Those differences could be explained by the diploid phasing of the Cabernet Sauvignon genome assembly and that multiple ISNT transcripts might correspond to a single gene locus. Nonetheless, similar relative amounts of Biological Process GO terms were found among the differentially expressed genes, confirming that the transcriptome obtained using Iso-Seq captured the transcriptional reprogramming underlying the main physiological and biochemical changes during grape berry development. In addition, gene expression analysis revealed that some private isoforms are significantly modulated during berry development, indicating that in addition to identifying the private gene space, the ISNT reference makes it possible to observe its expression. In conclusion, this study demonstrates that Iso-Seq data can be used to create and refine a comprehensive reference transcriptome that represents most genes expressed in a tissue undergoing extensive transcriptional reprogramming during development. In grapes, this approach can aid developing transcriptome references and is particularly valuable given diverse cultivars with private transcripts and accessions that are genetically distant from available genome references, like the non-vinifera Vitis species used as rootstocks or for breeding. The pipeline described here can be useful in efforts to reconstruct the gene space in plant species with large and complex genomes still unresolved.While San Joaquin Valley vineyards are currently fertilized with boron through the soil and foliage , some growers have expressed interest in applying boron via drip irrigation or “fertigation.” Fertigation is a relatively simple, cost-effective and efficient way to apply nutrients. However, irrigation water with more than 1 part per million boron can lead to vine toxicity, so the safety of boron fertigation is also a concern. Our research evaluates the safety and efficacy of boron fertigation in grapevines using drip irrigation. Boron is unique among the micronutrients due to the narrow range between deficiency and toxicity in soil and plant tissues. For grapevines, 25 liter plant pot this range is 0.15 ppm to 1 ppm in saturated soil extracts, and 30 ppm to 80 ppm in leaf tissue.

The goal of boron fertilization of grapevines is to keep tissue levels within this narrow range, since both deficiency and toxicity can have serious negative effects on vine growth and production. Fertilization amounts must be precise to avoid toxicity while providing adequate boron to satisfy grapevine requirements . On the east side of the San Joaquin Valley, boron deficiency of grapevines occurs on soils formed from igneous rocks of the Sierra Nevada. This parent material is low in total boron, which is crystallized in borosilicate minerals that are highly resistant to weathering. Boron deficiency is often associated with sandy soils and vineyard areas with excessive leaching, such as in low spots or near leaky irrigation valves. Vine symptoms of boron deficiency are more widespread and pronounced following high rainfall years, when greater amounts of soluble boron are leached from the root zone. In addition, snow melt water has very low levels of boron, and vineyards irrigated primarily with this water have a greater risk of deficiency. Boron is required for the germination and growth of pollen during flowering, and vines that are deficient in this micronutrient will have clusters that set numerous shot berries, small berries with a distinctive pumpkin shape. When boron deficiency is severe, vines produce almost no crop. Foliar symptoms appear in the spring: shoots have shortened, swollen internodes and their tips sometimes die, and leaves have irregular, yellowish mottling between the veins. Grapevines are also sensitive to too much boron. Toxicity is common on the west side of the San Joaquin Valley, where most soils are derived from marine sedimentary and meta sedimentary parent material that is rich in easily weathered boron minerals. Symptoms of boron toxicity include leaves that are cupped downward in the spring and that develop brown spots adjacent to the leaf margin in middle or late summer, intensifying and leading to necrosis as boron accumulates. Yields are reduced, the result of diminished vine vigor and canopy development. When foliar boron sprays are applied in excess in the spring, juvenile leaves become cupped within 2 weeks; however, vines quickly recover and yields are usually unaffected. Toxicity also occurs when boron fertilizer is applied in excess, regardless of the soil type, and this can lead to yield loss. Over-fertilization is the sole reason for boron toxicity on the east side of the San Joaquin Valley, so it is critical to establish how much boron fertilizer can be applied safely and effectively.

Our research investigated the uptake of boron by grapevines when fertilizer was applied with a drip-irrigation system.Research was conducted from 1998 to 2001 in a mature ‘Thompson Seedless’ raisin vineyard near Woodlake in Tulare County. The vineyard was planted in Cajon sandy loam on a recent alluvial fan associated with the Kaweah River. This soil is derived from granitic parent materials, and the surface soil is highly micaceous with a slight to moderate amount of lime. The underlying soil has a coarse, sandy texture. At the onset of this study, the vineyard’s boron status was in the questionable range for deficiency. The vine’s leaf petioles and blades contained about 30 ppm boron. While the foliage had no symptoms of boron deficiency, in the past the grower had observed sticking caps and pumpkin-shaped shot berries, which are indicative of boron deficiency. During the course of the research, the vineyard was drip-irrigated from April through October. The vineyard canopy covered 60% of the land surface during summer months and about 20 inches of water was applied during the season. Boron treatments consisted of applying fertilizer in varying amounts 3 weeks prior to bloom on May 18, 1998, and then again 3 weeks prior to bloom the following year, on May 3, 1999. Growers who fertigate grapevines with a drip system generally inject material into the irrigation water over a 45-to- 60-minute period at the beginning of an irrigation set. We simulated fertigation by applying Solubor, a soluble boron product , to a shovel-sized hole beneath drippers during the first hour of the irrigation set. By doing this, precise amounts of boron could be applied to each plot and plot size could be reduced. This technique has been used successfully in previous research with other nutrients . The experiment was designed as a randomized complete block with five treatments, five blocks and five vine plots . To evaluate the rate of boron uptake and accumulation in tissue with consecutive years of fertilization, grape tissue samples were collected in 1998 and 1999 at bloom and then again about 6 weeks later during veraison. Veraison is the stage of development where berries begin to soften and/or color. To evaluate carryover, leaf tissue samples were also collected at this Tulare County site at both bloom and veraison in 2001, 2 years after the fertilization was discontinued. In each case, 100 petioles and 50 blades were sampled per plot from the center three vines. Petioles and blades were taken opposite inflorescences during bloom, and recently matured leaves were sampled at veraison. Samples were oven-dried, ground in a Wiley mill and sent to the UC Davis DANR Analytical Laboratory for analysis of total boron. Statistical analysis was by ANOVA using least significance difference to separate treatment means. A second experiment was conducted in 1998 in Fresno County near Selma, in a mature Thompson Seedless raisin vineyard planted on Pollaski sandy loam and drip-irrigated.

The soil was formed in place from the weathering of softly to moderately consolidated granitic sediments. The particle size distribution of the surface soil is 63% sand, 25% silt and 12% clay. At the onset of the experiment, boron tissue levels were in the adequate range, 40 ppm. In both experiments, drip irrigations during the season were based on a schedule using historical evapotranspiration and developed for raisin vineyards in the San Joaquin Valley . The irrigation source was high-quality pump water with a boron concentration less than 0.1 ppm. The experimental design and methods were identical in both vineyards, except that the 1/16-poundper-acre boron treatment was omitted in the second vineyard. The Fresno County trial was discontinued after tissue samples were taken at bloom and veraison in 1998.At both the Tulare and Fresno county sites, black plastic plant pots boron uptake was rapid when fertilizer was applied in the spring. In both vineyards, applying boron at 2/3 or 1 pound per acre increased the boron concentration in blades by bloom, 3 weeks after application. Boron increased further in blades by veraison . In the Tulare County vineyard, boron in bloom tissue increased from a questionable deficiency range to adequate; at the Fresno location, boron in bloom tissue increased from 40 ppm to 54 ppm, a dramatic increase considering boron fertilizer was applied just 3 weeks prior. This indicates that boron uptake is rapid. None of the fertigation treatments resulted in either symptoms of boron toxicity or deficiency. Applying boron at 1/3 pound per acre or less did not significantly increase boron tissue levels by bloom or veraison at either site the first year. Fertigation over consecutive years was evaluated at the Tulare County location. Boron in grapevine tissue continued to increase with consecutive years of application. At the higher fertilizer rate , boron levels in blades increased from 35 ppm in control vines to about 60 ppm. We speculate that continuing with annual applications of 1 pound boron per acre would result in toxicity within 4 to 5 years. The 1/3-pound-per-acre rate significantly elevated boron in blades by veraison of the second year to adequate levels . There were no visual signs of toxicity in any of the fertilizer treatments, even when boron was applied at 2 pounds per acre in a single application. Boron levels in tissue remained unchanged 2 years after fertilization was discontinued at the Tulare County location . This indicates substantial treatment longevity with fertigation of a drip-irrigated vineyard. Rainfall during this experiment was below normal, which helped minimize leaching. Also, well-managed drip irrigation minimizes leaching. Under drip irrigation, salts tend to accumulate near the soil surface and 2 to 3 feet away from the drip line, with minimal water and salt movement below the root zone when irrigations are accurately scheduled . Boron concentrated more in the blades than in the petioles in response to fertilization. At the onset of the Tulare County experiment, boron concentrations in petioles and blades were similar at 31 ppm and 34 ppm, respectively. Fertilizing with 1 pound boron per acre for 2 consecutive years resulted in a 25% increase of boron in petioles but a 76% increase in blades . All fertilizer treatments increased boron in blades more than in petioles, indicating that blades should be sampled when monitoring the vines’ boron status following fertilization. Potential boron toxicity values at the time of sampling during the bloom period are 80 ppm for petioles and 120 ppm for blades, and in mid- to late summer are 100 ppm for petioles and 300 ppm for blades.Annual boron fertigation at 1/3 pound per acre elevated grapevine tissue levels from questionable to the adequate range within 2 years . In addition, tissue boron levels remained unchanged 2 years after fertilization was discontinued. This is probably because leaching was reduced by two factors: below-normal rainfall and accurately scheduled drip irrigations. After fertilization, boron was concentrated more in blades than in petioles, indicating that blades are the best choice for monitoring toxicity. Blade samples should be monitored on a routine basis and fertilizer amounts should be adjusted accordingly to avoid boron toxicity or deficiency. The results of this research can be applied to other drip-irrigated vineyards in the San Joaquin Valley under similar conditions: rapidly drained soils, high quality irrigation water, and low boron content in soil, water and vine tissue. In other regions of the state where winter rainfall is much higher, there would presumably be more leaching of boron fertilizer during winter months and less carryover time after fertilization is discontinued. In contrast, less leaching and greater carryover of boron would be expected in areas of less rainfall or on soils with finer texture and higher water-holding capacity. These variables underscore the importance of monitoring boron in tissue when developing a long-term fertilization program.The study of crop domestication has long been used as a proxy for studying evolutionary processes, such as the genetic effects of bottlenecks and the detection of selection to identify agronomically important loci .

To further explore links between management and soil fertility, we used the results from the PCA to formalize a gradient in management across all farms, and then used this gradient as the basis for comparison between Field A and Field B across all indicators for soil fertility. Using the ggplot and tidy verse packages , we displayed the difference in values between Field A and Field B for each indicator for soil fertility sampled at each farm using bar plots. We also included error bars to show the range of uncertainty in these indicators for soil fertility. Lastly, we further compared Field A and Field B for each farm using radar plots. To generate the radar plots, we first scaled each soil indicator from 0 to 1. Using Jenks natural breaks optimization, we then grouped each farm based on low, medium, and high N-based fertilizer application, as this soil management metric was the strongest coefficient loading from the first principal component . Using the fmsb package in R , we used an averaging approach for each level of N-based fertilizer application to create three radar plots that each compared Field A and Field B across the eight indicators for soil fertility. Farmers provided an overview of their farm operation, including farm size , the total number of crops each farm planted per growing season at the whole farm level, the types of crops planted in their field during the initial field visit , the type and amount of nitrogen-based fertilizer they applied on farm, and key aspects of soil health in their own words . Farm sizes ranged from 15 to 800 acres, with about one third of farms in the 15 – 50-acre range, drainage pot another third in the 100 – 450-acre range, and roughly a final third in the 500 – 800 acre-range. Farmers grew primarily summer crops, including tomato, a variety of cucurbits, strawberry, herbs, nightshades, root vegetables, and sunflower/safflower for oil.

