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 .

Policy discussions of the future of small farms, for example, emphasize the role of small farms in agricultural development in part because of their superior efficiency . This argument leans heavily on the inverse farm size – productivity relationship, but requires that small farms be more efficient with their use of all resources and not just land. Whereas a farm size – land productivity relationship does not provide clarity on this issue, a farm size – total factor productivity relationship does. In this light, we argue that the inverse relationship literature needs to shift its focus from land productivity to total factor productivity. In fact, empirical studies assessing the productivity – farm size relationship in the developed world, such as Garcia et al. , Alvarez and Arias , and Rasmussen , almost exclusively use measures of technical efficiency or total factor productivity. Similarly, the literature estimating national level agricultural productivity is clear in its use of total factor productivity as a preferred measure . We illustrate the importance of productivity measures with new empirical evidence on the farm size – productivity relationship across regions of Brazil from 1985 to 2006 . Our evidence is only suggestive because we are unable to correct for potential issues of measurement error in farm size, output, and inputs that have been identified in recent literature. However, this period in Brazil provides an excellent case study because it includes regions with relatively advanced agricultural sectors, those characterized by more traditional agricultural production, and others experiencing rapid agricultural transformation, allowing us to assess the farm size – productivity relationship and its dynamics at different stages of agricultural development. Using a pseudo-panel of farms aggregated at the municipality by farm size level, square black flower bucket we show that estimating the farm size – productivity relationship using land productivity is potentially misleading.

While we always identify an inverse relationship using land productivity, we find disparate results when using total factor productivity. In the modern agricultural regions of Brazil, we find a direct relationship between farm size and total factor productivity, and in the rapidly transforming region of the Center-West we identify dynamics that suggest the inverse relationship is disappearing over time. The analysis highlights that the relationship between total factor productivity and farm size has evolved with modernization, shedding some light on the issues raised by Mill over 150 years ago. The remainder of this paper is organized as follows. In Section 2 we seek to clarify the common measures, their relationships, and their advantages and limitations in empirical work. Section 3 presents the empirical exercise, generating new evidence on the relationship between size and productivity in several macro regions of Brazil. In Section 4 we summarize and conclude with policy implications.Farm size may be related to a broad range of economic outcomes, such as employment, poverty, inequality, food security, efficiency and growth. While these are important issues connected to the role of farm size in development, here, as with most of the literature on the inverse relationship , we focus specifically on the concept of productivity. The following discussion seeks to clarify the relationships between the various productivity measures most commonly used in the literature, allowing us to draw conclusions on the impact that choice of measure may have on finding an IR and the potential implications for policy.The relationship captured by is unconditional in the sense that it is the simple bivariate relationship between land productivity and farm size. Using land productivity as a measure is inherently limited—as would be any partial measure of productivity—whenever there is more than one factor of production.

