As is frequently noted, the green coffee scale insect is a persistent but relatively benign coffee herbivore, only rarely reaching important pest status, although with clear potential to do so . A casual walk on a coffee farm reveals what appears to be a regulating factor. Searching coffee bushes, one finds scale insects here and there and, importantly, a small species of beetle that is evidently feasting on them . The predatory beetle is Azya orbigera, in the family Coccinelidae. Without a doubt, this observation can easily lead to the conclusion that the relatively rare scale insect is kept under control by the relatively common coccinellid beetle. But a closer look reveals a dramatic variability: Some bushes are very heavily laden with the scale insects, and some have none at all. There is another classical ecological notion that emerges in this system. Surrounding the tree in which an Azteca nest is located is a region containing coffee plants that are routinely patrolled by the Azteca ants that were described above. The ants harvest the sweet secretions the scale insects produce and, in turn, scare away or kill the natural enemies seeking to attack the scales , a well-known mutualism . Because the coffee bushes located near the shade trees that contain Azteca nests are where the scale insect is at least partially protected from the predatory beetle and various parasitoids, this area represents a refuge for the scale insect. It is therefore tempting to conclude that the ant itself is an indirect herbivore on the coffee . Although such is the case at a very local level , because of the complexities induced by the beetle predator, such is not the case at a larger scale. The ants effectively provide an area of high food availability for the beetle. Furthermore, the ants protecting the scale insects also, inadvertently, dutch bucket for tomatoes protect the beetle larvae from its own parasitoids, providing an effective refuge for the beetle as well .

Predator–prey systems that contain a refuge are well studied in theoretical ecology , usually with an emphasis on their stabilizing properties. Expanding our view to a larger spatial scale, we deduce an evident contradiction from easily observable patterns. The scale insects are inevitably eaten by the predatory beetle unless they are protected by the ants. However, the ants cannot provide protection if they have not yet created a foraging pattern at the site where the scales are located. Therefore, the scale insect is unable to form a successful population unless under protection from the ants but is unable to attract the ant protection unless it builds up at least a small population. This pattern is well known in ecology as an Allee effect: An organism cannot form a successful population unless a critical number of individuals first become established, a mechanism generally understood to frequently be involved with the idea of critical transitions. In figure 4, we illustrate the system with a cartoon diagram approximately summarizing a simple population model . On one hand, as the dispersion of scales moves from a position far removed from the refuge toward it, the adult beetle predators that have already located the scales will tend to move with it, until they encounter the protective ants , as is presented in figure 4a. A snapshot at some particular time therefore might look like the pattern in figure 4b. On the other hand, as the dispersion of scales moves from a position within the refuge away from it, the encounter with the beetle predators will not occur until the scales are far removed from the refuge, as is presented in figure 4c. A snapshot at some particular time therefore might look like the pattern in figure 4d. Finally, combining the pattern of figure 4b with that of figure 4d, we obtain the combined graph presented in figure 4e. Note that there is a broad region in which the scales could be very high while at the same time could be very low, effectively depending on where the scales are dispersing from, a structure typically referred to as hysteresis. Selecting 20 different shade trees containing Azteca nests, we examined all coffee bushes within 2 meters of the nest and a number of bushes further removed .

We estimated the activity of Azteca ants on each of the bushes before counting the scale insects, to get an estimate of where the actual refuge was located . Note that the ant activity within 1 meter of the nest was high for almost all bushes surveyed , although positions greater than 1 meter awaty were highly variable, with some bushes having high activity levels and others having none. Further than 4 meters from the nest, ant activity was effectively nonexistant, and bushes further than about 4 meters from the nest were completely out of the refuge. Plotting the number of bushes with a saturated density of scale insects and those with less than 10 scales, we obtain a pattern corresponding quite closely to what is expected from the hysteretic pattern predicted by the theoretical considerations . A further complication enters with a more complete natural history understanding of the beetles and their larvae. Although the adult beetle can fly and therefore forage over long distances for its food source, the larvae are largely restricted to terrestrial movement; that is, they are restricted in space . Female beetles therefore must choose their oviposition sites in such a way that the larvae will mature in an environment that contains a locally abundant food source. One major food source for predatory beetles is the general kinds of insects that are relatively sessile and suck the juices from plants, precisely the characteristics of the green coffee scale. They are easy targets for predators because they are normally slow moving and have few defenses. The problem for a potential predator is that they are very frequently defended by ants, precisely in areas where they are good sources of food for a beetle larva. Consequently, a whole group of beetles has evolved the habit of seeking out ants and ovipositing in areas where ants are abundant and defending the hemipterans. These myrmecophilous beetles must obviously have a strategy of protecting their larvae from the aggressive action of the ants and of enabling oviposition in sites of high ant activity . In the case of the beetle A. orbigera, the larva is covered with waxy filaments that tend to stick in the ants’ mandibles whenever they try to attack it .

But more importantly, female beetles take advantage of an unusual behavioral pattern of the ants in order to oviposit where the scales are abundant . When a phorid fly attacks an ant, that ant exudes a pheromone that effectively says to the other ants in the general vicinity “Look out! Phorids attacking,” and the surrounding sisters all adopt a sort of catatonic posture, heads up, mandibles open, and stationary . Although the phorid is able to detect the alarm pheromones of the ant and is therefore attracted to it, it is unable to actually oviposit on the ant unless it sees some movement . Therefore, not only the ant under potential phorid attack, but also the sisters surrounding her assume this semistationary posture, a result of the very specific pheromone that alerts all ants in the vicinity that a phorid is lurking about. Remarkably, the adult female beetle is able to detect and react to this specific chemical, apparently using it as a cue that the time is propitious to enter into the ant-protected zone to sneak in some ovipositions . Therefore the phorid, in addition to being an important player in the Turing process that forms the basic spatial structure of the system, imposes a trait-mediated indirect interaction , in which the effect of the ant on the beetle is reduced. There is more to this story: first, from simple theoretical considerations and, second, from some evident natural history observations of the system. The theoretical considerations emerge from the knowledge that the refuge is dynamic. That is, past ecological theory has shown that when a prey species is able to retreat from its predator in a fixed refuge space, the basic instabilities of the predator–prey arrangement can be cancelled. But, in the present example, the refuge is effectively a pattern formed by another element in the system , blueberry grow pot the Azteca ant. And the Azteca ant is dynamic in the system, increasing its numbers in proportion to the resources it gains . If the scale insect population increases, there is more food for the ant, and it will therefore make more nests and expand its territory, creating even more refuge area for the scale insect. However, as the ant expands its area of influence , an increasing fraction of the area becomes refuge and, therefore, not available to the adult beetles . At the extreme, there must be some point at which the beetle is unable to find enough prey to continue its population expansion, because almost all of the area would now be a refuge for the scale insect. Therefore, theoretically, the inevitable expansion of the refuge would lead to the eventual local extinction of the beetle predator. It could, of course, be the case that this expected instability of the system does not express itself for diverse reasons or perhaps for an excessively long time. However, purely theoretically, it represents a potential problem for persistence of this control agent.

The theoretical problem is resolved by some very simple natural history observations. A fungal disease, known as the white halo fungus , almost inevitably becomes epizootic , especially when local population densities of the scale insect become large . The fungus can occasionally be found on isolated scale insects, but almost always is most evident when scale insects have built up a significant local population density, and such a buildup can only happen when they are under the protective custody of the Azteca ant.In the end, we see that the Azteca ant plays a key role in the control of this pest. On one hand it protects the scale insect from its adult beetle predator but only in the area of the refuge of the scale, which is defined by the ant itself . On the other hand, it permits the scale insect to build up such large local populations that the white halo fungus frequently becomes epizootic and drives the scale insect to local extinction. It is a curious inverse application of Gause’s traditional competitive exclusion principle, which might be expected to apply between the fungus and the beetle because they share this same food source. It seems unlikely, however, that the scale could be controlled completely by either the beetle or the fungal disease, except in the context of a spatial pattern generated by the Azteca ant . The massive expansion of the ants that might be expected theoretically never happens, partly because of the local effect of the fungal disease and the beetle larvae together reducing the scale insect population locally. Therefore, the dynamic nature of the ant cluster mosaic , always provides a small set of refuges that allows the beetle predator to be maintained throughout the coffee farm. From the point of view of the beetle, it is perhaps ironic that the beetle itself may be involved in the organization of the spatial pattern that is required for its own persistence . There is yet an additional complication. The fungal disease, once it arrives, multiplies extremely rapidly. But, as was noted above, it does not arrive in the first place unless the scale population is large and locally concentrated. Therefore, once the disease gets there, it increases to epidemic levels and wipes out the entire population of scale insects , creating a classical situation of boom and bust and hysteresis in space . Although it is a somewhat complicated argument that has been made in a couple of different ways elsewhere , the disease can clearly generate a locally chaotic dynamic trajectory. Furthermore, as the relevant population gets closer to the ant nest , the oscillations with its disease are expected to be more and more extreme. Eventually, they become so extreme that they transcend the boundaries of a critical value and both scales and disease completely disappear. Note that chaotic trajectories have boundaries , and the equilibrium point at zero is constrained within a basin of attraction.

The effect of cover crop presence on microbial community structure was also greater in some soil great groups, such as the Xeralfs, indicating that attributes associated with soil development can amplify effects of specific management practices like cover cropping. However, an isolated group of samples from alleys supporting grasses, legumes þ cereals or mustards were clustered together and associated with higher values in soil pH and clay content. All measured soil attributes also explained the most variation in microbial community structure in the variation partitioning analysis . Together, these findings suggest that soil chemical attributes and C and N pools played strong roles in structuring soil microbial communities .Bacterial communities tended to separate weakly, although significantly, with respect to presence and absence of tillage, but when looking within group factors through ADONIS a stronger effect of tillage emerged . For example, within soils with planted cover crops there was a stronger effect of tillage compared to across all soils . This may be due to the pre-plant preparation of soil by disking and rolling as well as incorporation of the cover crop into the soil. Similarly, within organic vineyards, tillage played a stronger role compared to conventional vineyards or across all vineyards , corresponding to lower soil C pools in organic vineyards . In this region, organic growers will till alleys to reduce competition between vines and cover crops and for weed control, and in at least one organic vineyard in this study, alleys had been tilled 4e5 times per vine growing season. Nonetheless, vertical hydroponic nft system vineyard soils in Napa are not intensively tilled in comparison to annual cropping systems with conventional tillage practices. This presents challenges in comparing effects of tilled treatments on taxa among annual and perennial cropping systems.