Farmers reported applying a range of external N-based organic fertilizers, including fish emulsion, Wiserg , pelleted chicken manure, and seabird guano, at varying rates . On the low end, farmers applied <1 kg-N/acre, and on the high end, farmers applied 90 – 180 kg-N/acre per season. About a third of farmers applied 2 – 25 kg-N/acre of N-based fertilizer. Farmer responses for describing key aspects of soil health were relatively similar and overlapped considerably in content and language . Specifically, farmers usually emphasized the importance of maintaining soil life and/or soil biology, promoting diversity, limiting soil compaction and minimizing disturbance to soil, and maintaining good soil structure and moisture. Several farmers also touched on the importance of using crops as indicators for monitoring soil health and the importance of limiting pests and disease. Discussion of the importance of promoting soil life, soil biology, and microbial and fungal activity had the highest count among farmers with ten mentions across the 13 farmers interviewed. Next to this topic, minimizing tillage and soil disturbance was the second most discussed with six of 13 farmers highlighting this key aspect of soil health. In addition to discussing soil health more broadly, farmers also provided in-depth responses to a series of questions related to soil fertility—such as key nutrients of interest on their farm, details about their fertility program, and the usefulness of soil tests in their farm operation— summarized in Table 2. When asked to elaborate on the extent to which they considered key nutrients, a handful of farmers readily listed several nutrients, including nitrogen, phosphorous, potassium , and other general macronutrients as well as one micronutrient .

Among these farmers that responded with a list of key nutrients, some talked about having their nutrients “lined up” as part of their fertility program. This approach involved keeping nutrients “in balance,” such as for example, monitoring pH to ensure magnesium levels did not impact calcium availability to plants. These farmers also emphasized that though nitrogen represented a key nutrient and was important to consider in their farm operation, tracking soil nitrogen levels was less important than other aspects of soil management, such as promoting soil biological processes, maintaining adequate soil moisture and aeration, or planting cover crops regularly. As one farmer put it, “if you add nutrients to the soil, and the biology is not right, the plants will not be able to absorb it.” Or, as another farmer emphasized, “It’s not about adding more [nitrogen]… I try to cover crop more too.” A third farmer emphasized, that “I don’t use any fertilizers because I honestly don’t believe in adding retroactively to fix a plant from the top down.” This same farmer relied on planting a cover crop once per year in each field, and discing that cover crop into the ground to ensure his crops were provided with adequate nitrogen for the following two seasons. While most farmers readily listed key nutrients, several farmers shifted conversation away from focusing on nutrients. These farmers generally found that this interview question missed the mark with regards to soil fertility. One farmer responded, “I’m not really a nutrient guy.” This same farmer added that he considered [soil fertility] a soil biology issue as much as a chemistry issue.” The general sentiment among these farmers emphasized that soil fertility was not about measuring and “lining up” nutrients, but about taking a more holistic approach. This approach focused on facilitating conditions in the soil and on-farm that promoted a soil-plant-microbe environment ideal for crop health and vigor. For example, the same farmer quoted above mentioned the importance of establishing and maintaining crop root systems, emphasizing that “if the root systems of a crop are not well established, that’s not something I can overcome just by dumping more nitrogen on the plants.” Another farmer similarly emphasized that they simply created the conditions for plants to “thrive,” and “have pretty much just stepped back and let our system do what it does; specifically, we feed our chickens whey-soaked wheat berries and then we rotate our chickens on the field prior to planting.

And we cover crop.” A third farmer also maintained that their base fertility program—a combination of planting a cover crop two seasons per year, an ICLS chicken rotation program, minimal liquid N-based fertilizer addition, and occasionally compost application—all worked together to “synergize with biology in the soil.” This synergy in the soil created by management practices—rather than focusing on nutrient levels—guided this farmer’s approach to building and assessing soil fertility on-farm. Another farmer called this approach “place-based” farming. This particular farmer elaborated on this concept, saying “I think the best style of farming is one where you come up with a routine [meaning like a fertility program] that uses resources you have: cover crops, waste materials beneficial to crops, animals” in order to build organic matter, which “seems to buffer some of the problems” that this farmer encountered on their farm. Similar to other farmers, this farmer asserted that adding more nitrogen-based fertilizer did not lead to better soil fertility or increase yields, drainage planter pot in their direct experience. Regardless of whether farmers listed key nutrients, a majority of farmers voiced that nitrogen was not a big concern for them on their farm. This sentiment was shared among most farmers in part because they felt the amount of nitrogen additions from fertilizers they added were insignificant compared to nitrogen additions by conventional farms. Farmers also emphasized that the amount of nitrogen they were adding was not enough to cause environmental harm; relatedly, a few farmers noted the absurdity and added economic burden of the recent nitrogen management plan requirements—specifically among organic farms with very low N-based fertilizer application. The majority of farmers also expressed that their use of cover crops and the small amount of N-based fertilizer additions as part of their soil fertility program ensured on-farm nitrogen demands were met for their crops. Across all farmers interviewed, cover cropping served as the baseline and heart of each fertility program, and was considered more effective than additional N-based fertilizers at maintaining and building soil fertility. Farmers used a range of cover crop species and often applied a mix of cover crops, including vetches and other legumes like red clover and cowpea , grains and cereals like oats . Farmers cited several reasons for the effectiveness of cover cropping, such as increased organic matter content, more established root systems, greater microbial activity, better aeration and crumble in their soils, greater number of earthworms and arthropods, improved drainage in their soils, and more bio-available N. Whereas farmers agreed that “more is not better” with regards to N-based fertilizers, farmers did agree that allocating more fields for planting cover crops over the course of the year was beneficial in terms of soil fertility. However, as one farmer pointed out, while cover crops provide the best basis for an effective soil fertility program, this approach is not always economically viable or physically possible. Several farmers expressed concern because they often must allocate more fields to cover crops than cash crops in any given season, which means that their farm operation requires more land to be able to produce the same amount of vegetables than if they had all their fields in cash crops.

Farmers also shared that in some circumstances, such as in early spring, they are not able to realize the full potential of a winter cover crop if they are forced to mow the cover crop early to plant cash crops and ensure the harvest timeline of a high-value summer vegetable crop. The cover crop approach to soil fertility takes “persistence,” as one farmer emphasized; another farmer similarly pointed out that the benefits of cover cropping “are not always realized in the crop year. You’re in it [organic agriculture] for the long haul, there is no quick fix.” Indeed, farmers who choose to regularly plant cover crops to build soil fertility, rather than just add N-based fertilizers, reported that they came up against issues of land tenure and access to land, market pressures, and long-term economic sustainability. To build on conversations about soil fertility, farmers also provided responses to interview questions that asked them to elaborate on the usefulness of available soil tests to gauge soil fertility more broadly—and then more specifically, the usefulness of soil tests in informing their soil fertility program and/or management approaches on-farm. Overall, only three of 13 farmers reported regularly using and relying on soil tests to inform their soil fertility program or aspects of their farm operation. These farmers offered very short responses and did not elaborate. For example, one farmer shared that they “test twice a year in general,” and that they “rely on the results of the soil tests to tweak [their] fertility program.” Another farmer said briefly, “We use soil tests… we utilize them to decide what to do to try to improve the soil.” A third farmer admitted that though he “used to do a soil test every year, literally used to spend hundreds of dollars per year on soil tests,” he found that the results of soil tests did not change year-to-year and were, as he put it, very “stable.” This particular farmer no longer regularly uses or relies on soil testing for their farm operation. The remaining ten farmers confirmed that they had previously submitted a soil test, usually once and most often to a local commercial lab in the region. These farmers expressed a range of sentiments when asked about the usefulness of soil tests, including disappointment, distrust, or both, particularly in the capacity of soil tests to inform soil fertility on their farm. Some farmers said directly, “I just don’t trust soil tests,” or “frankly, I don’t believe a lot in soil testing because it’s too standardized,” while other farmers initially stated they had used “limited” or “infrequent” soil tests, and then later admitted that they did not use or rely on soil tests on their farm operation. These farmers tended to focus on the limitations of soil tests that they encountered for their particular farm application. Limitations of soil tests discussed by farmers varied.

Across all farmers interviewed, including both first- and second-generation farmers, farmers stressed the steep learning curves associated with learning to farm alternatively and/or organically. While these farmers represent a case study for building a successful, organic farm within one generations, the results of this study beg the question: What advancements in farm management and soil management could be possible with multiple generations of farmer knowledge transfer on the same land? Rather than re-learning the ins and outs of farming every generation or two, as new farmers arrive on new land, farmers could have the opportunity to build on existing knowledge from a direct line of farmers before them, and in this way, potentially contribute to breakthroughs in alternative farming. In this sense, moving forward agriculture in the US has a lot to learn from agroecological farming approaches with a deep multi-generational history . To this end, in most interviews—particularly among older farmers—there was a deep concern over the future of their farm operation beyond their lifetime. Many farmers lamented that no one is slated to take over their farm operation and that all the knowledge they had accumulated would not pass on. There exists a need to fill this gap in knowledge transfer between shifting generations of farmers in order to safeguard farmer knowledge and promote adaptations in alternative agriculture into the future.Most studies often speak to the scalability of approach or generalizability of the information presented. While aspects of this study are generalizable particularly to similar farming systems in California such as the Central Coast region, the farmer knowledge presented in this study is not generalizable and not scalable to other regions in the US. To access farmer knowledge, pots with drainage holes relationship building with individual farmers leading up to interviews as well as the in-depth interviews themselves require considerable time and energy.

While surveys often provide a way to overcome time and budget constraints to learn about farmer knowledge, this study shows that to achieve specificity and depth in analysis of farmer knowledge requires an interactive approach that includes—at a minimum—relationship building, multiple field visits, and in-depth, multi-hour interviews. Accessing farmer knowledge necessitates locally interactive research; this knowledge may not be immediately generalizable or scalable without further locally interactive assessment in other farming regions. Local knowledge among farmers in US alternative agriculture has often been dismissed or overlooked by the scientific community, policymakers, and agricultural industry experts alike; however, this study makes the case for inclusion of farmer knowledge in these arenas. In-depth interviews established that farmers provide an important role in translating theoretical aspects of agricultural knowledge into practice. It is for this reason that farmer knowledge must be understood in the context of working farms and the local landscapes they inhabit. As one of the first systematic assessments of farmer knowledge of soil management in the US, this research contributes key insights to design future studies on farmer knowledge and farmer knowledge of soil. Specifically, this study suggests that research embedded in local farming communities provides one of the most direct ways to learn about the substance of farmer knowledge; working with the local UCCE advisor in combination with community referrals provided avenues to build rapport and relationships with individual farmers—relationships that were essential to effective research of farmer knowledge. Farmer knowledge of soil management for maintaining healthy soils and productive, resilient agriculture represents an integral knowledge base in need of further scientific research. This study provides a place-based case study as a starting point for documenting this extensive body of knowledge among farmers.

It is our hope that this research will inspire future studies on farmer knowledge in other contexts so that research in alternative agriculture can widen its frame to encompass a more complete understanding of farming systems and management motivations—from theory to practice. A fundamental challenge in agriculture is to limit the environmental impacts of nitrogen losses while still supplying adequate nitrogen to crops and achieving a farm’s expected yields . To balance among such environmental, ecological, and agronomic demands, it is essential to establish actual availability of nitrogen to crops . A holistic, functional understanding of plant N availability is particularly imperative in organic agriculture, as in this farming context, synthetic fertilizers are not applied and instead, production of inorganic N—the dominant form of N available to crops—depends on internal soil processes . In organic agricultural systems, farmers may seasonally apply cover crops or integrate livestock as alternative sources of nitrogen to crops—in addition to or in place of using organic fertilizers. In applying these alternative sources of nitrogen to soil, organic farmers rely on the activity of soil microbes to transform organic N into inorganic forms of N that are more readily available for crop uptake . Currently, the predominant way crop available N is measured in organic agricultural systems tends to examine pools of inorganic N in soil . Inorganic N, or more specifically ammonium and nitrate , represents the predominant forms of N taken up by crop species in ecosystems where N is relatively available, such as in non-organic agricultural systems that apply inorganic fertilizers . However, in organic systems, crop available N is largely controlled by complex soil processes not adequately captured by simply measuring pools of ammonium and nitrate. First, because nitrogen made available to crops is controlled by soil microbes—wherein crops only have access to inorganic forms of N after microbial N transformations occur to first meet microbial N demand—pinpointing the flow of N moving through inorganic N pools as a result of these microbial N transformations is necessary to accurately measure actual N availability to crops . Second, extensive recycling of N among components of the plant-soil-microbe system complicates relying solely on measurements of inorganic N pools, which do not reflect these dynamics .