If use of other factors vary systematically with farm size, the IR between land productivity and farm size may simply reflect more input intensive practices of small farms. Higher land productivity may reflect overuse of fertilizer, for example, which would not necessarily reflect any underlying productivity advantage of small farms. In such situations, estimates of the farm size – land productivity relationship introduces omitted variable bias into estimates of the underlying farm size – productivity relationship. From this perspective, a focus on the relationship between land productivity and the size of farms may be misplaced. Similarly, analysis using different partial productivity measures may result in conflicting policy recommendations. Indeed, Sen’s seminal contribution revealed precisely this type of systematic relationship between the intensity of labor use and farm size, leading to his formal exposition of the dual labor market hypothesis . Figure 1.2 illustrates the problem in the case of Brazil. While there is an inverse relationship between land productivity and farm size, there is a direct relationship between labor productivity and size. Analysis of the farm size and productivity relationship using labor productivity suggests that larger farms are more productive than are their smaller counterparts. Policy recommendations from the two partial measures of productivity would differ, underscoring the need for a comprehensive measure of productivity when identifying any relationship with farm size.We now provide an example using data on Brazilian agriculture. The intention here is not to explain the relationship between farm size and productivity by controlling for its potential determinants. Rather, we seek to use a regional analysis within Brazil to highlight how the choice of measure influences the observed relationship and how these patterns can change across stages of agricultural development. Our evidence is only suggestive because we are unable to correct for the measurement issues in farm size, outputs, and inputs that recent literature has focused on. We discuss this further below. The results provide an important counterpoint to much of the literature that has focused on countries in Africa and Asia where the overwhelming majority of farms have less than 2 hectares . Mean and median farm size in Brazil, in contrast, were around 65 and 10 hectares in 2006. The data come from the 1985, 1995/1996, and 2006 rounds of the Brazilian agricultural census. For confidentiality reasons, we constructed a pseudo-panel in which all farms in the census are aggregated into five farm size classes within each municipality of Brazil.9 Aggregation requires that we assume homogeneity within each observation . We call these “representative-farms,” as they reflect the average behavior of a given farm size in a given municipality. The pseudo-panel approach has been used recently to study agricultural productivity growth by Key and Rada et al. . Antmann and McKenzie demonstrate that, in the context of mobility studies, pseudo-panels can be used to consistently estimate parameters of interest. The averaging within cells in each period reduces the influence of individual-level measurement error, and the fact that it is not a true panel of farms makes it less vulnerable to non-random attrition. They show the approach is also robust to some forms of non-classical measurement error. We begin with 47,365 representative farms for all of Brazil across the three survey years. Due to concern about the comparability of a small number of extremely large observations, square black flower bucket wholesale we remove all representative farms in the Northeast and South over 4,000 ha and all of those over 5,000 ha in the North, Southeast, and Center-West. We then identify land productivity outliers taking into account the IR shown in Figure 1.1 and potential non-linearities. Thus, rather than trim the tails of the unconditional land productivity distribution, we use a quadratic specification to regress land productivity on farm size with municipal fixed effects and survey year dummy variables.

From this regression we identify and remove outliers, defined as all representative farms with residuals greater than four standard deviations from their size specific predicted values. Together, the data cleaning exercises remove 1.8% of the initial sample. The Census data were gathered by the Brazilian Institute of Geography and Statistics through end of season in-person farmer interviews based on recall. Output is measured as the real value of total agricultural production, deflated to 2006 with a price index developed from the data in Gasques et al. . Farm size is measured in hectares , and unlike in many African and Asian countries the overwhelming majority of farms operate a single plot. Additional factors of production used in the production function are family labor, purchased inputs including hired labor, and an index of capital. The number of male, female, and child family members working on each farm are used to develop a family labor index measured in adult male equivalents. The index assigns weights of 1.0 to men, 0.75 to women and 0.5 to children under 14. In 2006 around two thirds of family labor was provided by men, and over 90% of working family members were 14 years or older. The real value of purchased inputs, including expenditure on fertilizer, seeds, hired labor, fuel, energy, soil amendments, and other items, are deflated with the same price index used for output. A proxy for the total capital stock is calculated as a quantity index comprised of machine, animal, and