However, in Australia, a similar effect on Firmicutes was observed, in which no-till soils that had been tilled just once exhibited enrichment in Firmicutes . Furthermore, tillage seemed more important within Xeralfs compared to Fluvents or across all soils . For vineyards in Napa Valley, soil type tends to influence choice of tillage practice, in which Xeralfs and Fluvents are typically tilled while Xerolls and Xerults are not. Also, in Napa Valley, vineyards at higher elevations tend to be no-till due to rocky conditions and steeper slopes. Therefore, the effects of tillage and soil type are linked. Tillage disturbance creates shifts in soil nutrient availability and in aggregate size, composition, and stability, thereby changing the physical environment and resource availability experienced by soil microorganisms . This then can lead to shifts in soil microbial communities and microbially-mediated processes . One soil organic matter pool that re- flects both tillage disturbance and microbially-mediated processes is that associated with the fine soil fraction . As it is not always mineral associated , we will refer to it as ‘fine SOM’ instead of ‘organomineral complexes.’ Typically, fine SOM is thought to reflect residues that have been highly decomposed by soil microorganisms. Therefore, it is likely that fine SOM concentrations and measures of soil microbial activity, like respiration and potentially mineralizable nitrogen , reflect the microbial community structure . In our case, no till soils had distinct microbial community structure and the greatest concentrations of total and fine SOM and PMN compared to tilled soils, regardless of the time since tillage occurred . However, less recently tilled soils had highest diversity and richness, higher than no-till and recently tilled soils . At the same time, taxa that exhibited significant differences with tillage or time since tillage had occurred had greater relative abundances in tilled soils, suggesting that these taxa either had a greater stability in response to tillage disturbance or were selected in response to tillage, as compared to other taxa across all sites.

At the phyla level across all sites, no specific taxa had consistent decreases in relative abundance with tillage, suggesting that taxa most sensitive to tillage were consistent among sites. Interestingly, there was no clear overlap between soil microbial communities supporting specific kinds of cover crops and tillage status, suggesting that these practices had relatively independent effects on soil microbial communities . However, total cover crop biomass was not collected, and so any correlation of cover crop biomass production and its total contributions to labile soil resources with pre-plant tillage in fall, spring incorporation of cover crops by tillage or no-till is indeterminate. Further supporting the idea that soil resources drive diversity, compost addition was associated with an increase in overall bacterial diversity and changes in community composition. Increased diversity and relative abundances of certain taxa under compost application may be a response from increased availability of resources, especially as soils that received compost had lower C pools, or from microbial introductions from compost itself . Compost has varied origins and is derived from diverse materials, which might explain the lack of a consistent effect across all vineyards on particular taxa abundances, despite the consistent increase in phylogenetic diversity. As an example of the hierarchy of effects observed within groups , recency of tillage had a greater impact than tillage presence, in general, on structuring soil bacterial communities, especially when excluding no-till soils . An effect of recency of tillage was even resolved for groups in which tillage in general did not have an effect, such as within conventional vineyards and within Fluvents. Presumably, all vineyards were cultivated during their conversion from previous land-use types. Because tillage is known for its long-lasting impacts, even on soil microbial communities , all vineyards could be considered disturbed ecosystems. Therefore, it might not be a surprise that recency of tillage has a greater influence in structuring soil bacterial communities than the practice of tillage, in general. Tillage also is known for its short-term effects on soil resources and soil microorganisms, as shown in intensively cultivated vegetable crop soils and annual grasslands . In our case, less recently tilled soils had highest diversity and richness, above that of no-till and recently-tilled soils. This lends some support to the ecological concept of adaptive radiation, where an event gives rise to many new species expanding into new habitats or ecological roles in a relatively short time .

Other studies have supported the idea of adaptive radiation of bacteria particularly when species were absent from the medium prior to inoculation with the experimental bacterium , which could be analogous to adaptive radiation following the tillage-associated reduction of microbial biomass, richness, and diversity. However, further research is required to confirm the accuracy and wide applicability of such ecological concepts to microbial ecology.Bacterial community composition and diversity differed with conventional, organic, and bio-dynamic vineyard management. It is commonly known that these systems tend to differ in the types of pesticides and fertilizers used, and that pesticides and fertilizers affect soil microbial communities . However, since fertilizers and herbicides are typically only applied under the vine, and other pesticides are most commonly applied foliarly to vines, we do not expect these factors to play large roles in distinguishing our samples, which were taken from alleyways. Nevertheless, conventional, organic, and bio-dynamic vineyard management systems in our study also differed with respect to tillage, cover crop, compost application and practices specific to bio-dynamic like field sprays of cow manure and quartz silica as well as additives to compost , all factors that influence soil physical environment and resources available to microorganisms. Furthermore, differences in soils, climate, and sub-appellation may influence management decisions, impacting likelihood of a grower to adopt certain designations, whether conventional, organic, or bio-dynamic and observed distinctions among bacterial communities with respect to vineyard management systems. For vineyards, underlying practices embedded within the conventional, organic, nft hydroponic system and bio-dynamic management systems affected bacterial communities both in terms of biodiversity and overall community structure. Growers employ tillage as a water and weed management practice to prevent competition between vines and cover crops or weeds, particularly in organic and dry-farmed vineyards. Conventional systems were more likely to be no-tilldlikely due to the lack of a need for tillage as a water management or weed control practice. As previously discussed, tillage was associated with lower soil bacterial a-diversity and richness compared to no-till. Since organic vineyards were associated with tillage, we attribute the lower a-diversity and richness associated with organic vineyards to the impact of tillage. Studies in annual cropping systems have found the opposite effect or no differences between conventional, organic, and bio-dynamic management . This may be due to the different nature of conventional, organic, and bio-dynamic systems in vineyards compared to annual cropping systems.Soil bacterial communities were structured as a function of vineyard management practices and soil properties. As ranked by the highest ADONIS R2 -value, cover crop mix was the strongest management factor, but hierarchical effects of recency of tillage and compost additions on soil microbial structure were also noted. Our work supports the paradigm that vineyard management practices affect soil microbial communities through their suite of impacts on soil properties, but mechanistic studies will further elucidate the ecological role of specific taxa identified in these vineyard soils. The identification of distinctive soil bacterial communities related to soil resources and vineyard management indicates that soil bacterial community structures can be developed as a biological indicator of soil quality. This may provide a strategy to monitor soil quality or health in vineyard soils. This work also has opened the door for future assessments of interrelationships of vineyard management, microbial biodiversity, and agroecosystem services, especially as they relate to soil quality, soil health, vine health, and berry quality .

In a typical year, debates surrounding the state’s budget are among the most controversial matters addressed by Colorado state lawmakers. Because the current legislature is closely divided along party lines, many expected the budget to take center stage once again in the 2018 legislative session. Before the current session began, the Denver Post outlined some of the major items on the General Assembly’s agenda. Among the most pressing issues facing lawmakers were transportation funding, the opioid crisis, energy development, and the financial stability of the Public Employees’ Retirement Association , in addition to matters surrounding sexual harassment in the legislature . For the fourth consecutive year, divided party control exists in the General Assembly with Democrats holding a 10-seat advantage in the state House, while a slim Republican majority exists in the Senate with 18 Republicans, 16 Democrats, and one unaffiliated senator. At times the partisan differences between the chambers have been substantial. In prior legislative sessions, the issue of guns has been among the most controversial topics addressed by legislators as evidenced by the successful recall elections of two Democratic lawmakers over their votes on gun control bills in 2013 . During the current session, the Republican controlled Senate passed legislation in a party-line vote to allow Coloradans to conceal carry a firearm without a permit . With no Senate Democrats supporting the measure, the bill was dead on arrival in the House where Democrats hold the majority. A bill to ban bump stocks was recently defeated by Republicans in the State, Veterans, and Military Affairs Committee following a party-line vote. While political parties in Colorado remain bitterly divided on the issue of guns, other previously controversial measures witnessed unexpected compromise during this session such as increased funding for the program to provide driver’s licenses for undocumented residents. Beginning in August 2014, an estimated 120,000 undocumented residents could begin applying for driver’s licenses. Although the state issued 32,325 licenses through the program, it was troubled by a lack of staff and funding since demand outpaced the number of appointments offered by the state . Many expected further problems as the licenses first issued were due for renewal, and the program originally required all individuals to procure or renew their licenses in person. However, a bill recently passed in the Republican-controlled Senate provides additional funding to the program and allows existing licenses to be renewed online, among other changes . Following successful passage in the House, Governor Hickenlooper signed the bill in May. The passage of this bill into law demonstrates the possibility for bipartisan compromise in a divided General Assembly on controversial issues as well as debates surrounding spending priorities.

These findings and the reference genome will serve as a powerful platform to further investigate ”sub genome dominance” , facilitate the discovery and analysis of genes encoding economically important traits, and ultimately enable molecular breeding efforts in blueberry.Our goal was to obtain a high-quality reference genome for the high bush blueberry cultivar ”Draper,” which is widely grown around the world due to its excellent fruit quality. We sequenced the genome using a combination of both 10× Genomics and Illumina , totaling 324X coverage of the genome . These data were assembled and scaffolded using the software package DenovoMAGIC3 . The genome was further scaffolded to chromosome-scale using Hi-C data with the HiRise pipeline . The total length of the final assembly is 1,679,081,592 bases distributed across 48 chromosome-level pseudomolecules . The final assembly size falls within the estimated genome size of ”Draper” based on flow cytometry . The genome was annotated using a combination of evidence based and ab initio gene prediction using the MAKER-P pipeline . RNA sequencing data from 13 different gene expression libraries, representing unique organs, developmental stages, and treatments , and publicly available transcriptome and expressed sequence tags data of V. corymbosum in theNational Center for Biotechnology Information were used as transcript evidence. Protein sequences from Arabidopsis thaliana, Actinidia chinensis , and UniprotKB plant database were also used as evidence for genome annotation. We predicted a total of 128,559 protein-coding genes. Bench marking Universal SingleC opy Orthologs analysis v.3was performed to assess the completeness of the assembly and quality of the genome annotation. The annotated gene set contains 1,394 out of 1,440 BUSCO genes . Functional annotation was assigned using Basic Local Alignment Search Tool 2GO to reference pathways in the Kyoto Encyclopedia of Genes and Genomes database.