As an example, one previous study in organic vegetable systems showed examples where inorganic N pool sizes in the soil were measured to be low, yet there existed high production and consumption rates of inorganic N . This outcome highlighted that if the turnover of inorganic N is high—for instance, high rates of soil ammonium production exist in the soil with simultaneously high rates of immobilization by soil microbes and high rates of uptake by plants—measured pools of inorganic N may still be low . This study also showed that conversely, there may also exist situations when inorganic N pools are low and rates of ammonium and nitrate production are also low, in which case N availability would limit crop production. In organic systems especially, higher carbon availability as a result of organic management can increase these microbially mediated gross N flows, thereby increasing N cycling and turnover of inorganic N . Thus, we hypothesize that measuring total production of ammonium from organic N, or gross N mineralization, and subsequent total production of nitrate from ammonium, or gross N nitrification, may provide a more complete characterization of crop available N in the context of organic systems . Though the application of such diverse management practices on organic farms is known to affect rates of N cycling in soil , drainage pot measuring N flow rates as a proxy for crop available N is currently uncommon on working organic farms. The current historical emphasis on measuring inorganic pools of N in organic agriculture was originally imported from non-organic farming, wherein the Sprengel-Liebig Law of the Minimum was a widely accepted agronomic principle . In practice, this Law of the Minimum placed particular importance on using artificial fertilizers to overcome so-called “limiting” nutrients—namely, inorganic forms of N. Because inorganic N is relatively straightforward to measure, focus on quantifying pools of inorganic N has since become common practice among agronomists and agricultural researchers . However, the continued acceptance of the Law of the Minimum in organic agriculture underscores the gap in a functional understanding of organic agricultural systems, in particular the role of soil microbes in mediating N cycling. To understand crop available N more holistically, there is a need to measure actual flow rates of soil N—in addition to—static pools of inorganic N . Soil indicators that adequately capture N availability to crops are therefore necessary to move beyond the legacy of the Law of the Minimum in organic agriculture. Unpacking the soil processes that mediate flows of N may ultimately provide a more accurate characterization of soil N cycling and in turn, N availability to crops. Unfortunately, gross N mineralization and nitrification rates are very difficult to measure in practice, particularly on working organic farms . While net N flows are easier to measure in comparison to gross N flows and can provide a useful measure of N cycling dynamics as a complement to measurements of inorganic N pools, net N flows still pose serious limitations— namely that net rates cannot detect plant-soil-microbe interactions and therefore are not adequate as metrics for determining crop available N . In particular, relying on net N flows as a measure of N availability does not account for the ability of plants to compete for inorganic N, and assumes plants take up inorganic N only after microbial N demands are satisfied .

It is also possible that measuring soil organic matter pools could help indicate N availability because SOM supports microbial abundance and activity, and because SOM is also the source of substrates for N mineralization . Several studies have proposed measuring soil organic matter levels to complement measuring inorganic N pools, understand soil N cycling, and infer N availability . Assessing the total quantity of organic carbon and nitrogen within soil organic matter represents one established method for measuring levels of soil organic matter, and is more readily measurable than gross N rates. Additional indicators for quantifying “labile” pools of organic matter, such as POXC and soil protein, have also become more widely studied in recent years, and applied on organic farms as well . When used in combination with more established soil indicators that measure organic C and N pools , this suite of indicators may potentially provide added insight to understanding crop available N . Importantly, applied together these four indicators for soil organic matter levels may also more readily and accurately serve as a proxy for soil quality—generally defined as a soil’s ability to perform essential ecological functions key to sustaining a farm operation . Despite the availability of these soil indicators, very few studies have systematically examined the way in which SOM levels on working farms compare to N cycling processes, and specifically how SOM levels compare to microbially mediated gross N rates. Further, it is still unclear to what degree the interactions between soil edaphic characteristics and soil management influence N cycling and N availability to crops . For instance, soil texture may play a mediating role in N cycling, where soils high in clay content may limit substrate availability as well as access to oxygen, which in turn, may restrict the efficiency of N cycling . In this sense, it is important to understand the role that soil edaphic characteristics play in order to identify the underlying baseline limits imposed by the soil itself. Equally important to consider is the role of soil management in mediating N cycling. Compared to controlled experiments, soil management regimes on working farms can be more complex and nonlinear in nature due to multiple interacting practices applied over the span of several years, and even multiple decades. To date, a handful of studies conducted on working farms have examined tradeoffs among different management systems , though few such studies examine the cumulative effects of multiple management practices across a gradient of working organic farms. However, understanding the cumulative effects of management practices is key to link soil management to N cycling on working farms . Likewise, it is important to examine the ways in which local soil edaphic characteristics may limit farmers’ ability to improve soil quality through management practices. Though underutilized in this context, the development of farm typologies presents a useful approach to quantitatively integrate the heterogeneity in management on working organic farms . Broadly, typologies allow for the categorization of different types of organic agriculture and provide a way to synthesize the complexity of agricultural systems . Previous studies that make use of farm typologies found that differences in total soil N across farms are largely defined by levels of soil organic matter.

Blue elderberries were determined to be ripe when the berries in a cyme were deep purple, with or without the white bloom, and had no green berries present. Ripe elderberries were harvested by hand from all four quadrants of the elderberry shrub, totaling approximately 3 kg of elderberries. The berries were placed in clear plastic bags, stored on ice, and transported to the laboratory. A subsample was separated for moisture analysis, while the rest was de-stemmed and stored at -20 °C until analyzed. HPLC grade methanol , acetonitrile , phosphoric acid, ethanol, hydrochloric acid, and sodium hydroxide were purchased from Fisher Scientific . Ascorbic acid was purchased from Acros Organics . Formic acid, gallic acid, sucrose, chlorogenic acid, rutin, and catechin, and Folin-Ciocalteu reagent were purchased from Sigma Aldrich . Cyanidin-3-glucoside was purchased from Extrasynthese . Ultra-pure water was obtained from a Milli-Q water system . From each shrub, about 250 g of frozen berries were thawed in a glass container overnight at 4 °C. The following day, the thawed berries were mashed for 4 min by hand using a plastic pestle, then homogenized , and centrifuged at 3,000 rpm for 7 min. The supernatant was strained, collected, and weighed. A 15 mL aliquot of sample extract was stored in a 15 mL plastic tube at -20 °C for total monomeric anthocyanin analysis. The remaining supernatant was used to determine soluble solids, pH, and titratable acidity . One pooled sample was analyzed from each shrub and analyzed in duplicate analytical repetitions. A refractometer was used to determine soluble solids. It was calibrated with standard solutions of 5°, 10°, vertical gardening in greenhouse and 15° Brix made with sucrose and water. A 150 µL aliquot of elderberry juice was placed on the prism and read using the automatic setting. The pH was determined using a SevenMulti pH meter .

It was calibrated before each use using buffers at pH 4.0, 7.0, and 10.0. To determine TA, 10 mL of elderberry juice was diluted to 100 ml with nanopure water and mixed. This dilute juice was titrated to pH 8.2 using 0.1 N NaOH. The volume of 0.1 N NaOH used to achieve the desired pH was used to calculate the mg citric acid per 100 g fresh weight . For each of these analyses, duplicates were run on each juice. Elderberries were extracted by combining 5 g frozen berries with 25 mL MeOH:formic acid in a conical tube. The contents were homogenized, placed in a shaker without water at speed 7.5 for 20 min, then centrifuged at 3,000 rpm for 7 min. The supernatant was transferred to a 15 mL plastic tube and stored at -80 °C for no more than two weeks prior to analysis. Duplicate extracts were made from each shrub. TPC was determined using the Folin-Ciocalteu method. First, elderberry phenolic extract was diluted 1:4 with water. Each extract was analyzed in duplicate and averaged. In 10 mL glass tubes, 6 mL water was combined with 100 µL sample and 500 µL Folin-Ciocalteu reagent. After mixing and incubating for 8 min at room temperature, 1.5 mL 20% aqueous sodium carbonate was added. The tubes were mixed, covered with foil to avoid light exposure, placed in a water bath at 40 °C for 40 min, then cooled at room temperature for 15 min. The samples were read by a UV visible spectrophotometer at 765 nm and quantified using an external standard curve prepared with gallic acid . TPC is expressed as mg gallic acid equivalents per 100 g FW. Five grams of frozen berries were mixed with 25 mL of in a conical tube, which was then homogenized for 1 min at 7,000 rpm . The mixture was stored at 4 °C overnight, then in the morning, centrifuged at 4,000 rpm for 7 min. The supernatant was used directly for analysis. Three pooled samples were made for each hedgerow, each consisting of even amounts of berries from three distinct shrubs. Eachpooled sample was extracted once to give 3 biological replicates, and each extract was run in duplicate . The concentration of phenolic compounds in blue elderberry followed the method by Giardello et al. with some modifications.

Briefly, samples were analyzed via reversed-phase liquid chromatography on an Agilent 1200 with a diode array detector and fluorescence detector . The column used was a PLRP-S 100A 3 µm 150 x 4.6 mm at 35 °C, and the injection volume was 10.0 µl. Mobile phase A was water with 1.5 % phosphoric acid, while mobile phase B was 80%/20% acetonitrile/ mobile phase A. The gradient used was 0 min 6% B, 73 to 83 min 31% B, 90 to 105 min 6% B. The DAD was used to monitor hydroxybenzoic acids at 280 nm, hydroxycinnamic acids at 320 nm, flavonols at 360 nm, and anthocyanins at 520 nm. The FLD was used to monitor flavan-3-ols, with excitation at 230 nm and emission at 321 nm. External calibration curves were prepared using chlorogenic acid for phenolic acids, rutin for flavonols, and cyanidin-3-glucoside for anthocyanins , at the following concentrations: 200, 150, 100, 75, 50, 25, 10, 5, and 2.5 mg/L. Catechin was used to quantify flavan-3-ols and standards were run at 150, 100, 75, 50, 25, 10, 5, 2.5, and 1 mg/L. Compounds were identified based on retention time and spectral comparisons with standards. Information about the linear equations and lower limits of detection and quantitation can be found in Table S1 in the supplementary material. The LLOD was calculated as 3.3 times the standard deviation of the y-intercept of the curve divided the slope, while the LLOQ was calculated as 10 times those values.Several peaks appeared in the HPLC chromatograms that could not be identified using the above parameters. Chromatographic eluents of these peaks were collected individually and dried under vacuum. These extracts were reconstituted with mobile phase A, and 5 µL were injected into the HPLC- QTOF-MS/MS for accurate mass analysis . A Poroshell 120 EC-C18 column was used at 35 °C. Mobile phase A was 1% formic acid in distilled water, and mobile phase B was 1% formic acid in acetonitrile. The gradient used was 0 min 3% B, 30 min 50% B, 31-32 min 95% B, 33-38 min 3% B. The mass spectrometer was used in negative mode, and the mass range for MS was 100 to 1000 m/z while the range for MS/MS was 20-700 m/z. Collision energies at 10, 20, and 40 V were applied. The drying gas was set to a flow of 12 L/min at 250 °C, while the sheath gas was set to 11 L/min at 350 °C. The nebulizer was set to 40 psig, the capillary voltage was 3500 V, the nozzle was set to 500 V, and the fragmentor was set to 100 V. Data was analyzed using Agilent MassHunter Workstation Qualitative Analysis 10.0 .