tree capital stock sub-indices following Moreira et al. and Butzer et al. . The machine capital stock index values tractors of five horsepower classes, trucks, harvesters and other agricultural equipment using a constant set of sale prices drawn from the Instituto de Economia Agrícola in São Paulo. The stock of animal capital is measured in cattle equivalents of the nine most important animal stocks and aggregated with a set of time invariant relative prices . The stock of tree capital is measured as the present discounted value of expected future profits for thirteen different tree crops, using region-specific estimates of expected profits. The subindices are aggregated using region-specific weights estimated by regressing output on the three capital stock sub-indices in the base year 1985.13 Additionally, we control for unexpected shocks in rainfall and temperature to each municipality in each survey year utilizing data described in Wilmott and Matsuura . These quarterly shocks are measured as standardized deviations from 25-year moving averages ending in the year prior to each Census. The data are transformed into categorical variables capturing extremely low, below average, average, above average, and extremely high values relative to the historical municipal average. Weather shocks between -1 and 1 standard deviations are treated as normal weather years and are the reference category, with extremely high and extremely low values occurring at more than ±1.645 standard deviations. The data used are drawn from a nation-wide decennial census and are potentially subject to multiple sources of measurement error. The literature on measurement error and its implications for the IR has grown rapidly in recent years. Of greatest concern are non-classical types of measurement error that are correlated with farm size. Carletto et al. , Carletto et al. , Abay et al. and Dillon et al. examine measurement error in self-reported farm size relative to more accurate approaches to measuring land . They demonstrate clearly that farmers report area with error, that this error varies systematically with farm size, and that whereas small farms tend to overestimate farm size, large farms tend to underestimate their size. The implications for the IR literature are mixed, as Carletto et al. and Abay et al. find that the IR becomes stronger when measurement error in farm size is the sole correction made, but Carletto et al. and Dillon et al. both find that correcting for such measurement error partially mitigates the IR in some of their data but has no statistically significant impact elsewhere. Similarly, several recent papers have explored the implications of non-classical measurement error in output. Desiere and Jolliffe , Gourlay et al. , and Lobell et al. show non-classical measurement error in self-reported output when compared to “crop cuts” as the gold standard measure. Importantly, small farms overreport output more so than larger farms in their data. Conditional on GPS land measurement, the IR disappears in these papers when they utilize the more objective measure of output. Abay et al. explore measurement error in both farm size and output, and concur that in their data the IR disappears when land is measured objectively and then crop cuts are used to correct for measurement error in production. However, they caution that the IR strengthens when land is self-reported and measurement error in output alone is corrected. Lastly, measurement error in the use of inputs such as labor is potentially an issue. Relative to weekly surveys conducted in-person or by phone, end of season surveys of labor usage can contain substantial errors .

The four new fungicides were moderately to highly effective in reducing PRR and P. cinnamomi populations in rhizosphere soil of the avocado seedlings and rootstocks used. Overall, oxathiapiprolin was the most effective among fungicides evaluated. In experiments with Zutano seedlings, the efficacy of oxathiapiprolin at the low rate of 70 g/Ha was 2- to 33-times higher than that of the other fungicides and 2- to 4-times higher than that of mandipropamid, a CAA fungicide. In a study on managing P. capsici on peppers , the difference in effectiveness of oxathiapiprolin at 30 g/Ha as compared to the CAA dimethomorph at 262.5 g/Ha was similar to our study using the same FRAC codes of fungicides. In response to reducing PRR, avocado plants treated with oxathiapiprolin generally developed more shoot and root growth as compared with untreated plants. On the avocado seedlings and rootstocks used, fluopicolide, mandipropamid, and ethaboxam treatments also effectively reduced the incidence of PRR compared with the control. P. cinnamomi propagules in the rhizosphere soil were only significantly reduced on the Zutano seedlings and the Dusaâ rootstock. These latter treatments were often significantly more effective than potassium phosphite or mefenoxam; whereas fluopicolide often performed statistically similar to oxathiapiprolin. Still, the efficacy of potassium phosphite was demonstrated with significant reductions in PRR on the seedlings and rootstocks although its overall performance may have been compromised by the use of three P. cinnamomi isolates with reduced sensitivities to the fungicide in our soil inoculations. These results also could explain why potassium phosphite is still effectively used in managing PRR in California since many growers cultivate avocado trees grafted on the Dusaâ rootstock. Thus, flower buckets wholesale highly effective alternatives to mefenoxam and the phosphonates were identified by us for the management of avocado PRR.