Comparative genomic analyses assigned genes to 16,909 orthogroups shared by six phylogenetically diverse plant species including five eudicots , stackable planters each with distinct fruit types, and Zea mays as the out group. Transposable elements , both Class I and II, were identified and classified in the genome using the protocol described by Campbell et al.. Overall, 44.3% of the blueberry genome is composed of TEs . Consistent with previous reports, the most abundant Class I TEs were long terminal repeat retrotransposons , specifically the super family LTR/Gypsy followed by LTR/Copia, while for Class II transposons, the miniature inverted repeat superfamily hAT was the most abundant. The quality of the genome was further assessed by examining the assembly continuity of repeat space using the LTR Assembly Index deployed in the LTR retriever package. The adjusted LAI score of this blueberry genome is 14, and based on the LAI classification, this score is within the range of ”reference” quality . Estimation of the regional LAI in 3 Mb sliding windows also showed that assembly continuity is uniform and of high quality across the entire genome.The origin of high bush blueberry from either a single or multiple diploid progenitor species is a long-standing question. Previous reports have suggested that high bush blueberry may be an autotetraploid based on the segregation ratios of certain traits. However, an analysis of chromosome pairing among different cultivars revealed largely bivalent pairing during metaphase I , similar to patterns observed in known allopolyploids. To gain further insights into the polyploid history of high bush blueberry, we calculated sequence similarity and synonymous substitution rates between genes in homoeologous regions across the genome. The average sequence similarity is ∼96.3% among syntenic homoeologous genes. The average Ks divergence between syntenic homoeologous genes is ∼0.036 per synonymous site. The average Ks divergence between homoeologous genes can be used to not only identify polyploid events but also to estimate the divergence of the diploid progenitors from their most recent common ancestor. The Ks divergence between homoeologs in high bush blueberry is six times higher than that between orthologs of two A. thaliana lines that diverged roughly 200,000 years ago.

Based on the relatively high Ks rate between homoeologous regions across the genome, this suggests that tetraploid blueberry is unlikely an autopolyploid that was formed from somatic doubling or failure during meiosis involving a single individual . Furthermore, comparative genomics revealed that homoeologous regions are highly collinear, except a few notable chromosome-level translocations . These translocations were manually inspected and verified with both the raw sequence and Hi-C data. Rapid changes among homoeologous chromosomes is known to occur in newly formed allopolyploids. We also assessed the level of similarity and content of LTR transposable elements among the four haplotypes. As the most prevalent transposable elements in plants, LTR-RTs undergo continual ”bloat and purge” cycles within most plant genomes , resulting in a unique signature that may distinguish sub genomes in an allopolyploid. To examine the evolutionary history of LTR-RTs in the high bush blueberry genome, we calculated the mean sequence identity of LTR sequences among each of the four haplotypes . This analysis revealed that the majority of more recent LTRs are sub genome specific in high bush blueberry. In other words, the data suggest that LTRs prolifterated independently in the genomes of each diploid progenitor , following the divergence from their MRCA, but prior to polyploidy. The pair-wise LTR difference of the two ancestors is 2.4%–2.6%. With Jukes-Cantor correction and synonymous substitution rate of , the estimated time of divergence for the diploid progenitors from their MRCA is between 0.94 to 1.02 million years ago. These date estimates and the average speciation rate for temperate angiosperms suggests that high bush blueberry is either an allopolyploid derived from two closely related species or an autopolyploid derived from the hybridization of two highly divergent populations of a single species. To date the most recent polyploid event in high bush blueberry, we analyzed the unique LTR insertions present in each haplotype. Based on the pair-wise LTR difference between the four haplotypes, which is of 0.81%–0.89%, the polyploid event occurred approximately 313 to 344 thousand years ago.

The substitution rate of LTR sequences is likely different from that of protein coding genes. Thus, more accurate date estimates will be possible once the LTR substition rate in high bush blueberry becomes available from future studies. After allopolyploidization, one of the parental genomes often emerges with significantly greater gene content and a greater number of more highly expressed genes . The emergence of a dominant sub-genome in an allopolyploid is hypothesized to resolve genetic and epigenetic conflicts that may arise from the merger of highly divergent sub-genomes into a single nucleus. However, classic autopolyploids, formed by somatic doubling, are not expected to face these challenges or exhibit sub genome dominance since all genomic copies were contributed by a single parent. This was recently supported by genome-wide analyses of a putative ancient autopolyploid. It’s important to note that sub-genome expression dominance could still be observed in intraspecific hybrids and autopolyploids formed by parents with highly differentiated genomes. To explore this in high bush blueberry, we compared gene content and expression-level patterns between homoeologous chromosomes . While gene content levels were largely similar among homoeologous chromosomes, with a few notable exceptions , gene expression levels were highest for one of the four chromosome copies in the majority of gene expression libraries . Noteworthy, in the three fruit libraries, the most dominantly expressed often became the least expressed among the four homoeologous chromosomes or among the two lowest expressed copies . The most dominantly expressed in other Thissues remained so in developing fruit for only two of the chromosomes . These homoeologous chromosome sets have undergone the most structural variation, which may have modified gene expression patterns . These analyses are based on a single biological replicate from a plant grown in a growth chamber. Thus, the findings reported here should be considered as preliminary. Future studies should further explore sub genome expression dominance in high bush blueberry, stacking pots including at the individual homoeolog level, with additional biological replicates and across multiple environments.The progression of fruit development in blueberry is marked with visible external and internal morphological changes including in size and color . We profiled gene expression in fruit across seven developmental stages from the earliest stage through the final stage to identify genes differentially expressed during fruit development. Distinctive transitions in gene expression were observed between early fruit growth to start of color development and complete color change to ripened fruit. We found that the majority of genes upregulated during early fruit development were involved in phenylpropanoid biosynthesis, nitrogen metabolism, as well as cutin, suberin, and wax biosynthesis . In contrast, genes involved in starch and sugar metabolism were highly expressed at the onset of and during fruit ripening . Moreover, principal component analysis showed the first two components accounted for 84% of the variation and separated the developmental stages into three groups: early developmental stages, petal fall and small green fruit; middle developmental stages, expanding green and pink fruit; and ,late developmental stages, complete fruit color change, unripe and ripe fruit . Genes associated with cell division, cell wall synthesis, and transport were found to be expressed the highest during the earliest developmental stages , which is consistent with previous work on other fruit species. In addition to genes regulating cell prolifteration, defense response-related genes were also highly upregulated during the earliest developmental stages. During the middle developmental stages, genes regulating cell expansion, seed development, and secondary metabolite biosynthesis were highly expressed. During late developmental stages and as the berry transitions to ripening, late embryogenesis, transmembrane transport, defense, secondary metabolite biosynthesis, and abscisic acidrelated genes were highly over represented. Blueberry is considered a climacteric fruit; however,unlike the ethylene-driven fruit ripening in other climacteric species, abscisic acid has been demonstrated to regulate fruit ripening in blueberry. In summary, global gene expression patterns mirror the morphological and physiological changes observed during blueberry development .

We assessed the total antioxidant capacity in mature fruit across a blueberry diversity panel and the abundance of secondary metabolites responsible for its antioxidant activity in developing fruit. A diversity panel, composed of 71 high bush blueberry cultivars and 13 wild Vaccinium species, was evaluated for total antioxidant capacity in mature fruit using the oxygen radical absorbance capacity assay. Similar to previous reports, we observed a wide range in antioxidant capacity across cultivars, with ”Draper” having the highest levels of antioxidants . The observed variation in antioxidants among high bush blueberry, consistent with our results, were previously shown not to correlate with fruit weight or size . However, in another study, a correlation between fruit size and total anthocyanin levels was identified within a few select high bush blueberry cultivars but not across other Vaccinium species or blackberry. This inconsistency is likely due to sample size differences between studies. To further examine the antioxidant capacity in ”Draper” during fruit development, fruits from the seven aforementioned fruit developmental stages were assayed for antioxidant levels . The highest level of antioxidants was observed at the earliest ”petal fall” stage after which, the level of antioxidants declined during the middle and late developmental stages. This is consistent with previous reports on the antioxidant activity in blueberry during fruit maturation and similar to observations in blackberry and strawberry, wherein green fruit have the highest ORAC values. The antioxidant capacity in blueberry is influenced by various metabolites including anthocyanins. Using the same fruit development series, we quantified anthocyanin and flavonol aglycones in ”Draper” using liquid chromatography-mass spectrometry . Overall, as the fruit changed its exocarp color from pink to dark blue during ripening, delphinidine-type anthocyanins started to accumulate and were the most abundant compound in ripe fruit followed by cyanidin, malvidin, and petuni-din . Flavonols were also detected in all developmental stages, with quercetin glycoside being the most abundant , while myricetin glycoside and rutin were present at very low levels. Blueberry also has high levels of phenolic acids; among phenolics, chlorogenic acid was the most abundant. High levels of CGA were observed throughout fruit development, with the highest accumulation detected in young fruits . This correlates with the pattern of antioxidant capacity across different fruit stages, suggesting that CGA is one of the major metabolites contributing to high ORAC values in young developing fruit. CGA is derived from caffeic acid and quinic acid and has vicinal hydroxyl groups that are associated with scavenging reactive oxygen species.