Tentative identification was achieved by comparing the mass to charge ratio of the precursor and fragment ions to online libraries of compounds as well as using formula generation for the peaks in the spectra. The composition of blue elderberries is presented for the first time, which is key to understanding how this subspecies of Sambucus nigra compares to commercialized elderberry subspecies, S. nigra ssp. nigra and S. nigra ssp. canadensis. These data help to establish the blue elderberry grown in hedgerows in California as a viable source of berries and bioactive compounds. Data for the compositional assays is presented for the 2018 and 2019 harvest years as the average of all shrubs sampled in Table 2. The average moisture for the blue elderberries was 79.5 ± 1.5% in 2018 and 79.5 ± 1.6% in 2019, which is very similar to the levels found in wild elderberries in Spain 95. The average soluble solids found in blue elderberry ranged from 11.94 ± 2.08 to 14.95 ± 1.02 g per 100 g FW in 2018 and from 12.64 ± 1.86 to 17.09 ± 1.60 g per 100 g FW in 2019. These values are slightly higher than the soluble solids found in S. nigra ssp. cerulea grown in Slovenia29 and American elderberries grown in Ohio52. Compared to European and American elderberries evaluated in other studies, blue elderberries have similar levels of soluble solids 8,18,29,49,50,95. In the present study, the overall average content of soluble solids was significantly different between years, greenhouse vertical farming as blue elderberries harvested in 2019 had significantly higher average soluble solids than the elderberries harvested in 2018 . The pH in the blue elderberry ranged from 3.44 to 3.86 in 2018 and from 3.46 to 3.79 in 2019, with no significant difference found between harvest years. These values are slightly lower than the values found in European elderberry, which ranged from 3.9 ± 0.06 to 4.1 ± 0.04 with an average pH of 3.9 ± 0.2, and American elderberry, which ranged from 3.9 ± 0.04 to 4.5 ± 0.03 with an average pH of 4.2 ± 0.2 49 Another evaluation of pH in American elderberries had a range of 4.5 ± 0.08 to 4.9 ±0.12, higher than those found in the blue elderberry.52 The higher sugar and lower pH levels in blue elderberry could potentially impact taste and performance in food and beverages as compared with the European and American species. The average titratable acidity in blue elderberries ranged from 0.45 ± 0.08 to 0.77 ± 0.03 g citric acid per 100 g FW in 2018 and from 0.54 ± 0.06 to 0.77 ± 0.11 g citric acid per 100 g FW in 2019 with no significant difference found between harvest years. These values are lower than the total acids found by Mikulic-Petkovsek et al. 29 in S. nigra ssp. cerulea , but they are similar to the levels found in European elderberry 8,18,49,50 . Anthocyanins are a class of phenolics that contribute red, purple, and blue hues to fruits and vegetables, act as attractants for pollinators, and are potent antioxidants. European and American elderberries are well-known for containing high levels of anthocyanins 8,18,49. The anthocyanin content of elderberries strongly correlates to the antioxidant potential of the fruit, which may confer health-promoting properties 50,89, which is one reason why elderberries are used in supplements and value-added products. Elderberry is also used as a source of natural food colorants due to the levels of anthocyanins35. Understanding the levels of anthocyanins in the blue elderberry grown in hedgerows is critical towards establishing this native fruit as an additional and more sustainable elderberry. The average TMA measured in blue elderberry ranged from 34.2 ± 9.7 to 113.4 ± 18.2 mg CGE per 100 g FW in 2018 and from 43.1 ± 11.5 to 121.5 ± 11.5 mg CGE per 100 g FW in 2019 . TMA was variable between hedgerows in both years of harvest, with relative standard deviation values between 16% and 30%, yet there was not a significant difference in the overall average TMA between 2018 and 2019 . Furthermore, most hedgerows were not significantly different from the other hedgerows harvested that year despite significant differences in TMA values found between farms in both years . Regarding the age of the elderberry shrub, hedgerows 2 and 14 had two of the three highest concentrations of TMA in 2019 . This suggests that blue elderberries can be harvested from plants as young as two years without a significant loss of TMA concentrations. TMA values for the blue elderberries are lower than those found in other elderberry subspecies. In European elderberries, TMA levels range from 170 ± 12 to 343 ± 11 with an average of 239 ± 94 mg CGE per 100 g FW 49. A study of American elderberry grown in Ohio showed a range from 354 ± 59 to 595 ± 26 mg CGE per 100 g FW.52 In the present study, bare root prerooted cuttings of American elderberries were planted, along with blue elderberries, on Farm 1 in 2018, and three shrubs were harvested in 2019. These American elderberries had an average TMA value of 263 ± 5.4 mg CGE per 100 g FW, which is more similar to what has been observed in other studies on this subspecies. This suggests it is a subspecies difference contributing to the lower anthocyanin concentration in the blue elderberry and not the difference in growing conditions.

These inequivalent valleys at K and K0 lead to the valley Hall effect which, unlike the ordinary Hall effect, produces not only charge but also spin imbalance at the edges. The valley Hall effect has been understood in terms of the Berry curvature; the symmetries in 1 ML 2H-MX2 cause a sign change in the Berry curvature as one goes from one valley to an inequivalent valley in the BZ. This allows us to understand the valley Hall effect in terms of pseudospins, and provides possibilities to control the pseudo-spins by an external field. On the other hand, the Berry curvature is expected to vanish in the bulk because the bulk TMDCs have an inversion symmetry. However, one can imagine that the valley Hall in each layer could be nonvanishing—only the sum vanishes. This may naturally introduce the concept of “hidden Berry curvature,” a nonvanishing Berry curvature localized in each layer. Existence of hidden Berry curvature implies that the topology could be determined by local field; the local symmetry determines the physics. While experimental verification of a hidden Berry phase in the Bloch state is highly desired, standard measurements such as quantum oscillation cannot reveal a hidden Berry phase because these measurements represent an averaged quantity, with hidden quantity invisible. However, if we use an external field or surface sensitive technique such as angle resolved photo emission, then the direct measurement of such a hidden Berry curvature may be possible. In fact, the surface sensitivity of ARPES has recently been utilized in the measurement of hidden spin polarization. Then, the question is if Berry curvature can be measured by means of ARPES. In this regard, we note a recent proposal, based on a tight-binding model calculation on a simple cubic lattice with s and p orbitals, grow bucket that the nonAbelian Berry curvature is approximately proportional to the local orbital angular momentum in the Bloch state.

We use a similar approach and derived the relationship between OAM and the Berry curvature by using a three band, tight-binding model for in WSe2. We find that there is a linear relationship between OAM and the Berry curvature . Even though circular dichroism ARPES is not a direct measure of the OAM in the initial state in genera, it has been shown that CD-ARPES bears information on the OA. This fact can provide us a way to observe the existence of hidden Berry curvature by using CD-ARPES. In actual measurements, an important challenge lies in the fact that CD-ARPES has contributions other than the one from OAM. The most notable contribution comes from the geometrical effect, which is caused by a mirror symmetry breaking in the experimental geometry. Therefore, how we separate the Berry curvature and geometrical contributions holds the key to successful observation of the hidden Berry curvature. We exploit the unique valley configurations of TMDCs in the BZ to successfully disentangle the two contributions. The observed hidden Berry curvature has opposite signs at K and K0 as theoretically predicted. Moreover, we find the hidden Berry curvature exists over a wide range in the BZ. These features are consistently explained within the first principles calculations and tight binding description. ARPES measurements were performed at the beam line 4.0.3 of the Advanced Light Source at the Lawrence Berkeley National Laboratory. Data were taken with left and right-circularly polarized 94 eV light, with the circular polarization of the light better than 80%. The energy resolution was better than 20 meV with a momentum resolution of 0.004 Å−1 . Bulk 2H-WSe2 single crystals were purchased from HQ graphene and were cleaved in situ at 100 K in a vacuum better than 5 × 10−11 Torr. All the data were taken at 100 K. Figure 1 shows the crystal structure of 2H-WSe2 for which the inversion symmetry is broken for a ML.

In the bulk form of 2H-WSe2, the layers are stacked in a way that inversion symmetry is recovered. In the actual experiment, the contribution from the top layer to the ARPES signal is more than that from the sublayer, as illustrated by the dimmed color of the sublayer. Figure 1 schematically sketches the electronic structure with the hexagonal BZ of WSe2. The low energy electronic structures of 2H-WSe2 ML was found to be described by the massive Dirac-Fermion model, with hole bands at K and K0 points. These hole states at K and K0 points have local atomic OAM of 2ℏ and −2ℏ, respectively, which works as the valley index. The bands are then spin split due to the coupling between the spin and OAM. In the bulk, layers are stacked in a way that K of a layer is at the same momentum position as the K0 of next layer. Consequently, spin and valley symmetries are restored due to the recovered inversion symmetry and any valley sensitive signal should vanish. On the other hand, the in-plane nature of the primary orbital character of the Bloch states around the K and K0 points and the graphenelike phase cancellation as well as the strong spin orbital coupling strongly suppress the interlayer hopping along the c axis and make them quasi-two dimensional . In that case, the valley physics as well as the spin-split nature maybe retained within each layer as illustrated in Fig. 1 by the top- and sub-layer spin-split bands . In that case, one may be able to measure the hidden Berry curvature by using ARPES because it preferentially probes the top layer due to its surface sensitivity as, once again, illustrated by the dimmed color of the sub-layer. Since the signal is preferentially from the top layer, the situation becomes as if ARPES data are taken from the topmost layer of WSe2, for which the inversion symmetry is broken. As mentioned earlier, it was argued that OAM is directly related to the Berry curvature, which indeed has opposite signs at the K and K0 points as OAM does. Then, the hidden Berry curvature may be measured by using CDARPES, which was shown to be sensitive to OAM.

However, CD-ARPES has aforementioned geometrical contribution due to the broken mirror symmetry in the experimental geometry. In order to resolve the issue, we exploit the unique character of the electronic structures of TMDCs. The key idea is that, while the contribution from the geometrical effect is an odd function of k about the mirror plane, we can make the OAM contribution an even function. In that case, the two contributions can be easily isolated from each other. To make the OAM contribution an even function, we use the experimental geometry illustrated in Fig. 1. The experimental mirror plane, which is normal to the sample surface and contains the incident light wave vector, is precisely aligned to cross both K and K0 points. In such experimental condition, the Berry curvature is mirror symmetric about the experimental mirror plane and so is its contribution to the CD-ARPES. Then, the CD-ARPES is taken along the momentum perpendicular to the mirror plane , i.e., from K to K and K0 to K0 as shown in Fig. 1 by green dash-dot and brown dashed lines, respectively. We point out that we kept the same light incident angle for K-K and K0 -K0 cuts [note the color pair for the cut and light incidence in Fig. 1to prevent any contribution other than those from Berry curvature and experimental chirality. Figures 1–1 show data along the K0 -K0 cut. The dispersion is very symmetric with the minimum binding energy at the K0 point as expected. However, dutch bucket for tomatoes the intensity varies rather peculiarly; there appears to be no symmetry in the CD intensity in Fig. 1. The K-K cut in Figs. 1–1 shows a similar behavior. While the dispersion is symmetric , the CD intensity in Fig. 1 at a glance does not seem to show a symmetric behavior. However, upon a close look of the CD data in Figs. 1 and 1, one finds that the two are remarkably similar; the two are almost exact mirror images of each other if the colors are swapped in one of the images. This is already an indication that the CD data reflect certain aspects of the electronic structure that are opposite at the K and K0 points, most likely the hidden Berry curvature of bulk 2H-WSe2.In the calculation, the parameters are adjusted until the dispersion fits the experimental one and previous TB result. Then, the Berry curvature of the upper band is calculated based on the TKNN formula and its map is plotted in Fig. 3. The momentum dependent local OAM is obtained by density functional theory calculation. The resulting Lz map is depicted in Fig. 3. The in-plane components of the Berry curvature and OAM are also calculated but are found to be negligible over the whole BZ and thus are not presented. One can immediately note that the three plots of experimentally obtained IS NCD, Berry curvature from TB analysis, and local Lz from DFT calculation show remarkably similar behavior; their signs are determined by the valley indices and change only across the Γ − M line. In addition, all of them retain significant values quite far away from the K and K0 points. Our observation shows that IS NCD can be considered as a measure of the OAM and Berry curvature. We also find that IS taken with different photon energies shows no qualitative difference .

These observations support the notion that IS reflects an intrinsic property of the state, that is, OAM. For a more quantitative comparison, we plot IS NCD, Berry curvature and OAM along the high symmetry lines . Once again, IS NCD, Berry curvature and OAM show very similar behavior. As the Bloch states at the Γ and M points possess inversion symmetry, IS NCD, and Berry curvature as well as OAM are all zero. One particular aspect worth noting is their behavior near the Γ point. They are approximately zero near the Γ point but suddenly increase about a third of the way to the K or K0 point. Orbital projected band structure from TB calculation shows that this is when the orbital character of the wave function switches from out-of-plane dz2 and pz orbitals to in-plane dxy, dx2−y2 , px, and py orbitals. This behavior can be understood from the fact that the local OAM is formed by in-plane orbitals. These results strongly suggest that IS NCD is indeed representative of the Berry curvature and that the Berry curvature is closely related to the local OAM, at least for TMDCs. Characteristics of electron wave functions in the momentum space often play very important roles in macroscopic properties of solids. For example, topological nature of an insulator is determined by the characteristics of electron wave function at high symmetric points in the momentum space. The Berry curvature which is also embedded in the nature of the electron wave function in the momentum space determines the Berry phase and thus macroscopic properties such as spin and valley Hall effects. Through our work, we demonstrated a way to map out the Berry curvature distribution over the Brillouin zone and provide a direct probe of the topological character of strongly spin-orbit-coupled materials. This stands in contrast with transport measurement of spin and charge which reflect the global momentum-space average of the Berry curvature. In this regards, CD-ARPES can be a useful experimental tool to investigate certain aspects of the phase in electron wave functions if one can disentangle different contributions in the CD-ARPES. This work was supported by Research Resettlement Fund for the new faculty of Seoul National University and the research program of Institute for Basic Science . S. R. P. acknowledges support from the National Research Foundation of Korea . The Advanced Light Source is supported by the Office of Basic Energy Sciences of the U.S. DOE under Contract No. DE-AC02-05CH11231.In the momentum space of atomically thin transition metal dichalcogenides , a pair of degenerate exciton states are present at the K and K’-valleys, producing a valley degree of freedom that is analogous to the electron spin12–14. The electrons in the K and K’-valleys acquire a finite Berry phase when they traverse in a loop around the band extrema, with the phase equal in magnitude but opposite in sign at the K and K’-valleys, as required by the time-reversal symmetry.