Oxathiapiprolin used at low rates provided similar or better efficacy than the other fungicides. Oxathiapiprolin, fluopicolide, mandipropamid, and ethaboxam previously demonstrated high efficacy against selected foliar and root diseases of vegetable and tree crops caused by Oomycota organisms in greenhouse and field studies. Thus, the four fungicides were highly efficacious in reducing Phytophthora root rot of citrus caused by P. nicotianae and P. citrophthora . Oxathiapiprolin, fluopicolide, and mandipropamid were more effective in managing P. capsici on watermelon than mefenoxam or potassium phosphite . In other studies, oxathiapiprolin was shown to be highly effective in managing diseases of vegetable crops caused by Phytophthora species including P. capsici and P. infestans and controlled black shank of tobacco caused by P. nicotianae . Ethaboxam was shown to be an effective treatment for tomato late blight , as well as Phytophthora blight of pepper . Based on our studies, registration of oxathiapiprolin for use on avocado has been initiated through the Inter-regional Research Project No. 4 , and ethaboxam, fluopicolide, and mandipropamid are proposed for further development on avocado. Additional evaluations will have to be done under field conditions using rootstocks with different growth characteristics and susceptibilities to PRR. The availability of fungicides with new modes of action and options for rotation and mixture programs using previously registered and new fungicides will help reduce the risk of development and spread of resistance in P. cinnamomi populations in California avocado production. Growers currently rely heavily on the use of phosphonate-based fungicides, and as we demonstrated, pathogen populations are shifting towards reduced sensitivity to this fungicide class. Thus, there is an urgent need to register fungicides with new modes of action. In our greenhouse studies, overall treatment efficacy in reducing PRR and soil inoculum levels of the pathogen on the susceptible PS.54 was reduced as compared with the more tolerant Dusa rootstock, indicating additive effects of fungicide use and rootstock selection. In an integrated approach for a durable and effective management of PRR that allows the continued economical production of avocados in P. cinnamomiinfested soils, the use of tolerant rootstocks is critical along with irrigation management and cultural practices such as using mulching and planting in areas with good soil drainage.

There are Phytophthora species that can infect only one, or a few different hosts like Phytophthora infestans de Bary, and then there are species that can infect hundreds or even thousands of different plant species such as P. cinnamomi Rands . P. cinnamomi is of particular interest in California because it causes Phytophthora root rot of avocado, in fact, PRR is the most destructive disease of avocado production worldwide . PRR limits production of avocado by killing feeder roots which reduces fruit yield and can cause tree death . P. cinnamomi impacts other fruit crops such as peach, pineapple, and high bush blueberry, as well as affecting natural stands of eucalyptus, pine, and oak . Areas that have become infested with P. cinnamomi will never completely remove this pathogen from the soil. Current chemical treatments are being challenged by the emergence of isolates that are more virulent and less sensitive to potassium phosphite . The current challenges of PRR treatment of avocado necessitates a better understanding of the molecular and genetic basis of plant-P. cinnamomi interactions. Taking advantage of the wide host range of P. cinnamomi, we developed a detached leaf assay in Nicotiana benthamiana to elucidate the molecular and genetic basis of plant immunity against P. cinnamomi . The hemibiotrophic lifestyle of P. cinnamomi was confirmed in this model system through differential staining and quantitative PCR pathogen DNA quantification. The model plant, N. benthamiana , has been widely used to study the pathogenicity and virulence of similar broad range and root Phytophthora pathogens such as P. capsici , P. palmivora , and P. parasitica . Furthermore, several studies using model plants, crops, and tree crops to study pathogenicity, virulence, and fungicide efficacy of root rot pathogens such as P. sojae, P. capsici, P. parasitica, P. palmivora, P. cinnamomi, and P. ramorum have been performed using detached-leaf assays . Using the tools developed in previous studies and combining them with RNAseq analysis as well as functional assays using this model plant it becomes possible to gain a better understanding of plant defense responses against P. cinnamomi infection.