In addition to validating southwestern Ethiopia as a center of origin, the above results have suggested Yemen as one of the centers of domestication of C. arabica. If indeed Yemen were a center of domestication, today’s cultivated varieties of C. arabica should be genetically similar to Yemen cultivars. As predicted, Anthony et al found a number of AFLP and SSR markers present in Yemen cultivars to be similar in the Typica- and Bourbon-derived accessions. Their results fit accordingly with the historical data—that Typica and Bourbon genetic bases diffused from Ethiopian coffee introduced to Yemen , a center of domestication for C. arabica and the primary center of dispersal for coffee .While multiple types of evidences have been analyzed to trace the Ethiopian origin of C. arabica, archaeological evidence is still lacking. On the one hand, multiple sources affirm the strong linkage between coffee consumption and tiny porcelain/earthenware coffee cups, but on the other hand, recovery of such cups is rare. Not only would the sources of these cups help us trace the dissemination of coffee, but the cups themselves could be dated, confirming important dates in coffee history provided by other types of evidence. In addition to cups, other tools used to prepare coffee, such as a mortar and pestle to grind coffee beans, could carry valuable archaeological data. Promising excavation sites would include villages near the rainforests in southwestern Ethiopia, the Sufi monasteries of Yemen, and the trading ports of Yemen . Archaeobotanical evidence, such as seeds, pollen, phytoliths, etc., is almost nonexistent for C. arabica, nft channel which is unfortunate because these remains would prove crucial in verifying conclusions drawn from genetic evidence.Grapevine is an economically important crop worldwide with a global surface area of 7.45 million ha, which is mainly cultivated for wine making.

Califtornia stands out as the fourth leading wine producer in the world with 257,784 ha of wine grapes and 4.28 million tons of grapes harvested in 2018, leading to an annual economic impact of $57.6 billion . Nevertheless, winegrowers face the challenge of replanting their vineyards when grapevines are not producing due to diseases such as grapevine red blotch virus, trunk diseases, or other viral diseases such as leaf roll disease, or because the plant material is producing substandard fruit and consequently compromising the wine quality. However, several factors need to be taken into account when replanting, as improper establishment during this stage causes considerable economic loss to the industry. Arbuscular mycorrhizal fungi are soil-borne fungi that form mutualistic relationships with 80% of the superior plants . In viticultural regions, the AMFgrapevine symbiosis was pointed out as a key component of the vineyard system . Recent research suggested the key role that this symbiosis might play in facing environmental constrains . The application of mycorrhizal inocula has emerged as a reliable technique to enhance the agricultural productivity whereas reducing environmental costs . Frequently, these commercial inoculants consist of a single or few AM fungal isolates grown in plant culture or greenhouse conditions with annual grasses or forbs , hence they might not establish on woody grapevines that have different ecosystem preferences . It is well established that under controlled conditions AMF inoculation of grapevines promotes increased growth , drought tolerance , and nutrient uptake . Moreover, AMF protect grapevines grown in controlled conditions against pathogens through stimulation of key genes of the phenylpropanoid biosynthesis in leaves and inhibit their transmission by impairing the growth of nematode vectors in roots and their reproduction in soils . Although it is widely accepted that AMFgrapevine association improves grapevine growth and mineral uptake in vineyards , contradictory results were recently reported when studying the protective role of the symbiosis against pathogens such as Ilyonectria . Similarly, AMF inoculation may affect berry primary and secondary metabolism in response to environmental stresses when grapevines were cultivated under controlled conditions but little is known about their effect under natural conditions.

Additionally, rootstock genotype and type of inoculum could also influence the effectiveness of mycorrhizal inoculation and therefore the response of young vines to the environment . On the other hand, most wine grape producing regions are subjected to seasonal drought, but based on the global climate models an increase in aridity is predicted in the future. Hence, an optimized irrigation schedule would still be one of the most desirable tools to improve crop productivity and quality in historically non-irrigated viticulture areas where irrigation is expanded fast to mitigate environmental stress . In addition, in warm and hot viticultural regions such as Califtornia that rely on irrigation for crop production, water resources, especially groundwater, are becoming scarce due to extended drought periods and overuse by irrigated agriculture . Currently, winegrowers are aware of the importance of a sustainable viticulture that ensures the profitability in the future, without compromising berry quality. However, to the best of our knowledge little is known about the contribution AMF inoculation may have for implementing the effects of different irrigation amounts on the performance and berry quality of young grapevines under field conditions. Therefore, the aim of this study was to characterize the response of young Merlot grapevines to AMF inoculation subjected to two different irrigation amounts in their first productive year. This study was conducted in the Oakville Experimental Station . The vineyard was planted to Merlot clone 181 on 3,309 C rootstock in 2018 at 3 m × 2 m spacing in E–W orientation. The grapevines were spur pruned and trained to quadrilateral trellis system 1.38 m above vineyard floor with catch wires at 1.68 m. The experimental vineyard was drip-irrigated with one or two emitters spaced every 2 m along the drip line and with the capacity of deliver 3.8 L of water per hour. Natural vegetation was allowed to grow in alleys and mowed according to vineyard manager’s discretion, with a no-till system in place. The experiment consisted in a 2 × 2 factorial design with four replications of seven grapevine plots arranged in a split plot design. The commercial Myco Apply Endo Maxx inoculum consisted in a suspendable powder containing living propagules of Rhizophagus intraradices , Funneliftormis mosseae, Glomus aggregatum, and Glomus etunicatum containing 5,625 propagules/g.

The mycorrhizal inoculum was diluted in water to final concentration of 5.3 mg/L in order to achieve the manufacturer’s recommended rate of 10 g each 1,000 plants. The diluted AMF inoculum was applied in-field drench during 50 s around the trunk of each vine at the beginning of the growing season by using a 56 L spot sprayer. Although the inoculum manufacturer did not report other microorganisms accompanying AMF1 , it is known that commercial AMF inocula, obtained following industrial production processes, are home of a large and diverse community of bacteria with important functional plant promoting growth traits, that may act insynergy with AMF providing additional services and benefits . Therefore, non-inoculated vines received the same amount of a filtrate inoculum with the objective of restoring rhizobacteria and other soil free-living microorganism accompanying AMF and that play an important role in the uptake of soil resources as well as in the infectivity and efficiency of AMF isolates . The filtrate was obtained by passing diluted mycorrhizal inoculum through a Whatman filter paper Grade 5 with particle retention of 2.5 µm . Phosphorus amounts in the vineyard soil was measured before the experiment and was low, thus, that phosphorus level was sufficient to ensure adequate development of non-inoculated plants, even under water deficit and not excessive enough to decrease the mycorrhizal diversity in the vineyard and thereby the root colonization . Irrigation treatments started at the beginning of summer until harvest . Vineyard crop evapotranspiration was calculated by multiplying the reference evapotranspiration and the crop coefficient . Thus, hydroponic nft half of the inoculated and non-inoculated vines were irrigated to ensure the full of expansive growth that corresponded with the amount of water needed to restore the 100% of the ETc . The other half of inoculated and non-inoculated vines received half of the amount of water received by FI plants . Irrigation was applied weekly. Each treatment had four replicates consisting in 7 grapevines, 3 of which were sampled and the 4 on distal ends were treated as border plants. Intraradical AMF colonization was estimated before treatment application , 3 months after treatment application , and at harvest . Root samples from three grapevines per replicate were collected at a depth of 15 and 20 cm away from the vine trunk by using a fork, and stored in zip bags for further analysis. Then, each replicate root sample was washed with water in the sink, cleared, and stained according to methods described in Koske and Gemma . AMF colonization was determined by examining 1-cm root segments under the microscope . Then, intensity of the intraradical mycorrhizal colonization was calculated for each treatment/replicate as described previously by Torres et al. . Briefly, the extension of mycorrhizal colonization was determined by estimating the product of the mycorrhizal colonization in width and length according to a scale range between 0 and 10 where 0 is complete absence of fungal structures. The extension of each treatment/replicate was calculated as the sum of the product of mycorrhizal colonization in width and length divided to the number of root segments. Then, the incidence of mycorrhizal colonization was estimated by dividing the number of root segments with presence of fungal structures and the total observed segments.

Finally, the intensity of the colonization was calculated as the product between the extension and incidence, and the result was expressed as percentage of colonization. Relative mycorrhizal dependency index was calculated following Bagyaraj : RMD = Leaf fresh weight of I vines × 100/Leaf fresh weight of NI vines. This index allows establishment of the crop dependency upon the mycorrhizal symbiosis for reaching its maximum growth for given environmental conditions. All the growth parameters were measured on the three middle vines in each replicate and the values were averaged for the replicate value. Green pruning was carried out before the cluster development to avoid the excessive vegetative growth and ensure a good balance between the growth of vegetative and reproductive organs of the grapevines. Removed shoots from the three middle grapevines were weighed. Trunk diameter was measured with a carbon fiber composite digital caliper . At harvest, leaves were removed and leaf area was measured with a LI- 3100 Area meter . Clusters were harvested and weighted to obtain the yield per vine. Measurements were performed on the three middle grapevines within each replicate and averaged.Thirty berries were randomly collected from the middle vines within each replicate and immediately processed. Berries were weighed and gently pressed by hand to squeeze the juice. Total soluble solids were determined using a temperature compensating digital refractometer . Must pH and titratable acidity were determined with an autotritrator . TA was estimated by titration with 0.1 N sodium hydroxide to an end point of 8.3 pH and reported as g/L of tartaric acid. For flavonoid analysis 20 berries were randomly collected from each treatment-replicate and after gently peeling, skins were freeze-dried . Dried Thissues were ground with a Thissue lyser . Fifty mg of the resultant powder was extracted in methanol: water: 7 M hydrochloric acid to simultaneously determine flavonol and anthocyanin concentration and profile as previously described by MartínezLüscher et al. . Briefly, extracts were filtered and analyzed using an Agilent 1260 series reversed-phase high performance liquid chromatography system coupled to a diode array detector. Separation was performed on a reversed-phase C18 column LiChrospher R100, 250 mm × 4 mm with a 5 µm particle size and a 4 mm guard column of the same material at 25◦C with elution at 0.5 mL per minute. The mobile phase was designed to avoid co-elution of anthocyanins and flavonols and consisted in a constant 5% of acetic acid and the following gradient of acetonitrile in water: 0 min 8%, at 25 min 12.2%, at 35 min 16.9%, at 70 min 35.7%, 65% between 70–75 min, and 8% between 80–90 min. The identification of flavonoid compounds was conducted by determining the peak area of the absorbance at 280, 365, and 520 nm for flavan-3-ols, flavonols, and anthocyanins, respectively. Identification of individual flavan-3- ols, anthocyanins, and flavonols were made by comparison of the commercial standard retention times found in the literature.