As an effect of this bill alone, the California Energy Commission estimates that the state will need to triple its electricity power capacity in the renewable sector to achieve this goal. In 2022, the California Air Resources Board passed a plan mandating that all new cars sold in California be electric starting in 2035. The combination of these two laws creates a desperate need for increased electricity production capacity fueled by renewable energy. As more of the California economy ’electrifies’, the need for clean energy sources will only increase. The timelines of SGMA, SB 100 and the CARB mandate align well with one another to form an ideal environment for farmers to transition from traditional crop production to energy production. Policymakers could leverage these alignments to incentivize solar energy infrastructure investment and lessen farmer losses from water scarcity. The aim of this paper is to identify agricultural land parcels in the San Joaquin Valley that would provide both private and social benefit from switching to solar energy generation. This paper analyzes crop choice from both a private farmer’s and a social planner’s perspective and will rank land parcels based on the estimated total benefits generated by permanently transitioning agricultural land to energy production. I will analyze usable farmland in the San Joaquin Valley that has been fallow for at least one recent growing season and use computed water application and revenues per acre for different crops to find relative sensitivities to water price shocks induced by continued water scarcity and regulation. A wide range of crops are grown in the region, nft growing system and crop choice drives most of the variation in revenue and water cost per acre. I will compare traditional crop revenues with projected solar energy revenues to determine if a land use transition would be privately profitable. Current water application to the land parcel and total acreage will determine the water savings and added solar generation capacity .

Growers in California have experienced increasingly varied precipitation and, consequently, surface water availability since the 1980s . 75% of California’s rain and snow occurs in the top third of the state, far from where the bulk of the agricultural activity occurs . In response to this reality, multiple water projects were created by the state to move water from where water is relatively plentiful in the north to the parched southern population hubs and central agricultural regions. Moving this water expends energy, and those requesting water delivery bear the cost. The price of water varies heavily by region due to variation of relative water availability, and is a large part of farmers’ variable costs of producing an acre of crop. The amount of precipitation is hugely important in farmer cropping decisions, and land allocation choices vary based on the relative wetness or dryness of the growing year. In figures 2 and 3, crop cover and fallow land in the SJV for growing years 2010 & 2014 are shown by hydrologic region. 2010 represents a year with relatively typical precipitation, and 2014 was a drought year in the midst of historic drought conditions lasting from 2012- 2016 . In each figure, I display the crop cover choices and fallow land from two years relatively close to one another, but with very different surface water availability. Panels and show fallow land in each of the hydrologic regions that make up the San Joaquin Valley. Comparing these figures, there is a pronounced increase in fallow land from the ’wet’ year to the ’dry’ year . Differences in crop mix for farmers are to be tied to the precipitation conditions they grew under. Comparing panels and of figure 2, the marked decrease in double cropping activity in the central portion of the San Joaquin River in 2014 is apparent. In the same panels in figure 3, deciduous tree fruits and nuts are nearly wiped out by the dry conditions, and the acreage of cotton planted decreases as well. Surface water availability plays a massive role in farmers’ land use and crop mix decisions. Relevant literature in the agricultural economics field study farmers’ adaptation decisions when facing water scarcity. Hagerty finds that in the short-term, California farmers operating irrigated land choose to fallow some or all of their usable land when confronted with water scarcity.

This finding is supported visually by the increase in the fallow land acreage from 2010 to 2014, as shown in figures 2 and 3. Water is more costly in years with decreased precipitation for two reasons: less surface water is available and groundwater levels are lower, which means that water is more expensive to pump. Hagerty estimates that a 10% decrease in annual surface water level predicts a 3.6% decrease in farm revenues for the growing season due to inability to grow high-value annual crops that are generally more water intensive than the more stable perennial crops. Further, when facing long-term water scarcity, Hagerty finds that California-based farmers adapt by permanently removing fallow land from cultivation. This retired agricultural land becomes grassland, which can be used to graze cattle, or is left untouched. This kind of unirrigated rangeland has a mean revenue of $11, where the mean revenue of the least water intensive crop category is $622 with mean water needs of 1.31 acre-feet per acre . Although grain has the smallest mean water needs per acre, the volume of water needed to cultivate any crops successfully is a massive cost to farmers. Delivery of water alone averages around $250 per acre-foot in the San Joaquin Valley, and water right permits can cost over $30,000 to obtain . Farmers who have no choice but to stop irrigating some or all of their land are suffering huge losses as compared to those that are able to shift land toward less water intensive crops. These losses are even greater when compared to the average revenue per acre of utility-scale solar production. Annually, renting land to solar energy generators could earn between $1,000 – $1,500 per acre of farmland . This value is larger than returns from cultivating most annual crops , and some perennial orchard crops . In addition to crop choice, political factors like access to water rights impact a farmer’s decision to fallow a piece of land. Smith finds that growers with lower priority water access are more likely to fallow their land, whereas farmers with better access tend to make water conservation choices that are less costly. Growers who have higher priority water rights are more likely to make smaller adjustments to planting decisions when water supply is constrained, like planting earlier or planting varietals that develop quickly.

This means there are also distributional impacts of water scarcity, and farmers who may be historically excluded or limited in their water access will be hurt more by the continued scarcity in the coming decades. Taken together, the agricultural water scarcity literature suggests that agricultural land in the San Joaquin Valley that is currently oscillating between active and fallow will be taken offline in years to come, with potentially devastating consequences for farmers’ economic well-being. If farmers were able to shield themselves from climate-related income risk with solar energy generation, they may be more able to tolerate increasing water costs caused by SGMA-induced scarcity and increased drought frequency.Although rooftop solar PV panels are easily installable in neighborhoods across California and the American Southwest, there are unique challenges and benefits associated with scaling up solar energy generation to the farm level. Electricity transmission lines are a major limiting factor in building out utility-scale solar energy, vertical hydroponic nft system and current infrastructure is concentrated in residential distributed generation areas and areas with existing large-scale solar generation . However, to its benefit, utility-scale farming may not be plagued by the solar rebound effect that is present for residential solar generation. The household solar rebound effect is the ratio of the increase in total electricity consumption to the amount of energy generated from a household’s solar panel system . Various studies investigate the percent solar rebound effect in the US and abroad, with estimates ranging from 12% to as much as 50% for an individual household’s rebound effect . The increase in electricity usage driven by adoption of residential solar PV diminishes the positive externalities that solar adoption provides. Oliver argues that SRE is avoided when bringing utility-scale solar generating sites because the very drivers that cause the phenomenon on an individual household level do not exist. Utility-scale solar decouples households’ electricity consumption decisions from the generation itself, which avoids the need for additional policies to induce adoption. This makes utility-scale solar relatively more energy efficient than distributed generation or rooftop solar tends to be due to the solar rebound effect. Utility-scale solar generation is commonly defined as solar projects with more than 5MW of generation capacity . For utility-scale solar energy generation, there are two dominant technologies farmers could choose to use on their farms: primary photovoltaic or concentrated solar power . CSP uses mirrors to amplify solar radiation, making it a more efficient, but more expensive, system. Typical fixed solar PV panels are less energy efficient, but a much more accessible and widely adopted tech- nology. There is substantially more information on energy generation using fixed solar PV, both in economic literature and in practical experience from users of the technology. In this analysis, I will assume all farmers who switch to solar energy generation will use a fixed PV system, and all costs associated with installing the system are equal across farmers. I will assume additionally that all adopting farmers have the same electricity generating capacity per acre of land, and thus equal revenues from using an acre of land for solar. This requires that all PV systems installed by farmers have the same energy conversion efficiency. In reality, solar panel systems can have a variety of features that increase sunlight exposure, like rotating in accordance with the optimal sun angle . I will assume all farmers choosing to produce solar energy will use ground-mounted PV panels with equal energy conversion rates and equal installation costs. Equal electricity generating capacity across farmers also requires that all farm plots receive equal amounts of usable solar radiation per acre. Figure 5 shows statistics for two different measures of solar radiation: direct normal irradiance and global horizontal irradiance . Both are used in determining solar PV generating capacity, though GHI is most commonly used to calculate fixed solar panel generating potential . Average daily GHI in the U.S. is shown in the map in figure 4. Visually, it is clear that the majority of solar resources are concentrated in the Southwest. Analyzing average daily DNI and GHI values, I find that the SJV has substantially more energy-generating potential than the rest of the Americas and California, with less variation. What little variation there is has a relatively small impact on energy generating ability, and thus revenues per year. Using the resource ranking system from NREL , all land in the SJV falls into the top four of the ten categorizations of solar potential based on GHI values. Thus, the San Joaquin Valley has ample solar resources to support utility-level generation. Currently in the valley, some land is already used for utility-scale solar generation. The PPIC estimates that the existing 3GW of capacity in the SJV takes up 15,000 – 25,000 acres of land, with projects averaging a density between 5-8MW per acre . By comparison, there were over 170,000 fallow acres of land in the same area in 2023 alone . Because of the existence of these solar projects, there is already some infrastructure to support the distribution of the energy currently generated in SJV. In order to feed utility-scale amounts of electricity into the California energy system, solar farms must be connected to high-voltage transmission lines, which are defined as those able to handle 69 kV or more . Figure 6 shows the various existing transmission lines over the active agricultural land in the SJV. Although Ayres et al. estimate that more high-voltage transmission lines will need to be built to handle incoming solar projects, the existing infrastructure can be built upon, and is near much of the active agricultural land. As a result, some land is already being used for energy generation, and energy transmission lines have been installed across the valley to distribute the harvested solar. Above, figure 6 shows transmission lines that are able to carry utility-generated electricity.

Importantly, rather than resting on an inverse farm size – productivity relationship, policy that seeks to impact both equity and efficiency should focus on ensuring that smallholders have access to the productivity gains experienced by their larger counterparts. Thus, policies that help build human capital, facilitate adoption of new technologies, and enhance access to markets via a reduction in transactions costs will continue to be indispensable for reducing rural poverty in developing countries.The regularity with which an inverse relationship between farm size and land productivity is observed led to many theoretical explanations for the phenomenon. Early explanations centered around multiple market failures , asymmetric information , and risk aversion among farmers . A second set of explanations emphasized empirical issues such as systematic measurement error in farm size and/or output and omitted variables . Empirical studies have typically found that existing theory fails to fully explain the observed inverse relationship, generating a body of mixed and at times contradictory evidence. Chapter 1 illustrates how the choice of productivity measure can alter the relationship observed and how it can obscure a changing relationship between farm size and total factor productivity, the more relevant productivity measure. A dynamic relationship was found between farm size and total factor productivity in the rapidly modernizing agricultural regions of Brazil, contributing to an emerging literature that documents changing farm size – productivity relationships as agricultural sectors modernize and develop . This is consistent with Helfand et al. , hydroponic bucket whose findings suggest that both the larger commercial farms and smaller family farms in Brazil have advantages in harnessing technical change and achieving rapid gains in productivity.

In this paper the hypothesis of a dynamic farm size – productivity relationship is extended to the context of Mexico, identifying the relationship in a panel of family farms from the Mexican Family Life Survey and testing for changes over the sample period of 2002-2009. Mexico is an interesting case for assessing changes in the farm size – productivity relationship because of its long history of land reform and the recent agricultural policy reform associated with the North American Free Trade Agreement in the 1990s. These policies are a prime example of the Washington Consensus, liberalizing markets for land, agricultural inputs, and agricultural output in Mexico with the objective of spurning the modernization, competitiveness, and productivity of the agricultural sector and the broader economy. An environment with such market reforms, if successful, is expected to diminish the multiple market failure explanation of the inverse relationship between farm size and productivity, and any observed inverse relationship might weaken accordingly. We test for changes in the farm size – productivity relationship and, contrary to expectations, find that an inverse relationship exists and has remained strong in the wake of Mexico’s market reforms. We explore the relationship further by estimating a stochastic production frontier, an approach often applied in developed economy agriculture but infrequently applied in developing economy contexts. While frontier productivity growth has increased rapidly for larger farms, eliminating the inverse relationship at the frontier, the average relationship has remained unchanged due to more rapidly increasing technical inefficiency amongst the larger farms in the sample. This finding highlights the need for, and echoes calls for, policies that support family farms’ transitions towards modern agriculture and adaptation to market liberalization in Mexico.