Previous transcriptomic studies on avocado and model systems provides important information on plant gene expression in response to infection by P. cinnamomi. Avocado defense gene expression has been analyzed three separate times over the last eight years . Mahomed and Van den Berg used the tolerant avocado rootstock Dusa to study the gene expression changes after P. cinnamomi inoculation. By comparing expressed sequence tags and 454 pyrosequencing they were able to identify six defense related genes. The defense genes identified encoded: cytochrome P450-like TBP , thaumatin, PR10 , metallothionein-like protein, MLO transmembrane protein encoding gene, and a gene encoding a universal stress protein . In a follow up study, again on the resistant avocado rootstock Dusaâ , 16 additional defense genes encoding: WRKY transcription factors, phenylalanine ammonia-lyase , beta-glucanase, allene oxide synthase, allene oxide cyclase, oxophytodienoate reductase, 3-ketoacyl CoA thiolase, Fbox proteins, ethylene biosynthesis, isoflavone reductase, glutathione s-transferase, cinnamyl alcohol dehydrogenase, cinnamoyl-CoA reductase, cysteine synthase, quinone reductase, and NPR1 were differentially expressed after P. cinnamomi infection. Reeksting et al. found up-regulated transcripts corresponding to cytochrome P450, a germin-like protein , flower harvest buckets and chitinase genes after P. cinnamomi infection using microarray technology. It has been stated , that an important difference between gene expression in avocado and model systems is that the salicylic acid response is only seen in infected avocado, which is associated with a defense response to biotrophic and hemibiotrophic pathogens. It has been further asserted that P. cinnamomi infection of model plants initiates the jasmonic acid and ethylene pathways associated with necrotrophic pathogens. Although there are differences between expression patterns in avocado and the numerous model plants that have been studied to better understand plant defense to P. cinnamomi, there are also many similarities. Model plants used to better understand plant defense gene response to P. cinnamomi infection include; Zea mays, Arabidopsis thaliana, Lupinus angustifolius, Castanea sativa , Eucalyptus nitens, Lomandra longifolia, and most recently N. benthamiana . The gene expression in susceptible model hosts such as L. angustifolius and N. benthamiana can be compared to tolerant hosts like A. thaliana and L. longifolia to identify differences that may be associated with resistance to P. cinnamomi. Santos et al compared the gene expression between a susceptible and resistant variety of chestnut. They found that genes encoding for proteins involved in pathogen recognition proteins , were significantly upregulated in the resistant variety especially before inoculation. Six out of eight defense related genes including; WRKY31 and LRR-RLK’s were more highly expressed in the uninoculated C. crenata when compared to the uninoculated C. sativa. This increased basal defense to P. cinnamomi may contribute to this variety’s resistance. Gene expression in E. nitens in response to P. cinnamomi infection included up-regulated overrepresented gene ontology terms related to JA and ET signaling . Interestingly, pathogenesis-related gene 9 was down-regulated and represents a cross-species effector target during P. cinnamomi infection. Functional genomics and validation of these defense genes has only been performed in one study in A. thaliana. Eshraghi et al. reported that an auxin Arabidopsis mutant was more susceptible to P. cinnamomi infection than the wild type indicating the role of auxin pathways in P. cinnamomi defenses. The main challenges for the identification of P. cinnamomi resistance genes in avocado are the lack of tools available for functional genomic studies and limitations associated with tree crop biology. Next-generation sequencing has provided some information on the expression of defense-related genes in avocado infected with P. cinnamomi. However, the lack of the genome sequence and absence of functional genomic tools for avocado makes it difficult to determine and confirm their contributions to resistance against P. cinnamomi.