For that we measured whether the passive individual was in front of the ramp by the time the actor arrived at the location where the food had been released. after releasing the food, the actor moved to the food location in 237 of those 287 trials . Passive individuals were in front of the ramp by the time the actor arrived in 76 occasions . We found no differences between conditions . We found that actors did not approach the released food in 50 trials in which they released it. A majority of those trials were direct food test trials . This makes sense since actors spent some time obtaining the food reward placed inside the handle. Nevertheless, in a great majority of these trials the actors ended up obtaining the food reward from the handle before the passive individual finished her last reward. Interestingly though, this behavior predominantly occurred in three of the six days. Furthermore, we only found one case in which the actor showed an intention to approach the partner by getting closer to him.The results of the study suggest that days of gibbons managed to solve a competitive food task where one dyad member had the opportunity to pull and activate a release mechanism containing five potential food rewards for both partners. When gibbons had the opportunity to obtain an extra reward from their actions , they almost always acted, avoiding mutual deffection. In contrast, in an indirect food test condition where gibbons could not obtain the extra rewards from their pulling efforts, their likelihood to pull and release potential food rewards dropped significantly in comparison to the direct food test condition. In our opinion, two primary reasons could explain this pattern of results. First, it is possible that gibbons were more motivated to pull when they could directly benefit from the extra reward inside the handle. Similarly, blueberry package gibbons would have significantly pulled more often in the indirect food test condition compared to the no food control because they could still obtain some rewards.

Clearly, gibbons showed that they did not just act for the sake of pulling the rope. Most likely, their actions were motivated by the prospect of obtaining rewards, especially when those were easier to access. While this reason is very plausible, it does not necessarily account for why gibbons did not pull for 90 s in almost 40% of the indirect food test trials. This is especially surprising if we consider that actors benefitted more than passive partners in this condition. In other words, gibbons did not seem to interpret the situation as beneficial for actors. If that were the case, we would have expected gibbons to pull more often in indirect food test trials. Thus, the second possible explanation for our results is that gibbons interpreted the situation as a conflict of interest and hesitated to pull to avoid losing rewards in favor of the passive partner. This interpretation would be in line with previous findings in chimpanzees, bonobos and common marmosets. Thus, given the two non-mutually exclusive explanations, it remains unclear whether gibbons deffected in indirect food test trials due to a reduced motivation to act because they could not access the extra reward attached to the handle or because they wanted to avoid the possibility of losing rewards to their partner. So far, we have mainly discussed gibbons’ decisions whether to pull or not. In other words, did they try to maximize their own rewards when their partners pulled? The main source of potential conflict between participants lied on the possibility that passive individuals could position themselves in front of the release mechanism during direct and indirect food test trials. In direct food test trials, this could be particularly beneficial for passive partners given that actors could lose some valuable seconds trying to obtain the extra food reward attached to the handle. However, we found that actors actually obtained most of the rewards in both conditions, with a special advantage over passive partners during indirect food test trials. In fact, in only one dyad of gibbons the passive individual obtained more rewards than the actor in both test conditions.

Furthermore, passive individuals rarely took advantage of the situation and they did not distinguish between conditions. That is, during direct food test trials passive partners did not benefit from the time that the actors spent trying to obtain the reward located inside the handle. In that sense, gibbons did not interpret the situation as a social dilemma in which they could benefit more than their partner. Yet, gibbons also did not solve this task cooperatively. For that to be the case, dyad members would have needed to benefit more or less equally on both conditions and they would have not hesitated to manipulate the handle in indirect food trials. It is also very unlikely that gibbons’ decisions were driven by proactive prosocial motivations such as releasing food rewards to favor their dyad members given that actors benefited the most from their own actions. One possible explanation to understand why actors obtained more rewards than passive partners is that both individuals approached the handle during direct food test trials to obtain the reward, although only one individual pulled the handle. This occurred in 27.6% of the direct food test trials in which an individual pulled the handle. This possibility could partially explain why passive gibbons rarely position themselves in front of the release mechanism during direct food test trials, but it cannot explain why in indirect food test trials they did not take advantage of their passive role. In fact, in indirect food test trials passive partners approached the handle in 10% of trials. An alternative explanation is that the dominant individual pulled and obtained the majority of rewards. However, there are numerous reasons to suggest that a dominance component cannot fully explain our pattern of results. First, only three of 12 individuals released rewards in less than 20% of the direct and indirect food test trials. The result suggests that although they did not solve the task cooperatively, in half of the days both individuals exchanged roles relatively often. Furthermore, our results are also in line with literature suggesting that there is no clear dominance of one sex over the other and that gibbons engage in food sharing in both captive and natural settings.

Importantly, conflict avoidance does not seem to be relevant here either. Cofeeding events occurred three times as often than displacements events, suggesting that individuals were usually tolerant with each other, as it has been observed in other populations. Relatedly, gibbons never hoarded the blueberries. They ate them as soon as they got them. Furthermore, these tolerance may be mediated by the length of time that days had spent together. In our study, the length of dyad predicted how equally gibbons divided the five food rewards. A third alternative explanation is that once a gibbon decided to manipulate the handle, the other one totally disengaged from the task, as if acknowledging a sort of property claim. This could explain why passive partners did not take an advantageous position in front of the release mechanism and why, as a consequence, actors did not face a social dilemma in many trials. after all, actors benefit more than passive partners despite the costs to pull the rope, understood as the possibility to lose rewards due to the distance they had to cover and the time lost to return to the location where the food was released. Nevertheless, this is unlikely because passive individuals still obtained a significant fraction of the food rewards . All these previous arguments cannot fully explain why passive partners rarely took advantage of their position, especially given how successful this strategy was: passive partners obtained almost 75% of rewards when they positioned themselves in front of the release mechanism by the time the actor manipulated the handle. We thus propose that passive gibbons did not always take advantage of their partner actions because of the combined processes of motivation from the side of the actor and a general high level of social tolerance towards inequities. That is, individuals that were more motivated to obtain food and more attentive were also more likely to take the actors’ role in our task. Trough participation, they could become more aware of the situation as a whole and react faster to obtain the rewards despite the potential costs of pulling the rope. This gave them an advantage over their passive partners, whom at the same time tolerated actors obtaining the majority of rewards . Importantly, tolerance towards reward inequities also came from the perspective of the actors. Indeed we found that in ffy trials individuals from five of the six days seemed to adopt a prosocial attitude towards their passive partners by letting them access all the released rewards. Future studies should improve different aspects of our setup to continue exploring gibbons’ decision-making strategies when individuals’ interests collide. Te main weakness of our design is that we were not able to separate days of gibbons before the experimental sessions. In that sense we could not train them with the different task contingencies as it is usually the case in this type of settings but see. It is thus possible that some individuals were more skillful than others, blueberry packaging and that might have affected our results. Nevertheless, all individuals approached the appara.Thus and obtained rewards and only one never pulled from the handle during the course of the study. Moreover, despite the fact that gibbons distinguished between conditions with food and the no food control, their latencies to act did not differ between the indirect food test trials and the no food control trials. This could be interpreted as strategic behavior in the indirect food test trials if the gibbons were waiting for their partners to act. It is possible that with longer trials we would have found a significant difference between gibbons’ latencies in indirect food test trials and no food control trials.

In that sense, future changes in the trial time or the food rewards can better assess whether gibbons strategize to solve conflicts of interest. Relatedly, it is possible that gibbons were more motivated to act during direct food test trials compared to indirect food test trials because there were more rewards in play . It has been found that at least great apes are able to distinguish between these two amounts when they are presented at the same time. To our knowledge, however, gibbons have never been tested with these quantities. Nevertheless, in our scenario gibbons did not necessarily need to discern between these two quantities because the two amounts were never presented at the same time. Thus, although it is possible that this difference could have played a role in their performance, it is more parsimonious to think that their motivation to pull in direct food test trials was due to the high probability to eat the extra reward while pulling the handle. Future studies may use different reward constellations varying in quantity and/or quality to continue shedding light on gibbon socio-cognitive performance. Finally, given the quasi-experimental nature of our task, we did not always capture the social dilemma scenario we envisioned. Future tasks should implement designs in which cooperative acts are clearly costly for those individuals willing to volunteer. In addition, given our restricted sample size we could not test species differences or the presence of individual biases . The present study advances our understanding of how tolerance may allow primates to solve potential conflict over food rewards. In our study gibbons exhibit high degrees of social tolerance . Passive partners tolerate that actors obtain higher benefits in a majority of trials while actors often actively forego opportunities to maximize rewards . Relatedly, gibbons engaged in cofeeding events relatively often. One possibility is that such a high degree of social tolerance towards conspecifics results from gibbons’ unique pairliving social system compared to other great apes, although future studies should inspect this relationship in more detail. Overall, the inclusion of gibbons in studies exploring the nature of primate socio-cognitive abilities is critical. It will help to elucidate the nature of our prosocial motivations and their relationship to specific socio-ecological pressures and ultimately to understand how they have evolved since the last common ancestor with all living apes.One experimenter interacted with the apes during a test session while a second experimenter recorded the session and scored the subjects behavior .

The Tanaka Farm executives are ethical, good people who want the best for their workers and their local community. They have a vision of a good society that includes family farming and opportunities for social advancement for all people. They want to treat their workers well and leave a legacy for their children. They participate in churches and non-profit organizations working toward such hopes in society. They asked for my opinions on how the labor camps could be improved for the workers. After a picker strike in which explicit racist treatment of the pickers in the fields was brought to light, the growers were visibly surprised and upset. They promptly instructed all crop managers to treat all workers with respect. 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. Rob Tanaka is a tall, bearded man with a kind, gentle personality. He is in charge of agricultural production of the farm, planning everything from planting to harvest and overseeing those in charge of each crop. His office is located in a small house in the middle of the berry fields, several miles from the main offices. He spends most of his time in this office, although he also works via laptop in the small lounge of the main office building and visits the fields often. His primary concerns relate directly to farming—weather, insects and birds, soil quality, and labor—although he is also concerned by the survival of the farm. Over several conversations in the small lounge in the main office building, Rob described to me his anxieties related to his work and the farm’s techniques to buffer their vulnerability.In this conversation, Rob indicates his primary worries regarding the most important variables affecting not only his job but the feasibility of the farm business as a whole—labor, weather, urban growth, regulations, pe grow bag and the market. He explains that this family farm has developed a ‘‘portfolio of crops’’ in order to buffer their vulnerability to the market.