The proceeding section discusses agricultural policy in Mexico, providing context for the empirical analysis. This is followed by an introduction of the empirical methodology, a description of the data, and the presentation of empirical results. Policy recommendations for Mexican agriculture and research implications conclude.The institutional structure of Mexican agriculture continues to reflect agricultural policies implemented after the Mexican Revolution of the early 20th century. Land policy of the 1934 Agrarian Code established the ejidos – tracts of communally held land with individual plots farmed by designated households – as a principle tool for redistributing land and property rights to peasants. Agrarian communities, a distinct form of land tenure located predominantly in the South where farmers had pre-existing claims to agricultural land, were similarly formed although to a lesser extent. A dual system of agricultural tenure emerged, with ejido farmers on the one hand and private landowners on the other. Within both the ejido and private farm sectors there exists both the larger, commercially oriented farms and the smaller predominantly subsistence farms. It is in this context that Berry and Cline first studied the farm size – productivity relationship in Mexico. Drawing from the Mexican Agricultural Census of 1940 and of 1960, they compared land productivity of small and large private farms. They found land productivity of small farms to be 6.5 times larger than that of larger farms in 1940, but just 3.5 times as large by 1960. More importantly, when output per unit of land and capital was measured, a more comprehensive measure of productivity, small farms were 1.7 times more productive than large farms in 1940 but just 0.8 times as productive in 1960. This early evidence illustrates that an inverse relationship between farm size and land productivity is neither necessary nor sufficient for an inverse relationship between farm size and more comprehensive productivity measures, similar to the findings of chapter 1 in the context of Brazil.

Berry and Cline hypothesized that the changing productivity ratios reflected a shift from livestock to crops on large farms, facilitated by government investment in infrastructure, provision of credit, and other supportive policies. As the birthplace of the Green Revolution, Mexican agriculture experienced productivity growth throughout this period, notably becoming net exporters of important staples such as wheat and maize. A weakening of the IR between farm size and land productivity accompanied this period of agricultural modernization and development, as did a reversal of the IR between farm size and output per unit of capital and labor. More recent research using farm-level panel data from the Mexico National Rural Household Survey , a household survey statistically representative of 80% of rural Mexico, showed evidence of an inverse relationship between farm size and productivity in 2003 and 2008 . By estimating an average production function and a stochastic production frontier, they find an inverse relationship between farm size and land productivity, farm size and average TFP, and farm size and TFP along the production frontier. They conclude that the observed farm size – TFP relationship was driven, in part, by larger farms being further from the frontier . Mexican agriculture in the early 20th century is an interesting setting for studying the farm size – productivity relationship because of the policy changes and market reforms associated with The North American Free Trade Agreement going into effect in 1994. As part of an economy-wide reduction in tariffs, agricultural tariffs were gradually eliminated over a 14-year span ending in 2008. The liberalization of agricultural trade exposed the Mexican agricultural sector to increased competition and imports from Northern neighbors. As a result, a flood of cheap imports has led to a decline in the price of staple crops for many Mexican farmers . For Mexican agriculture, NAFTA was part of a broader program of reform and market liberalization. One important change was the Program for the Certification of Ejido Rights and Titling of Urban Plots , which included reform of the ejido system of land tenure. Following a constitutional amendment, Procede facilitated the new option for ejidos to privatize individual parcels that could then be mortgaged, rented, or sold. Further, agricultural rights to ejido parcels ceased being contingent upon actual agricultural production, strengthening property rights for the ejido sector. Importantly for the private sector, stackable planters the practice of expropriating large private holding for the formation of ejidos was ended. By securing property rights and integrating ejidos into the market, these changes were expected to increase opportunities throughout the rural farm sector. A World Bank evaluation of the ejido reforms found that, while Procede had been widely successful in securing property rights, often in the form of certificates of agricultural rights, the program had not led to widespread land transfers and ejido farms remained credit constrained at the turn of the century. A second set of policy changes affected the manner in which government supported agricultural input and output markets. Policy shifted away from heavily subsidizing inputs and providing price supports for output towards a system of direct transfers for those impacted by increased international competition. In general, producers of staple products have suffered due to increased competition with relatively cheap imports whereas exports of high-valued horticultural products have benefited . The Program for Direct Assistance in Agriculture , primarily an income support program, offered per hectare payments to any farms with a history of producing any of nine key staples prior to 1993 that were actively farming one of those crops. An important change to the program in 1995 allowed participation of any farm producing any legal crop that had previously qualified for the program.

Further changes to the program in 2001 included higher per-hectare payments for farms under 5 hectares and a shift of the timing of payments to the start of the planting season. Alongside Procampo is Alianza para el Campo, a suite of programs designed to increase agricultural productivity primarily through investment in infrastructure and extension assistance. As government programs withdrew, farms became increasingly reliant upon markets for access to key agricultural inputs such as fertilizer, pesticides, and seed and for access to credit. Although government credit programs have scaled back, well functioning credit markets have not appeared in rural Mexico and access to credit markets is not widespread, inhibiting access to key inputs and modern technology. As in other developing country contexts, market concentration in both input markets and post harvest processing and marketing has hurt the profitability of family farms and generated economies of scale in transacting with the agricultural supply chain. We hypothesize that the farm size – TFP relationship is likely to be changing over time in the wake of Mexico’s NAFTA-era reforms, much as it appears to have done in Mexico during the Green Revolution and in Brazil’s modernizing agricultural regions . This hypothesis rests upon the assumptions that market imperfections contribute to any pre-existing IR in Mexican agriculture and Mexico’s NAFTA-era market liberalization has improved the efficiency of agricultural input and output markets. Beyond the farm size – productivity relationship, agricultural productivity is important to Mexico for both rural economic development and poverty reduction. According to data from the World Bank,2 agricultural output made up 3.6% of Mexico’s GDP but employed 13-14% of the workforce in 2015. Further, approximately62% of Mexico’s rural population is impoverished when using the national poverty line, suggesting that agricultural productivity has a potentially important role in Mexico’s rural economic development and efforts to reduce poverty. There are similar implications for trends in migration, as increasing agricultural productivity on family farms facilitates the ability to generate adequate livelihoods and effectively support families, reducing an important push factor in migration decisions.As discussed in chapter 1, land productivity is a partial measure of productivity and does not account for the use of inputs other than land. Where other inputs are used in production, failing to account for the use of those resources potentially introduces bias into estimates of the relationship between farm size and productivity if the intensity of input use varies with farm size. Controlling for all inputs in agricultural production can be accomplished with estimation of a production function, uncovering TFP, the comprehensive and preferable measure of productivity. We use two complementary approaches to explore the relationship between farm size and TFP with a panel of Mexican farms. First, we use an average production function to estimate average TFP and its relationship with farm size. Second, we use a stochastic production frontier to estimate both TFP along the technological frontier and technical inefficiency, identified as deviations from the frontier. The frontier analysis identifies any relationship between farm size and frontier TFP and any relationship between farm size and technical inefficiency. As is standard in the literature , we view TFP change as a combination of changes in the technological frontier and changes in the deviations from the frontier.

The removal of underripe berries was also evident by the difference in color among treatments. For BA, the rejected treatments were significantly lighter in color; however, the color of the sort and control treatments was very similar, whereas a similar trend was observed in the CS treatments. Wines made from GN generally did not follow these trends; possibly because sorting parameters were too aggressive for this cultivar, resulting in a high percent rejection of optimal berries. This may have minimized potential differences between reject wine with the other treatments. Another possibility is that color differences in the GN fruit did not correspond to differences in sugar content. From these results, it may be concluded that, when using color as a criterion, optical sorting based on ripeness level was successful but may be dependent on variety and fruit variability. Additionally, the impact on the resulting wine is likely dependent on the initial variability in grape ripeness. The optical sorter was successful in removing MOG. This result was reflected in the phenolic analyses; reject treatments were generally higher in total phenolics and tannin, most likely due to the greater proportion of MOG included in the must. The decrease in anthocyanins is likely due to the higher percentage of green, underripe berries in the reject treatment musts. A study that made wine with the addition of MOG found that this addition significantly increased the phenolic and tannin content in the resulting wines. Despite the differences observed in the phenolic composition of the reject wines, the control and sort treatments were very similar for all three varieties. This is in contrast with some previous studies that have found wine made from optical sorted fruit had significantly different levels of phenolics. One study found that optical sorting led to wines with higher levels of total phenolics. It should be mentioned that the researchers here did whole cluster pressing for their control wines , hydroponic nft system whereas the sorted wines were destemmed. It is possible that higher levels of phenolics were extracted due to the damage caused by the destemming process on the seeds and skins.

Another study found that wine made from optically sorted grapes that were machine harvested generally had lower levels of phenolics; levels that were similar to the same wines made from a handpick treatment. Given that the rejects were, in general, significantly higher in total phenolics and tannin than the control and sort treatments, it can be suggested that optical sorting has the potential to decrease the phenolic content in wine; however, there was not enough MOG to show a large impact in the current study. Optical sorting likely has a greater impact on mechanically harvest fruit due to generally higher levels of MOG observed from this harvest method. Some differences were found among treatments in the aroma profiles of the wines. Few compounds differed significantly between sort and control treatment and, in general, the reject treatments had greater concentrations of higher alcohols and control and sort treatments had greater concentrations of ethyl esters. The higher ethanol content of the sort and control treatments as well as their lower pH can lead to a higher production of esters. In general, reject treatments contained significantly more suspended solids then the control and sort treatments for all varieties studied. Research has shown that high levels of suspended solids during fermentation can lead to greater production of higher alcohols. Descriptive analysis indicated only one significantly different attribute among GN treatments and only two significantly different attributes among BA treatments. BA control and sort wines were associated with the “alcohol” descriptor which correlated with the higher ethanol levels in these treatments compared to the reject treatment. Similarly, there were only three significant attributes among the CS treatments. “Alcohol hotness” related to ethanol content as previously described. The control and sort treatments were also rated significantly higher in “apple” and “sweet” aromas compared to the reject treatment.

Some studies have shown that higher levels of ethanol can increase the perception of sweetness in a wine. However, as King et al. noted, there is disagreement in this regard, as other studies have shown that ethanol content can either decrease or have no effect on the perception of sweetness. Thus, this may not be a sufficient explanation as to why the control and sort wines were rated significantly higher in sweetness. Perhaps the higher concentration of total phenolics and tannin in reject wines could explain the difference given that phenolics in wine contribute to bitterness and astringency. From the PCA in Figure 6, it can be noted that “bitter” and “drying” are more associated with reject wines. Although these attributes are not significantly different among the treatments there appears to be a trend which could impact the perception of sweetness. It is possible that reject wines were rated lower in “sweet” due to the higher concentration of phenolic compounds thus decreasing the perception of sweetness. The higher perception of sweetness in the control and sort wines may also be attributed to the higher intensity of the “apple” aroma, which the judges could have associated with a sweet taste. One study found that retronasal aromaperception of fruity compounds increased with an increasing level of sweetness in a model wine solution. The authors also noted several other studies which found that aroma compounds can enhance the perception of sweetness in different foods and beverages. Another study found that samples described as “fruity” were also often associated with a “sweet” aroma. This provides further evidence that the judges in the current study may have associated these attributes together. The overall sensory differences were minimal, and the wines were determined to be similar. The results from this study largely agree with results from previous studies investigating the effects of optical sorters. It is possible that there was not enough variation in the starting material of the current study for optical sorting to have a large impact. Optical sorters may be used to greater effect during vintages with inconsistent ripening, issues with raisining, or large amounts of berry damage, possibly caused by either birds and/or fungal infections. Future research should investigate the impact of optical sorters in these scenarios. Keeping It Living developed from the content and discussions surrounding the 1997 American Association for the Advancement of Science symposium entitled “Was the Northwest Coast of North America ‘Agricultural’?: Aboriginal Plant Use Reconsidered.”