The N. benthamiana model plant provides the opportunity to conduct functional genomic studies to determine the role of defense response genes to P. cinnamomi resistance that is not yet available in the avocado system or other tree hosts. Model plants including A. thaliana , L. angustifolius , and Medicago truncatula have been previously reported as susceptible hosts for this oomycete pathogen and have been used to study P. cinnamomi pathogenesis and plant responses to this pathogen. Although whole genome sequencing was available for these pathosystems, functional assays were not conducted with the exception of one study in Arabidopsis implicating the auxin signaling pathway with defense response against P. cinnamomi . Conducting RNAseq studies in N. benthamiana system at different time points during the infection process will provide a foot-hold into the defense gene expression pattern during P. cinnamomi infection and will allow us to conduct functional studies of selected defense genes using this N. benthamiana–P. cinnamomi pathosystem. Differentially expressed pathways and genes can be then validated by RT-qPCR in N. benthamiana and in avocado inoculated with P. cinnamomi using a detached leaf assay. Functional validation of the most promising genes can be done in N. benthamiana by transient over expression or silencing to determine their contribution to P. cinnamomi resistance. If similar expression patterns are found in avocado it is reasonable to consider this gene a good candidate for marker assisted breeding or biotechnology in avocado. As genomic tools for avocado quickly become more available the methods developed in this system will become more applicable to this fruit tree crop. RNAseq analysis of infected N. benthamiana roots can complement this system by identifying what genes are universally expressed in the plant in response to P. cinnamomi infection and what gene expression is unique to the roots. Functional genomics are lacking in avocado; therefore, the objectives of this study were i) to establish a model system to look at defense gene expression in response to P. cinnamomi infection, ii) validate differentially expressed defense genes using overexpression in the same N. benthamiana model system, and iii) establishing connections to similarly expressed defense genes in avocado in response to P. cinnamomi infection. This information will help to select candidate defense genes in avocado for marker assisted breeding or biotechnology. The average total million reads for the sequenced mock-inoculated N. benthamiana samples were 66, 75, 75, 81, and 70 million for the 6, 12, 24, 36, and 48 hpi time points respectively. The average total reads for the inoculated N. benthamiana samples were 145, 123, 80, 62, and 70 million reads for the 6, 12, 24, 36, and 48 hpi time points respectively. The average percentage of reads mapped for the five-mock inoculated time points was between 86 and 88%.

At the end of the harvest season, when the seasonal farm workers prepare to return home, established workers sell their good hunting dogs for up to $1000 pesos to migrant workers who purchase them using the earnings from the harvest season. In the process of describing the everyday-lived-experience of farm workers, is important to also recognize that the experience of the finqueros themselves is often overlooked, which in turn encourages a shallow understanding of the complexity of the problems faced by migrant workers in coffee plantations. Similar to what Holmes describes in the case of migrant farm workers in US agriculture, the increasingly corporatized market “squeezes growers such that they cannot easily imagine increasing the pay of the pickers or improving the labor camps without bankrupting the farm” . As he continues, “perhaps instead of blaming the growers, it is more appropriate to understand them as human beings doing the best they can in the midst of an unequal and harsh system” . The struggle in coffee plantations is experienced on its own way by the finqueros, who find themselves “squeezed” between the pressure of the market, increasing indebtedness and the social stigma that accompanies large plantations in this region. The finqueros I interviewed for this work were generally concerned about the living conditions of their workers and expressed future plans to improve mostly infrastructure, but find themselves with their hands tied in the face of low prices and few economic benefits from the premiums offered by the specialty market. On the one hand finqueros most catch up with current trends that include roasting their own coffee, which requires special infrastructure, special training, as well as high investments. On the other hand, growers have also had to incorporate the touristic aspect of their plantations, create and recreate the colonial stories that forged these places, build attractive bungalows and spas, black plastic plant pots wholesale and sell coffee as a whole new “experience of the senses”, that includes biodiversity conservation at its center and the recasting of colonial narratives .