In another conversation, Rob told me about a recent meeting of the farm executives about being a ‘‘great company.’’ He explained that every time he heard the word ‘‘great’’ all he could see in the discussion was profitability to shareholders. This made him angry and he said, ‘‘We already are a great company, and if this is what being a great company means, then I want to be a good company.’’ He described his frustration with the farm becoming more corporate and bureaucratic. He liked it more when it was a small family business and he ‘‘didn’t have to go through all these hoops to write a check.’’ These excerpts show Rob Tanaka concerned with the farm’s survival for future generations in the midst of a difficult market while resisting becoming another corporate agribusiness.Another of the executives is Tom, a lean white man in his late 40s brought in by the Tanaka family to help the farm compete on the international small fruit market. Tom has an office in the trailer with the other main executive offices, although he has taken more care to decorate it than most, proudly displaying a colorful painting of workers picking strawberries in China—one of the very places against which he is competing. Previously, Tom was in charge of processing and marketing for a large Mexican strawberry producer. At the Tanaka Farm, his job starts before sunrise, when he calls his competitors and potential buyers in Poland, China, and then Chile. Later in the day, he can take breaks to meet friends or eat out. He daily attempts to find a competitive advantage by changing the fruit grown in various fields or by buying fruit from other farms to process and then sell. Over the course of several months, Tom describes the stark competitive disadvantages of the farm in domestic and global terms.Tom paints a stark picture of the effects of global free markets in the context of large economic inequalities. He worries daily about competition with the Califtornia variety of berries along with the stretching of its flavor via food science. Although Tom is dedicated to his job, starting work before the sun rises, he does not have much hope for the future of berry farms in the Pacific Northwest nor in the United States in general. The farm executives are anxious to ensure the survival of the farm for future generations in the midst of bleak economic trends. They work long days, worrying about many variables only partially within their control and doing their best to run a family farm that treats its workers well. They are very aware of their own structural vulnerability. They also have some control over their own schedules.

They take breaks when they choose to eat or work out, talk on the phone or meet with a friend. They have comfortable houses, private and clean indoor bathrooms and kitchens, insulation and heating, and quiet. They have private indoor offices with phones and computers as well as employees ‘‘under’’ them .Most of the administrative assistants are white, along with a few Latino US citizens. All are female. They work seated at desks in open spaces without privacy. They are in charge of reception, interacting with white local residents and business people as well as with Mexican farm workers. Sally is the year-round front desk receptionist. She is a lean, white woman, approximately 40 years old, often smiling. She grew up in the same town in which the farm is located and lives with her husband and children in a relatively small house. Sally tries to treat the workers well and turning around the desk when she first arrived was one step in this direction. She helped arrange loans for the Mexican farm workers one year when the picking date was moved back and the workers were living out of their cars, waiting without money or food. Crew bosses and farm executives regularly reprimand her for being too nice to the workers. She has been told to be ‘‘more quick,’’ ‘‘less friendly.’’ In addition, she feels disrespected by the people ‘‘above her’’ , treated like a ‘‘peon.’’ They sometimes give her advice on her work or give her jobs to do without the common courtesies of ‘‘please’’ or ‘‘thank you.’’ Maria is 30, a bilingual Latina from Texas. Her great grandparents moved to the United States from Mexico. She lives in the nearest labor camp with heat and insulation. She works several positions May through November, sometimes at the front desk with Sally, sometimes in the portable unit where pickers can ask questions and pick up mail in the afternoon. On Fridays, she works in the wooden shed where paychecks are passed out to workers in a long line. Her first summers on the farm, including the summer she was pregnant, she picked berries and worked with a hoe. After four years with the hoe, she was moved up to desk work due largely to her ability to speak English fluently. Like many other workers on the farm, she first heard of indigenous Mexicans while working on the farm. She explained her work to me while we sat in the portable, occasionally interrupted by a picker seeking their mail.

The crop managers are in charge of all details involved in the efficient production of a specific crop, from plowing to planting, pruning to spraying, picking to delivery, growing bags and finally to processing. They have private offices in the field house amidst the berry fields nearby the largest labor camp, although they also spend a fair amount of time walking through the fields overseeing. During harvest, they begin by 5 a.m. seven days a week and finish in the early evening. They can take a break when they choose to eat, run errands, or go quickly home. The crop managers worry about the availability of machinery, the effects of weather on the crops, and the docility of their labor force. They have some control over how much the pickers are paid, and they have several field bosses below them enforcing their instructions. Jeff is a 30-year-old white man who recently finished a degree in agricultural marketing at a university in Califtornia. He manages blueberries and raspberries. Jeff told me about his job as he drove his large white pick-up with two large dogs in back. We drove to an agriculture store to buy large concrete drains for the blueberry fields and to Costco to buy tri-tip steaks for a potluck at his church. He explained several simultaneous tasks in the raspberry fields to illustrate the many things a crop manager has to oversee. The thing that causes him the most anxiety is having multiple bosses on a family farm without a strict chain of command. He also worries about weather, and about harvest crews: ‘‘It is what it is, you know. Sometimes people walk out and sometimes people pick. It’s kind of like the weather, you can’t really predict it and you don’t really have control over it, but usually it ends up working out all right.’’ He went on, ‘‘We make the prices fair, so if the crew walks out [on strike], we just say ‘hey, we’ll be here tomorrow’ and that’s the way it is. They can come back if they want.’’ He told me that all the people on raspberry machines are Latinos from Texas whereas those picking blueberries are ‘‘O-hacan’’ , although he also told me that he cannot really tell the difference. That week, Jeff was in the midst of budgeting for next year, trying to predict the crop yield. He predicts based on bud count: for each fruit bud in the fall, he expects seven berries the following summer, although a freeze could make the fruit smaller or kill the buds altogether.After I turned off my tape recorder, Scott wanted to hear more about my interest in crossing the border with some of the Triqui indigenous Oaxacan workers. First, he told me I should get permission from the federal government. Later, he changed his mind and said the problem with that would be that they would ask for all my information about where I crossed. He was afraid the government would then shut down that route ‘‘and we wouldn’t have any workers anymore.’’ He explained that almost 90 percent of the pickers are undocumented. The profiles of the crop managers bring into focus the practical attempts from the management to run a good, ethical farm in the midst of difficult conditions. In addition, Scott is clearly concerned about the direct effects of immigration and border policies on his labor force. Like many farmers I interviewed, he knows that current US farming practices would be impossible without undocumented Latin American migrant workers.Several supervisors, often called ‘‘crew bosses,’’ work under each crop manager. Each directs a crew of 10 to 20 pickers. They walk through the fields, inspecting and telling workers to pick more quickly and carefully. The crew bosses are under constant supervision from the crop managers, although they can take short bathroom breaks and they often carry on light-hearted conversations with coworkers. Most crew bosses are US Latinos, with a few mestizo Mexicans and one Mixteco indigenous Oaxacan. They live in the insulated, year-round labor camp. Some of the crew bosses call the Oaxacan workers derogatory names. The crew boss most often accused by pickers of such racist treatment has a daughter, Barbara, who is also a crew boss. Barbara is a bilingual Latina from Texas in her early twenties who has worked the harvest at the farm for 11 years. She attends a community college in Texas every spring and hopes to become a history teacher. She is upset that other crew bosses call Oaxacan people pinche Oaxaco or Indio estupido . She explains to me that Oaxacans are afraid to complain or demand better working conditions because they do not want to lose their jobs. She describes a farm policy stating that if a crew boss fires a picker, they can never be hired by anyone else on the farm. She explains, ‘‘It’s unfair. I think there should be checks and balances.’’ Her family learned English in Texas as well as in the farm-sponsored English classes each night after work.

The results of the PCoA analysis with 34 markers also produced three groups. The species group was clearly separated from the other two groups. The distinction between the O34-16 group and the TSL group was less clear . The O34-16 group contained nearly all of the subsp. sylvestris accessions, however within that group, there was no clear distinction between the cultivated and wild forms . To differentiate the wild sylvestris accessions from cultivated sativa forms, further analyses focused on only the O34-16 group. The Ward and UPGMA hierarchical clustering methods divided the 165 accessions of the O34-16 group into two clades. Seventy-six cultivated V. vinifera subsp. sativa accessions, including the powdery mildew resistant ‘Matrassa’ were in one group, and the second group consisted of 89 sativa and sylvestris accessions. When the Ward clustering method was applied to this second group of mixed accessions, there were again two clades. These four V. vinifera accessions are ancient cultivars and are likely transitional forms with the wild ancestor sylvestris. The powdery mildew resistant accession DVIT3351.27 was in this clade. The second clade had three less well-defined sub groups: the first contained six sylvestris accessions including the powdery mildew resistant accession O34-16; the second group contained accessions of V. vinifera subsp. sativa collected from Pakistan and Turkmenistan and one accession labeled V. jacquemontii; and the third group was a mix of wild sylvestris or feral types that were collected from Iran, Iraq, Turkmenistan, Pakistan and Russia, vertical farming system and five incorrectly identified accessions – three of which were labeled as V. jacquemontii, and the other two were collected from China.

Two distinct clades were revealed when clustering analysis was applied to the 40 wild sylvestris accessions . The first clade contained ten sylvestris accessions obtained from Turkmenistan, four accessions from Iran and two from Afghanistan. The Turkmenistan accessions were collected from the Kopet Dag mountain range, which defines the border between Turkmenistan and Iran on the east of the Caspian Sea. The powdery mildew resistant accession O34-16, collected near the town of Shirvan, Iran, was in this clade. Shirvan is near Mashhad, an important trade hub on the ancient silk route located on the other side of the Kopet Dag mountain range . Therefore, it was not surprising to see these accessions positioned in one clade. The second clade consisted of accessions collected from Georgia, Armenia and Iran. The powdery mildew resistant sylvestris accession DVIT3351.27, collected from Alaverdi, Armenia, was in this group. These results in conjunction with analyses that included the entire O34- 16 group suggest that the two wild sylvestris accessions could have acquired powdery mildew resistance from different genetic backgrounds. Gene diversity indices for each group are shown in Table 2. The average FIS value for the Species group was higher than the other two groups. This group consisted of only 29 accessions as compared to 165 accessions in the O34-16 group and 186 accessions in the TSL group. The average FIS for the O34-16 group was 0.10; expected heterozygosity was higher than observed for all but one of the 34 markers. The average near zero FIS value for the TSL group suggests that they are a panmictic population in Hardy-Weinberg equilibrium. Values for the differentiation index among the three groups were very low . These results indicate that there is no clear differentiation among these groups due to the presence of transitional forms that bridge the groups and indicate active gene flow among them, implying that domestication and selection is underway.Because two of the newly discovered powdery mildew resistant accessions were collected as sylvestris, it was important to confirm their true type based on morphological traits. Flower sex phenotype and seed morphology are two key criteria used to differentiate subsp. sylvestris from cultivated sativa forms .