It is a compilation of exceptional work done by many scholars who have studied Northwest Coast Native communities from Oregon to Southeast Alaska. In each chapter, the authors present evidence from historic accounts and oral histories describing the management of plants for improved productivity. The long-standing construct is that Northwest Coast populations did not practice plant cultivation and instead relied almost exclusively on harvesting of marine resources and gathering of native fruits for sustenance. The book’s editors and contributing authors challenge this perspective. They suggest that the common view is based on the assumptions codified in the historical accounts from the seventeenth and eighteenth centuries and perpetuated by many anthropologists who visited with community members in the nineteenth and twentieth centuries. Although archaeological studies have provided plenty of evidence for the antiquity of Northwest Coast fishing practices, climate conditions in this region are not adequate for the preservation of plant remains. As such, there is no physical evidence of the history of indigenous horticultural or agricultural management. In light of this dilemma, the authors approach the subject from an ethnographic standpoint, utilizing past accounts and modern perspectives to reconstruct plant management by the indigenous peoples from Oregon to Southeast Alaska. The authors deftly organize the ethnographic evidence describing harvesting, seed collection, planting, and cultivation practices used by indigenous communities in this region. More than three hundred indigenous plants used by these communities are described and/or listed in this volume. In the introduction, nft channel the editors identify the need for a reconstruction of our understanding of indigenous resource management. The rest of the chapters are separated into two groups: concepts and case studies. In the first of the five concept chapters, Bruce D. Smith describes how the historic characterization of the Northwest Coast peoples as “affluent hunter gatherers” was based on the mistaken assumption that these people were not using agricultural techniques to enhance the productivity of useful indigenous plants. He calls into question the dualistic perspective that communities are either hunter-gatherers or agriculturalists. In the next chapter, Kenneth M. Ames describes the evolutionary intensification of food production systems in the Northwest Coast and elsewhere. He identifies food storage as essential for the development of the social complexity observed in these sedentary communities and offers a perspective on the implications of increased food production in complex hunter-gatherer societies. In chapter 4, Nancy J. Turner and Sandra Peacock provide a broad overview of the nature of peopleplant interactions in these communities and present some specific examples of plant resource management. Next they describe the “continuum” of indigenous plant-management activities practiced by these communities. In the concept section’s last chapter, Turner, Robin Smith, and James T. Jones describe ownership patterns for the plant resources used, illustrating how each group developed its own system of ownership based on environmental and cultural factors. The second section offers informative case studies of plant use from numerous Northwest Coast areas. Wayne Suttles describes the ownership, management, and harvest of camus bulbs by the Coast Salish. Their management techniques included loosening the soil, weeding out grasses, transplanting, and burning above ground vegetation after harvest.

Early ethnographers used the terms semiagricultural and protohorticultural to describe these practices. Suttles suggests that the cultivation of camus may have been described as protohorticultural because lilies were common in European flower gardens at the time of contact. Melissa Derby describes how precontact Chinook villages of the Lower Columbia River were situated adjacent to the wetlands where the wapato grew. She makes the case that the level of social complexity of the Chinookan people is related to their management of wapato as an agricultural commodity. Dana Lepofsky and her colleagues present direct and indirect evidence for the use of controlled burning in indigenous agroecosystems in British Columbia’s Fraser Valley. Next, James McDonald uses historical documents to describe how the Tsimshian managed horticultural plants for food production. For example, an account from 1859 documents the members of this community farming “potato” . Other visitors observed plant management for the harvest of berries, crab apples, maplewood, ferns , hemlock bark and sap, lichen, devils club, and skunk cabbage. Remarkably, the individuals who described community ownership of specific berry patches simultaneously maintained the view of the Tsimshian lands as an unmanaged wilderness. McDonald is the only author who states the obvious: it benefits the colonizers to perpetuate this myth because it enables them to justify the appropriation of the land on the grounds that it is in need of management. In chapter 10, Madonna Moss describes Tlingit horticulture in Southeast Alaska, the northernmost portion of the Northwest Coast. Moss characterizes the Tlingits’ precontact management of indigenous plants as a system of selective harvesting. The exception was tobacco, which was grown prior to European contact using the horticultural management techniques of seeding, weeding, and fertilizing. She proposes that it was their expertise with tobacco that enabled these people to raise the horticultural crops introduced in the eighteenth century successfully. In the final case study, Douglas Deur describes the creation and maintenance of estuarine gardens by indigenous communities. Keeping it Living is a shining example of scientific reevaluation and concentrated inquiry of a long-held perspective, and it is as necessary as it is exemplary. Litigation involving Indian claims in the modern era often revolves around the complex and expensive reports prepared by ethnohistorians, historians, anthropologists, and other experts. Any claim involving the meaning of a treaty provision or whether a tribe qualifies for gaming on lands acquired after 1988 or even whether a tribe should be federally recognized will involve this battle of experts. Tribal victories in the Sioux Nation’s Black Hills land claim, Pacific Northwest and Great Lakes treaty fishing rights, and eastern land claims would have been unobtainable without careful expert testimony.

We calculated daily energy requirements for birds under field conditions as M =  2.5, where W is the weight of an average insectivorous bird on coffee farms . We calculated the weight of an average insectivorous bird by averaging body masses of 33 insectivorous resident and migrant bird species reported to consume CBB on Jamaican and Costa Rican coffee farms , or predicted to consume CBB based on morphology and diet breadth . Sherry et al. found that CBB made up 5%–10% of the diet of three Neotropical migratory warblers by number of individuals consumed; we used these percentages to estimate how many calories, and therefore how many CBB, birds potentially eat. Avian consumption rate of CBB was constant, with even effort across the coffee season. For avian densities, we used estimates from Karp et al. of 3 to 14 birds per ha, because these densities include known CBB predators on coffee farms in Costa Rica.Parameters for our Leslie matrix for coffee berry borers are broadly consistent with expectations and general knowledge . For example, our conversion of fecundity to a daily value, F1 = 1.341, is consistent with published literature stating that 1–2 eggs are laid per day by CBB . Model projections showed that across a 185-day CBB breeding period starting at the point of first ovipositing, an initial population size of 100 female dispersers would produce 1.3 million offspring, resulting in a new adult population of 70,245 females . Assuming  99% of colonizing females successfully bore and oviposit in a coffee cherry on Day 0, the first generation of new dispersing females does not appear until day 37. At Day 38, the adult population begins to increase, and continues to do so exponentially.The daily growth rate of this population converged on 1.042. Sensitivity analysis revealed that survival of adult females had the largest impact on overall population growth , followed by daily survival of pupa , juveniles , eggs and larvae and dispersing females . In addition to modeling growth with 100 initial colonists , grow bag for tomato we projected the population growth of low and high starting populations calculated from observed weekly alcohol-lure trap catches during peak dispersal .

Comparing the three population projections, peak number of dispersers at Day 185 varied considerably, with 162, 3259, and 8768 daily dispersers for low, medium, and high colonizing populations, respectively. In the high population projection, the adult population toward the end of the growing season reached over 18,800 individuals. Note that because these are density-independent models, the number of CBB does not depend on plant density. However, the impacts of the CBB population on yield would depend on coffee plant density. To reduce the final adult population by 50%, the daily survival rate of dispersing females would have to be reduced from 0.99602 to 0.83202. This change represents a 16.4% reduction in daily survival when dispersing. The number of CBB that birds need to eat to reduce the adult population at this rate was driven by the initial population size as a straight line, y = 79.23 N0 . At medium starting population , birds need to consume 7628 CBB during the borer breeding season, while at high starting population , about 20,500 dispersing CBB must be consumed by birds. Daily consumption rates by birds would have to increase over time as the CBB population grows and could vary from 15 to 750 CBB being consumed a day, depending on starting population size . Overall, we calculated that for every female CBB in the initial colonization, birds need to consume 79 CBB to reduce the end of season population by half.We estimated that the caloric content of a 195 μg adult CBB to be 1.09 calories per gram dry weight, or 0.00109 kcal. At 5%–10% of a bird’s daily diet based on number of prey items, birds would consume <7 CBB per day. This represents 0.03%–0.05% of daily caloric requirements of our average insectivorous bird. At these feeding rates, our models suggest that by the time of peak dispersal, 4, 88, and 236 birds are required at low, medium, and high starting population sizes, respectively, to reduce CBB populations by 50% on day 185 .Our model suggests that avian predation is likely to be effective at reducing CBB populations by 50% only during small infestations , or during the early stages of larger infestations .

Birds appear unable to successfully suppress medium and large infestations because the number of CBB that need to be eaten in a season requires higher bird densities than are reported in the literature. Karp et al. estimated 4–12 birds/ha of species that are confirmed or suspected CBB predators. Flocks of migratory birds on coffee farms are estimated at 19/ha and 24/ha , but these values are also short of our estimates of necessary densities for suppressing larger CBB outbreaks. One caveat to our conclusions is that our calculations were based on CBB accounting for 5%–10% of a bird’s daily diet . This assumption meant birds would only eat a set maximum of 7 CBB per day. Sherry et al. reported up to 116 CBB in the stomach contents of a single warbler, suggesting under certain circumstances in the field, birds eat more CBB. Generalist insectivores, particularly Neotropical migrants, have flexible foraging preferences and would likely feed opportunistically on CBB in response to dramatic dispersal peaks. Therefore, birds might be expected to increase feeding rates as CBB disperser abundances increase, though it may depend on the relative abundances of other prey. Better data on CBB consumption rates by birds under different circumstances would improve our estimates of the circumstances under which birds can control CBB populations. A second caveat is that bird densities used in the model may not represent the potential for CBB control because bird densities depend on the structure of the agricultural landscape, which the current model does not consider. On coffee farms, birds are more abundant when native tree cover is highest and natural forests are close by . Across tropical and temperate regions, the propensity for birds to forage on farms, and thus exert pressure on agricultural pests, is correlated with the physical complexity and diversity of the agroecosystem . For example, birds make more frequent foraging trips to apple orchards with high native tree coverage . In alfalfa fields, edge habitat complexity supports greater avian richness leading to lower pest abundances . Under some circumstances, the density of birds foraging in certain areas may behigher than average densities would imply, leading to greater control potential than our models suggest.

More generally, our CBB population model is density independent and assumes environmental conditions and sufficient resources to allow CBB populations to increase without restriction. As a result, our model is limited, as it does not consider localized effects of weather and temperature fluctuations on CBB developmental time , nor characteristics of coffee farms that influence both CBB infestation and bird density. We assumed maximal capacity for CBB population growth and used estimates of bird densities from the literature that only included birds known to consume CBB, perhaps underestimating the potential for avian control. Models are an important tool for estimating population dynamics, but as with any species, the growth potential for CBB and availability of its predators, is context dependent. Our study echoes Kendall et al.’s conclusion that, grow bag for blueberry plants even though errors in model construction are common, these seldom change qualitative conclusions. From our population matrix, CBB daily growth rate converged on λdaily = 1.042 around day 124, with an observed rate of population change across the entire coffee-growing season of 705 . Our λdaily is higher than Mariño et al.’s reported lambda of 1.32 over  50– 56 days, which corresponds to λdaily ≈ 1.006 . Part of this discrepancy may come from the fact that Marino et al. combined vital rates across life stages with different time steps. Nonetheless, both models are consistent in predicting rapidly growing populations. Observed CBB population growth rates are similar to ours: Baker, Barrera, & Rivas, calculated a 1.067 growth rate in wild populations and RuizCardenas and Baker reported 1.047 in CBB reared in laboratory settings. In their sensitivity analysis, Mariño et al. reported that adult female survival, and transitions from larva to pupa and pupa to juvenile had high sensitivity in contributing to population growth rate, with adult survival the highest . We found a similar peak sensitivity value for female adult survival in our matrix , supporting the idea that CBB population growth is most sensitive to adult survival rate. Interestingly, dispersal survival from our matrix was estimated to have low impact on population growth , even though this life stage is when CBB are vulnerable to bird predation. Thus, our analysis superficially suggests that population control once CBB are established should focus on reducing adult survival rather than on trapping dispersing females , if the same impact on numbers could be achieved. However, dispersing females are much more accessible to control methods like spraying fungal bioinsecticide than are adult females, which are inside the coffee cherries, so despite the tremendous difference in sensitivity values, management of an established population is likely to be more cost effective by continuing to focus on dispersing females . Population models specific to CBB have been criticized for not being representative of wild populations, since more generations are estimated through modeling than are observed in field studies . We analyzed CBB population growth using a deterministic model, with an even distribution of dispersal and a fixed predation pressure. While CBB dispersal is continuous, there can be dramatic intraseasonal peaks in numbers that were not captured by our model . In addition, reported longevity of female CBB varies widely from 55 to 380 days, though some studies looked at CBB reared on artificial diet . Refinements of survival in natural settings would, therefore, improve models of CBB population growth, and the potential for control by birds. If field data on CBB vital rate stochasticity become available, and bird densities opportunistically increase during CBB peak numbers, it could affect our conclusions about the capacity of birds to control larger CBB outbreaks. Based on our analyses, there is a population density of CBB above which their capacity to produce more adults exceeds the ability of birds to control their numbers, at least to limit the population size by 50%. This positive density-dependent relationship between population growth and density is an Allee effect , and escape from predation is one mechanism for this phenomenon . In general, predator-driven Allee effects can occur when predators are the main driver of prey dynamics and when predators are generalists as are insectivorous Neotropical migrants . Additionally, predators can exert strong pressure when prey availability is not temporally or spatially limited—a potential limiting factor in the coffee system, since CBB are only available to birds during dispersal. Variation in starting population size is likely dependent on how recently CBB have colonized in an area, timing of trapping , the size of the farm , and the extent to which farmers used control measures the previous year . We found that only under very low initial population sizes of CBB could birds be expected to suppress pest numbers by 50%. We note that earlier, stronger CBB suppression by birds would lead to lower infestation numbers later in the coffee season, but this might require selective foraging by birds, depending on relative abundances of other prey species. In conclusion, our models suggest that birds can control CBB under some circumstances, depending on the relative size of the starting CBB population and existing local bird density. To put this idea into practice it is important to remember that managing farms for bird habitat does not always result in pest reduction. Birds may not prey on the pest of interest or birds might cause pest numbers in increase by preying on insect predators that normally regulates the pest population . Aside from predators, pest species are also impacted by the agricultural environment directly . In fact, on coffee farms where bird densities are higher in shade, CBB infestations are also higher , possibly because CBB native range is in humid, shade forests of Africa . It is important that future modeling include such habitat-specific factors to understand Our research helps quantify the densities under which birds have the potential to control CBB populations.