As one of them puts it: “el turismo hace maravillas” . In addition, in order to increase economic gain, finqueros have also started to diversify their income, not only through tourism, but also through the production of ornamentals, cardamom, timber, and medicinal plants, which marketable value increases when being planted along with coffee. Low and unstable coffee prices, in combination to a changing climate and disease outbreaks, add to the struggle of coffee growers, which blends with the problem of low productivity of their shade-grown coffee plantations, and labor shortages for this region7 , a problem that is not new to the region . To add to this problematic, Renard points out: “ The liberalization of the international coffee market combined with a sharply reduced state intervention engendered the control over coffee production by a few transnational companies and the collapse of the economy of small producers. Combined with natural disasters whose effects were not addressed by the neoliberal state, this situation caused the region to be bypassed by Guatemalan labor that now prefers direct migration to the United States” . Moreover, in the past decade, finqueros in Soconusco and Central America were also challenged by two important coffee leaf rust disease outbreaks caused by the fungus Hemileia vastatrix, that practically swept entire coffee plantations in the region in 2008 and 2013 . This disease is highly associated with climate change , another important environmental challenge that is projected to increase climatic variability and the intensity of rain for this region . At the center of the imaginary is the shade-grown coffee farm, which is offered to the world as a steward of the land, a guardian of endangered species, a place for retreat within lush gardens overlooking a seemingly natural, remote land. However, within the wrinkles and creases of this portrait lies the experience of farm workers laboring in the fields, the struggles, the joys, and the stories that give meaning to this place.

Considering that various visions, knowledge, and experiences converge within the coffee plantation, we can begin to understand it as a co-produced space, one that is constructed through the ecological views and social relations of diverse actors that produce this space : the market and the consumers, the workers and their everyday labor experiences, the owners with their own struggles and desires, and dominant conservation narratives. In some ways, the convergence of ecological knowledges in the coffee plantation, the alternative market boom, and the conservation narrative sold in “First World” cafeterias, has created a particular coffee tropical imaginary. In this sense, coffee produced on shaded and biodiverse plantations is often targeted toward a specific environmentally conscious, upper class consumer that engages with these narratives by both directly buying the coffee as commodity, and through ecotourist vacations to coffee plantations. Shaded plantation coffee is also presented as a luxurious commodity associated with a type of tropical imaginary that, in actuality, is produced at the expense of farm workers’ living and working conditions. This work questions the practices and narratives surrounding biodiversity conservation in the context of farm workers’ lives. Farmworkers in coffee plantations are a highly vulnerable sector in the coffee production chain. In these labor-intensive systems, they not only suffer unfair living and working conditions, but also face fears and anxieties posed by conservation practices and discourses: the need to harvest coffee in the dense vegetation or abundant leaf litter, and the strict regulation around the use of resources to supplement their daily diets. Multiple imaginaries have shape this landscape dominated by coffee. On the one hand, neoliberal market trends in coffee production– which have brought the multiple certification schemes we can find in the supermarket– have imposed dogmatic regimes around the production of coffee , which– as I have shown– are at odds with people’s needs and desires. On the other hand, scientists have often promoted an imaginary around shade-grown coffee production, which reminds us of a natural or seemingly natural portrait, in which humans are nonexistent . These imaginaries, supported by an exclusionary narrative of biodiversity conservation, obscure the lived experience of farm workers. I also bring attention to an important problem in organic production, which is the fact that it does not question social conditions, particularly of farm workers, despite presenting itself as a label with social responsibility. Issues such as poor wages, structural violence, social segregation, and racism are aspects of the daily lives of farm workers in systems that depend heavily on migrant labor . However, there is a strong emphasis on ecological sustainability goals, that ignore such issues. The social implications of these labels and discourses about conservation in a labor-intensive system are striking. Therefore, in the practice of questioning our current food regime, we must reflect and recognize how narratives of conservation might reinforce farm workers’ marginalization. A change of paradigm in the conservation narrative in shaded coffee plantations should acknowledge workers’ experiences, but not only the ways in which farm workers experience injustices in the plantation, such as prohibitions, unequal pay, forced labor, bodily pain, and unfair living conditions; also, the potential subtle and creative ways of contesting them, which challenges a potential passive and subjugated vision that their experiences might provoke on the reader. For example, disregarding hunting prohibitions, using the work in coffee plantations to reproduce the peasant living back at home, appropriating land in abandoned areas of the plantation, and gossiping and character assassination of powerful figures within the hierarchy of the plantation , all as an act of autonomy or “everyday resistance”. Similarly, I acknowledge the fact that plantation owners also find themselves squeezed in various narratives: the push to be more ecologically sustainable, the unforgiving reputation that many of them receive by the media and the adjacent ejidos, black plastic plant pots bulk the push to be more productive in a competitive market while being socially just, all within a reality of low coffee prices, and increasing indebtedness to international buyers and powerful corporations, such as Nestle and Starbucks.