The flower phenotype of the subsp. sylvestris accessions collected from Armenia, Georgia and Turkmenistan could not be determined because they were young potted plants. Flower phenotype data for 15 wild V. vinifera accessions was obtained from GRIN, the National Germplasm Resource Information Network [31]. A combination of two DNA markers was used to differentiate male, hermaphrodite and female flower phenotype for the set of 380 accessions. Field phenotypic observations for the 95 accessions from the Vassal collection matched the flower phenotype predicted by DNA analysis with only one exception – ‘Yhsouh ali’ , which was recorded as a female, but DNA analysis indicated it was a hermaphrodite. These test results indicate that the combination of both markers is a reliable system to determine flower phenotype. DNA marker-based flower phenotyping of the 40 wild forms of V. vinifera subsp. sylvestris and all ten newly discovered powdery mildew resistant accessions are presented in Table 4; the results for all other accessions are presented in Additional file 11: Table S10. The flower phenotype was undetermined for 11 accessions due to ampliftication failure with one or both markers. Phenotypic observations differed from genotypic results for only three accessions. Two accessions in the species group, C-166-025 and DVIT1159.3, are recorded as male, but are hermaphrodite based on the DNA analysis. The third anomaly was the cultivar ‘Neeli’ , which was scored as a hermaphrodite, but is listed as a female plant in the GRIN database. DNA marker analysis of flower sex in the V. vinifera subsp. sativa group of cultivars found that 223 were hermaphrodite, 57 were female, and five were identified as male . One of the five males, ‘Kala Kostan’ is recorded as a female in GRIN; the flower phenotype could not be verified for the other four genotypically male cultivars. Eighteen of the 40 V. vinifera subsp. sylvestris accessions were male, including newly identified powdery mildew resistant accession, DVIT3351.27. Eight accessions were female, including resistant accession O34-16 . Fourteen others were hermaphrodite. Seeds were extracted from ten of the wild sylvestris that H.P. Olmo collected from Iran and Afghanistan .

The combined results from seed morphology and flower sex phenotyping, revealed that 14 accessions designated as sylvestris are likely not pure sylvestris, but instead hybridized forms of native wild species and cultivated varieties. interestingly, three accessions from H.P. Olmo’s O series, which are male, based on genotypic analysis, bear fruit . The flower phenotype of the accession O34-26 was scored differently in each of three years on GRIN. Similarly, observations of the flower phenotype for O34-55on GRIN varied from year-to-year between hermaphrodite and female. O35-47, the third genotypically male accession has been recorded as a hermaphrodite. The flower sex of the 12 powdery mildew resistant accessions was also determined: the sativa accessions ‘Husseine’ ‘Soïaki’, ‘Sochal’, and ‘Vassarga tchernaia’ are female vines; the other six including ‘Kishmish vatkana’ and ‘Karadzhandal’ are hermaphrodites . Two of the new powdery mildew resistant accessions are clearly V. vinifera subsp. sylvestris. O34-16 is a female vine with obvious wild type seed morphology . The accession DVIT3351.27 is a male flowered V. vinifera subsp. sylvestris.In this study, we exploited available genetic information on the powdery mildew resistance locus Ren1 to identify additional germplasm that shared a Ren1-like local haplotype, and then attempted to clarify the evolution of powdery mildew resistance and its domestication in cultivated V. vinifera subsp. sativa. Ten new powdery mildew resistant accessions were discovered that possess a Ren1-like local haplotype, which was earlier identified in ‘Kishmish vatkana’ and ‘Dzhandzhal kara’ from Central Asia. We discovered that powdery mildew resistance is present in two V. vinifera subsp. sylvestris accessions, a taxon considered to be the progenitor of the cultivated form sativa. Four of the resistant accessions ‘Vassarga tchernaia’, ‘Chirai ’, ‘Late Vavilov’ and ‘Khalchili’ are obscure varieties with few records in the ViThis International Variety Catalog or the European ViThis database. The first three accessions were obtained from germplasm collections in Uzbekistan, Tajikistan, and Turkmenistan, respectively; Harold P. Olmo collected ‘Khalchili’ from Afghanistan in 1948. The other four resistant sativa accessions are better known. ‘Husseine’ was also collected from Afghanistan and it is available worldwide with records in 20 germplasm collections with 61 synonyms. ‘Matrassa’ was acquired from the Azerbaijan collection, and is available in 15 collections with 26 synonyms. ‘Soïaki’ is found in 10 collections with 3 synonyms. ‘Matrassa’ and ‘Soïaki’ are listed by Russian grape breeders as cultivars for high quality table, sparkling and dessert wines. The eighth resistant sativa accession ‘Sochal’ is only held at two collection sites in the USA. Plant inventory records indicate that cuttings of ‘Sochal’ were obtained in 1971 from the N. I. Vavilov institute of Plant industry, Leningrad. Eight of the newly identified accessions carrying Ren1-like local haplotypes were acquired from five neighboring countries of Central Asia and the Caucasus, all major junctions for trade on the ancient silk route for thousands of years. It is not hard to believe that selected grape germplasm, vertical farming racks favored for desirable fruit characteristics, was moved back and forth in the form of seeds and cuttings from one region to another, where they were likely crossed with local varieties in remote isolated valleys and villages in different regions. In addition to the identification of eight new powdery mildew resistant accessions, this study also gathered information on the genealogical relationships. A likelihood based method that determines potential parent progeny relationships without any prior knowledge revealed four first-degree relationships. We identified ‘Vassarga tchernaia’ as the female parent of ‘Kishmish vatkana’ and verified ‘Thompson seedless’ as the male parent. ‘Vassarga tchernaia’ and ‘Sochal’ shared a first-degree relationship, sharing at least one allele at 42 markers. Both are female vines with reflexed stamens and seeded fruit. It is difficult to determine the direction of the relationship between ‘Sochal’ and ‘Vassarga tchernaia’. Nevertheless, both of them are female vines, resistant to powdery mildew, and produce seeded fruit. ‘Sochal’, ‘Vassarga tchernaia’ and ‘Kismish vatkana’ are not found in historical collection/ breeding records and may have been disregarded due to undesirable fruit attributes, e.g. loose clusters, and small seeded berries, which did not saThisfy selection criteria for that particular region.

The other two first-degree relationships identified in this study were between ‘Late Vavilov’ and ‘Karadzhandal’, and between ‘Khalchili’ and the powdery mildew susceptible ‘Yarghouti’. All four arehermaphrodites and only ‘Karadzhandal’ is well known with a recorded history. One of the important findings of this study is that four of the new powdery mildew resistant cultivars ‘Chirai obak’, ‘Husseine’, ‘Matrassa’ and ‘Soiaki’ are not directly related to any other accession in this study or in the complete Vassal collection. This implies that the story of powdery mildew resistance in cultivated varieties is complex and what we have revealed in this study may not be the complete picture due to extinction or missing cultivars in our collections. It is likely that a thorough search of germplasm collections in Central Asia would unearth more resistant germplasm. With the exception of ‘Matrassa’, STRUCTURE placed all seven new subsp. sativa powdery mildew resistant cultivars in the TSL group, even though they were collected from different regions of Central Asia. These results suggest that selection and active flow of desirable plant material was common in this region of grape domestication and that multiple breeding efforts were underway to saThisfy the local tastes for quality grapes. The TSL group also indicates that breeding efforts were also directed at seedlessness as ‘Thompson seedless’, one of the ancient varieties, was a popular parent for a large number of table grape cultivars. Two of the resistant accessions in this study belong to the subsp. sylvestris, which prompts many questions. Are these two accessions truly wild sylvestris that have never been cultivated or are they hybrids between wild and cultivated forms? What is the direction of the gene flow for powdery mildew resistance – did these two sylvestris accessions acquire resistance from cultivated forms or did the resistance come from wild types to cultivated forms? O34-16 is a female vine with seeded fruit, and seed shape typical of the sylvestris type grapes – small round seeds and short beaks. The accession DVIT3351.27 is a male vine. Dioecy is one of the key traits distinguishing the wild sylvestris from the cultivated sativa. Additionally, the male flower phenotype is only associated with wild ViThis species. According to the model of Antcliftf , flower phenotype is controlled by a single major locus with three alleles: male dominant to hermaphrodite , which is dominant to the female . In the wild, one should find only male and female vines in the absence of gene flow from hermaphroditic cultivated varieties.

Further analysis was based on 403 unique accessions: 296 from the Davis collections and 107 from the INRA Domaine de Vassal germplasm collection. Additional file 3: Table S3 presents the fingerprint profiles of the 403 unique accessions based on 19 SSR markers – one marker from each grape chromosome. Twenty-three accessions were removed from the study set. The number of alleles per marker and percent of missing data were calculated for the remaining 380 genotypes with 34 markers . Based on the collection records, the study set of 380 unique accessions consisted of 306 genotypes of V. vinifera subsp. sativa, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of ViThis species from northern Pakistan, Afghanistan and China. A minimum of 9 and maximum of 44 alleles were observed with SSR markers VVIq52 and VVIv67, respectively. The average number of alleles for all markers was 22. There were 7 markers with 5% or more accessions that had missing data .Prior to phenotypic evaluation for powdery mildew resistance, the entire set of 403 accessions was genotyped for linkage with the powdery mildew resistance locus Ren1 at four SSR marker, which span 8.1 cM genetic block on chromosome 13. The resistance linked allele of 260 defined by marker VMCNg4e10.1 was observed in 47 accessions that included V. amurensis, V. romanetii, Muscadinia rotundifolia and wild V. vinifera subp. sylvestris accessions. The majority of the accessions with allele 260 for marker VMCNg4e10.1 did not have allele 216 at the marker UDV124. However, cut flower bucket a missing allele at either marker could have been due to a recombination event. Eleven accessions, including ‘Karadzhandal’ and ‘Kishmish vatkana’ had alleles that are in linkage with the Ren1 locus at the two distal markers, VMCNg4e10.1 and UDV124 that are in linkage with the Ren1 locus .