The molecular underpinnings of color variation and fruit shape in Fragaria are mostly unknown or unreported, although clearly of interest for development of molecular markers for breeding purposes to meet changing consumer tastes. In strawberry, antioxidant compounds such as polyphenols and ascorbic acid are important nutritional traits. Yet these are difficult traits to assess as they are influenced not only by genotype, but by the growing environment and by developmental stage. Forexample, levels of the bio-active nonflavonoid polyphenol, ellagic acid , is higher in achenes from ripe fruit of the F. vesca cultivar Yellow Wonder than in achenes from ripe fruit of F. × ananassa cultivar Calypso. A complication for improving fruit nutrient quality is that EA levels are higher in achenes than in receptacles of all cultivars tested, and EA is found primarily at small green stage. In addition, the mode of inheritance of EA content is yet to be elucidated. Previously unidentified bio-active compounds, such as the acylphloroglucinol glucosides discovered in F. × ananassa while examining the enzymatic properties of recombinant F. vesca chalcone synthases, may also exist in Fragaria species. With the availability of modern methods in metabolomics and allied fields, discovery of additional bio-active compounds is likely, and these methods can be applied to direct molecular approaches to improving fruit quality. In the future, metabolic flux analysis should also enhance our ability to delineate what biochemical pathways are good targets for fruit quality improvement as well and to predict what modifications may influence fruit quality parameters.There has been ample progress in recent years in describing the genetic architecture of disease resistance in cultivated strawberry. Many resistances appear to be primarily conferred by one or two major loci or large-effect QTL, including to Phytophthora fragariae, Xanthomonas fragariae, Phytophthora cactorum, Fusarium oxysporum f.sp fragariae, Colletotrichum gloeosporoides, and Colletotrichum acutatum.

For P. cactorum, additional minor loci have recently been identified. On the other hand, resistances to Verticillium dahaliae and Podosphaera aphanis appear to be quite complex, grow bag with no major loci identified to date. This suggests that genomic prediction approaches for these two diseases would be most effective. However, with the advent of the “Camarosa” genome, an opportunity exists to characterize Mildew Locus O genes in strawberry toward potential gene editing solutions. Elucidating the genetics of resistance to M. phaseolina should be a high priority in the future, given the recent spread of this pathogen in important production regions and the lack of effective controls for this disease. In addition, no resistance genes have been reported against gray mold caused by Botrytis cinerea. Instead, it seems most likely that any small differences in tolerance to this disease among cultivars results from morphological variations in flower structures, fruit firmness, etc. Because strong resistance to B. cinerea is not likely to result from conventional breeding, a gene editing solution may be most viable. Where disease resistances are conferred by one or a few genes, genetic and breeding approaches to characterize and increase resistance are straightforward. In the cases where classical R genes are involved, the development of custom-capture libraries and single-molecule resequencing of captured target sequences has been quite effective for identifying causal gene variants. In fact, such a resource has now been developed for cultivated strawberry in the form of a RenSeq library based on the “Camarosa” reference and resequencing of a number of elite cultivars and breeding lines. Combining this resource with mapping and association genetics approaches should help uncover subgenome-specific variants underlying known loci and lead to the cloning of R genes in octoploid strawberry. Given the tremendous allelic diversity present in strawberry and the large copy numbers and highly repetitive coding sequences typical of R genes, assembling long reads from single-molecule realtime sequencing should be helpful to this endeavor. Hand in hand with characterization of R genes, we recommend the characterization of pathogen populations in order to understand the durability of resistances.

The paradigm of a gene-for-gene arms race has been long established, but a more accurate assessment of the durability of resistance could arise from an understanding of the selective forces operating on pathogen effectors. Dual RNA-seq technology can help uncover the dynamic interactions of pathogen and host. Both the pathogen and the host transcriptomes are simultaneously captured and analyzed in silico to distinguish species specific transcripts. For some complex interactions, single cell transcriptomics coupled with protein and metabolite analysis may be helpful. What new insights into disease resistance in strawberry could be gained simply from studying the population structures of causal pathogens? Would identifying and characterizing pathogen effectors give us meaningful insights into the control of pathogens through breeding and other means? It is intriguing that some recently discovered resistance loci in strawberry confer very strong resistances and yet have apparently been durably effective in commercial production for many decades. Cloning the first R genes and pathogen effectors involved these interactions will help us to understand why.The Genome Database for Rosaceae is the central repository and datamining resource for genomics, genetics, and breeding data of Rosaceae, including strawberry and related crops such as almond, apple, apricot, blackberry, cherry, peach, pear, plum, raspberry, and rose. The volume and type of data generated for strawberry research has markedly increased in the past ten years. This includes whole-genome assembly data, RNA-seq data, multiple SNP arrays, increased numbers of QTL, and more genotypic and phenotypic data. The massive volume of data generated by the strawberry research community, combined with active curation, integration, further analyses and tool development by the GDR team has resulted in marked expansion in the data and functionality available for strawberry. In addition to the near-complete chromosome-scale assembly for F. × ananassa, two draft genome assemblies for F. × ananassa are available. Four genome assemblies, including the newest v4.0, are also available for F. vesca. New and much improved annotation v4.0. a2, including 34,007 protein-coding genes with 98.1% complete Benchmarking Universal Single-Copy Orthologs , is available. For older assemblies F. vesca genome v1.1 and v2.0, additional annotations are also available: v1.1.a2 and v2.0.a2, respectively. The draft genome assemblies of four wild diploid Fragaria species and of Potentilla micrantha a species that does not develop fleshy fruit but is closely related to Fragaria, are also available. In addition, the whole genome of F. iinumae has recently become available. GDR now provides a reference transcriptome that combines published RNASeq and EST data sets. The GDR team provides additional computational annotation for both predicted genes of whole-genome assemblies and RefTran datasets with homology to genes of closely related or model plant species and assignment of InterPro protein domains and GO terms. The genome assembly and transcript data can be accessed through the Fragaria genus and species pages, Gene/Transcript search page, JBrowse and BLASTX. The octoploid “Camarosa” genome, F. iinumae v1.0, and both annotation versions of F. vesca Genome v4.0, are used in a synteny analysis with whole-genome assemblies from 18 Rosaceae species using MCScanX with results available to view and search through the Synteny Viewer. GDR hosts 29 genetic maps for Fragaria species, most of which contain trait loci and can be viewed and compared through the MapViewer. Detailed data on 505 QTLs and 5 MTLs for 124 horticultural traits, and 171,115 genetic markers for Fragaria that includes 154,739 SNPs are available, as well as SNP data from the iStraw 90 K array for cultivated strawberry. The SNP data is accessible through JBrowse tracks, downloadable files and can be searched and downloaded from the SNP Marker and All Marker search pages. The Marker search page now includes filtering by trait name, which allows users to search for markers that are near and/or within QTLs using the associated trait name. Phenotyping data from the public projects such as RosBREED are available from GDR. In addition to the “Search Trait Evaluation” page, the public breeding data can be queried and downloaded using the Breeders toolbox.

A new module in GDR, grow bag gardening the Breeding Information Management System , now provides breeders and breeding project teams with tools to easily store, manage, archive and analyze their private or public breeding data. The availability of whole-genome assembly and SNP array data for the cultivated octoploid strawberry, along with wealth of QTL data that are integrated in the community database with data from other related crops are expected to accelerate research and practical tools such as DNA tests. BIMS in GDR will help breeders not only to organize their data but also to utilize the tools and resources that are available for strawberry improvement.The strawberries found in markets around the world today are produced by cultivated strawberry Duchesne ex Rozier, a species domesticated over the past 300 years . F. ananassa is technically not a species but an admixed population of interspecific hybrid lineages between cross-compatible wild allo-octoploid species with shared evolutionary histories . The earliest F. ananassa cultivars originated as spontaneous hybrids between F. chiloensis and F. virginiana in Brittany, the Garden of Versailles, and other Western European gardens in the early 1700s, shortly after the migration of F. chiloensis from Chile to France in 1714 . Their serendipitous origin was discovered by the French Botanist Antoine Nicolas Duchesne and famously described in a treatise on strawberries that biologists suspect included one of the first renditions of a phylogenetic tree . Even though those studies predated both the advent of genetics and the discovery of ploidy differences in the genus, the phylogenies were remarkably close to hypotheses that emerged more than 150 years later . The early interspecific hybrids were observed to be more phenotypically variable than and horticulturally superior to their wild octoploid parents, factors that drove the domestication of F. ananassa. The increase in phenotypic variability can be directly linked to an increase in nucleotide diversity and heterozygosity, and presumably to the introduction of complementary favorable alleles that were not found in either parent. Hardigan et al. showed that hybrids between F. chiloensis and F. virginiana have nearly double the genome-wide heterozygosity of their parents. With the mysterious origin of the spontaneous interspecific hybrids solved , breeding and cultivation shifted to F. ananassa, which supplanted the cultivation of the wild relatives and forever changed strawberry production and consumption worldwide . The romanticized and widely recounted story of the origin of cultivated strawberry, while compelling, oversimplifies the complexity of the wild ancestry and 300-year history of domestication, for which we have an incomplete understanding . One of our motives for reconstructing the genealogy of cultivated strawberry was to shed light on the origin and diversity of the wild founders and the breeding history. The only pedigree-informed studies of the breeding history of cultivated strawberry focused on an analysis of the ancestry of 134 North American cultivars developed between 1960 and 1985 . They identified 53 founders in the pedigrees of those cultivars, estimated that 20 founders contributed approximately 85% of the allelic diversity, and concluded that North American cultivars had originated from a genetically narrow population . Others have reached similar conclusions , and the notion that cultivated strawberry “displays limited genetic variability” has persisted . Gaston et al. were possibly alluding to the absence of morphological diversity on par with that found in tomato . Nevertheless, the genetic narrowness hypothesis has not been supported by genome-wide analyses of DNA variants, which have shown that F. chiloensis, F. virginiana, and F. ananassa harbor massive nucleotide diversity and that a preponderance of the alleles transmitted by the wild octoploid founders have survived domestication and been preserved in the global F. ananassa population . Hardigan et al. proposed an alternative to the “limited genetic variability” hypothesis , arguing that genetic variation has not been reduced by directional selection or population bottlenecks in certain populations. One of the consequences predicted by this hypothesis is the persistence of a high frequency of unfavorable alleles in domesticated populations. The domestication of cultivated strawberry has followed a path different from that of other horticulturally important species, many of which were domesticated over millennia and traced to early civilizations, e.g., apple , olive , and wine grape . Although the octoploid progenitors were cultivated before the emergence of F. ananassa, the full extent of their cultivation is unclear and neither appears to have been intensely domesticated; e.g., Hardigan et al. did not observe changes in the genetic structure between land races and wild ecotypes of F. chiloensis, a species cultivated in Chile for at least 1,000 years .