In some way, finqueros benefit from the conservation narratives and the imaginary of shade grown coffee plantations, as they are able to accommodate their coffee with much more identity and value in the market. Finally, this research invites all of us as scientists, tourists, and coffee consumers to rethink our political actions as we construct the spaces that we visit, study, and imagine. In a time of increasing violence towards immigrants, and a food regime increasingly dominated by corporations, it is pertinent to ask how our actions change and perpetuate current neoliberal models, that are ultimately detrimental to the lives of people that live with and from coffee. Coffee is an important agricultural system for Latin America, supporting millions of farmers and national economies. A large portion of coffee in Latin America is produced under the shade of forests, making this habitat important for the conservation of biodiversity and ecosystem functions, as well as the sustenance of human livelihoods. Through the analysis of species interactions and human lived-experiences I provide a glimpse to the social and ecological complexities of organic shade-grown coffee plantations. Shaded coffee plantations are complex socioecological systems constructed through our scientific understandings of ecological interactions, insects and other organisms, as well as by the experience of people making a living in these spaces. My work contributes to our understanding of complexity through the lens of humans and non-humans, and paints a portrait of shade grown coffee that shows Los claroscuros del café, or the disambiguation of this space. On the one hand, my research contributes to our understanding of the mechanisms that maintain species diversity and complex interactions in complex agroecosystems. From an agroecological perspective, resource heterogeneity, and the availability of a diverse suit of resources, including food, nesting and connectivity resources can promote species richness and biological pest control in coffee systems. My research highlights the importance of conserving specific resources for insects in the face of increasing agricultural simplification. From a political ecology perspective, my research brings attention to an overlooked aspect of shadedcoffee systems, which is the lived experience of farm workers, and indirectlyinvites all of us to rethink our political actions as we construct the spaces that we study. Highly parallel genotyping has become an important component of genomics. Hybridization of genomic DNA and RNA to microarrays has been used in the past for detection of polymorphisms between genotypes. However, the previously available arrays for complex genomes only provided limited transcriptome coverage. We developed an array designed to maximize transcriptome coverage while maintaining the possibility of performing other analyses. Our custom designed Lettuce GeneChipW combined the benefits of overlapping probes across unigenes, similar to that demonstrated by Gresham et al. for yeast, with the use of anti-genomic probes to maximize the possible coverage of unigenes while maintaining the sensitivity to detect polymorphisms and retaining appropriate controls to normalize and correct for background noise. The tiling path design allows for multiple assessments of hybridization differences between lines for single positions rather than single assessments of a few positions as obtained with most expression arrays. We developed custom scripts for analysis of our hybridization data taking into account the multiple probes covering a single position as well as filtering out poorly performing probes. We used recent advances in high throughput sequencing technology to validate our SPP calls as well as filter out potentially unreliable data. Genomic DNA and cDNA are two options for hybridization to an array for SFP detection. The decision of which to use becomes more difficult as genome size and complexity increases. DNA as well as cDNA are both viable targets for species with smaller genomes such as Arabidopsis and rice. However, with larger and more complex genomes such as barley, cDNA was indicated as a more reliable option for hybridization even with the added difficulty of subtracting out expression effects. The genome of lettuce is nearly 17x larger than Arabidopsis although it is half the size of barley. Given the difficulty of accounting for spatiotemporal expression effects as seen in cDNA, we focused on developing methods to use genomic DNA. Rostokset al.suggested that genomic DNA may be a feasible target in larger genomes with added replication. With the redundancy of the overlapping probes in the lettuce array, the need for additional replication was reduced because they provide technical replicates within a chip.