The germplasm set was then evaluated for alleles at sc47-18 and SC08-0071-014 that flank each side and co-segregates with the Ren1 locus. ‘Karadzhandal’ and ‘Kishmish vatkana’ fingerprint profiles were used to determine whether the allele of 249 defined by the marker sc47-18 and the allele of 143 defined by the marker SC08-0071-014 were linked to resistance. These are the two alleles that co-segregate with the Ren1. Allele 249 for marker sc47-18 was common: 80 of the 403 accessions shared it. Nearly all of the 47 accessions that carried the allele 260 for marker VMCNg4e10.1 also had allele 249 for marker sc47-18, confirming the tight linkage between these two markers . The allele 143 for marker SC08-0071-014 was rare; only 17 accessions in the entire data set carried it . Six accessions had the allele 143 for marker SC8-0071-014, but did not carry the resistance associated alleles at all tested markers . ‘Khalchili’ and ‘Khwangi’ had 143 flanked by 249 at sc47-18. Two of the V. vinifera subsp. sylvestris accessions had alleles 143 and 260 on the opposing flanks for marker VMCNg4e10.1; ‘Matrassa’ and a third sylvestris accession had the 143 allele and no resistance associated allele on the opposite flank. These six accessions are potential recombinants. Two Chinese species accessions, V. romanetii and V. yenshanensis had the 143 allele, but neither of them carried a resistance-associated allele at the other three markers. In the case of these two examples, we speculate that the presence of the 143 allele is either due to size homoplasy, or the alleles at other markers are lost due to recombinations. In 2009 and 2010, resistance to powdery mildew was evaluated on a 0 to 5 scale on all accessions from Davis that carried alleles linked to resistance at one or more markers . Four other accessions were evaluated in 2012 . The year effect was significant; disease pressure was more severe in 2010 . However, the susceptible controls were highly susceptible and resistant controls had no or minor symptoms in three test years . The location in the field test plot was not significant, indicating that the close-spaced field evaluation site with no spray was an efficient and cost effective way to screen for resistance .

‘Karadzhandal’, a known powdery mildew resistance accession was evaluated both years and had a powdery mildew resistance score of < 1. ‘Kishmish vatkana’ the other previously known powdery mildew resistant accession was under quarantine as part of the importation process and could not be evaluated. Accessions with Ren1-linked alleles at only one of the flanking markers exhibited no resistance to powdery mildew in the field test . The V. vinifera subsp. sativa cultivars: ‘Husseine’, ‘Khalchili’, ‘Late Vavilov’ and ‘Sochal’ were resistant. These four accessions had mean scores for leaf and cane PM symptoms ranging from 1.08 – 2.42 in 2009 and 0.83 – 2.42 in 2010 . In 2012, in a much smaller evaluation, two accessions from wild V. vinifera subsp. sylvestris were identified as resistant from field evaluations: O34-16, collected from Shiravan, Iran, had all four resistance-linked alleles; and DVIT3351.27, collected from Armenia, had the resistance allele at one of the flanking markers on each side. Mean leaf symptoms scores were 0.4 and 0.7 for DVIT3351.21 and O34-16, respectively . The powdery mildew resistant accession ‘Karadzhandal’ at Davis had similar marker profile to accession ‘Kara djandjal’ and the newly identified resistant accession ‘Husseine’ had identical marker profile to ‘Kandari noir’ inthe Vassal collection. Both of these accessions were found to be resistant in greenhouse screens carried out at Vassal. ‘Chirai oback’ and ‘Vassarga tchernaia’, which had all four Ren1-linked SSR marker alleles, were resistant based on greenhouse screening in France. The other two powdery mildew resistant accessions were ‘Soïaki’, which had resistance-linked alleles with four markers, and ‘Matrassa’, which had resistance-linked alleles with two markers on one side, have not been evaluated for disease symptoms. In total, this study identified and verified eight new accessions that are powdery mildew resistant. ‘Soïaki’ and ‘Matrassa’ were identified as potentially resistant based on marker analysis. Their disease resistance needs to be verified in a field or greenhouse screen.Probability of identity analysis found that nine markers were sufficient to identify unique accessions in the study set . The paternity exclusion probability for a single locus ranged from 10.6% to 72.6% . A cumulated probability of exclusion of 100% was reached using only 7 markers for paternity and 3 markers for a parent pair. The simulation for parentage analysis identified a LOD score threshold of 5.0 to assess a potential single parent and 4.0 to assess a parent pair with 34 SSR markers. Six newly identified resistant accessions ‘Husseine’, ‘Chirai obak’, DVIT3351.27, O34-16, ‘Soïaki’ and ‘Matrassa’ were not related to any other accession in the set; two of these are V. vinifera subsp. sylvestris.

The presence of powdery mildew resistance in unrelated genetic backgrounds is a very important result of this study that suggests that powdery mildew resistance in Central Asia is complex and potentially represent orthologous and paralogous homology for the Ren1 locus, first identified in ‘Karadzhandal’ and ‘Kishmish vatkana’. A second important inference from these results is that there maybe many more powdery mildew resistant accessions within V. vinifera subsp. sativa and Central Asian ViThis species and further exploration is needed. This resistance could be the result of intentional breeding efforts involving material collected and curated in the early 1900s at multiple institutes set up by the Russian geneticist Vavilov, or the result of unintentional breeding and selection of resistant material in an earlier period of domestication and selection over thousands of years. More importantly, identification of powdery mildew resistance in accessions of V. vinifera subsp. sylvestris indicates that the resistance is present in wild germplasm. There were four parent-progeny relationships identified in this study; two involved the previously published powdery mildew resistant accessions . ‘Vassarga tchernaia’ was conclusively identified as the female parent of ‘Kishmish vatkana’; it also shared a parent-progeny relationship with ‘Sochal’ although the direction of the cross is unknown. ‘Karadzhandal’ and ‘Late Vavilov’ share one or both alleles with all 42 SSR markers . The powdery mildew resistant accession ‘Khalchili’ was shown to have a first-degree relationship to ‘Yarghouti’ .A 620 bp region that includes the resistance associated 143 bp allele from marker SC8-0071-014 was sequenced for the 12 powdery mildew resistant accessions and two susceptible V. vinifera subsp. sylvestris . Two accessions of Chinese species that had a 143 bp fragment at SC8-0071-014 were also sequenced. The sequences were nearly identical for all fourteen V. vinifera accessions except for occasional single nucleotide polymorphisms between both unrelated and genetically related accessions. The sequences of the two Chinese species, V. romanetii and V. yenshanensis were very different from one another and from the V. vinifera sequence, obvious examples of size homoplasy, where two alleles are identical in size but result from independent events .For the 12 powdery mildew resistant accessions, including the two previous known powdery mildew resistant accessions ‘Kishmish vatkana’ and ‘Karadzhandal’, genetic analysis was expanded to a 26 cM genomic block with six SSR markers including the Ren1 region . Six of the newly identified powdery mildew resistant accessions, including O34-16, a V. vinifera subsp. sylvestris, had similar alleles similar to ‘Kishmish vatkana’, flower display buckets and ‘Karadzhandal’ with six SSR markers . SSR marker allelic comparison of two other resistant accessions indicated that a recombination event had occurred between markers at different junctions. The wild subsp. sylvestris accession, DVIT3351.27 had complex allelic combination of markers surrounding the Ren1 region suggesting a different genetic origin of powdery mildew resistance.The genetic diversity of the core set of 380 Central Asian accessions was evaluated with hierarchical clustering , principle coordinate analysis , and a model-based clustering method implemented in the program STRUCTURE. All three analysis methods generated three groups with data from 19 or 34 markers. The delta K value calculated from the output of STRUCTURE was 45.0 at K = 3 compared to less than 5.0 at all other values of K. The three groups determined by PCoA were similar to those produced by STRUCTURE . The Q-values assigned by STRUCTURE for 380 accessions in three groups are displayed in Additional file 9: Table S9. Group A contained 29 ViThis species accessions, nearly all of which originated in China. The Q-value for membership in this group was 0.90 or above for 25 accessions. ViThis yenshanensis and B-166-016, an accession labeled as ViThis spp., both collected from China had Q-values split between the group A and B. A second V. yenshanensis accession, also collected from China, had Q values split between group A and C. ‘Khir Ghuluman’, collected by H.P. Olmo in Afghanistan, had Q-values split among all three groups indicating it was a possible hybrid of a local species and cultivated varieties. ‘Khir Ghuluman’ was labeled as V. vinifera, presumably because it is a cultivated variety in Afghanistan. None of the previous and newly identified powdery mildew resistant accessions were in this group. Group B contained 165 samples, a mix of both V. vinifera cultivars and wild V. vinifera subsp. Sylvestris accessions. Three new powdery mildew resistant accessions were placed in this group with Q-values of 0.80 and higher. O34-16 and DVIT3351.27 were collected as subsp. sylvestris, and ‘Matrassa’ was collected as subsp. sativa. For clarity, this group will be referred to as O34-16 from this point onward in the manuscript. Thirty nine accessions collected as subsp. sylvestris were in this group, 36 of which had Q-values of 0.80 or higher. Two Chinese ViThis species accessions, 588650.a and B-166-019 were in this group, and are most likely hybridized forms. All four accessions of V. jacquemontii collected from Pakistan were also in this group. The Q values of these accessions, one as high as 0.97, suggest that these accessions are not pure species and may be hybrid or mislabeled forms . Group C was named after ‘Thompson seedless’ to indicate that the group consists primarily of table grape cultivars. Two previously identified and seven of the new powdery mildew resistant accessions were in this group . The group consisted of 185 accessions labeled as V. vinifera subsp. sativa and one accession of subsp. sylvestris – O35-64 collected from Iran by H.P. Olmo. The Q values for this particular accession placed it in groups A and C. ‘Kala Khostan’ with a group C Q-value of 0.66 is the only other accession in this group with association to the species group. All but 10 of the remaining 184 accessions had group TSL Q-values of 0.70 or higher .

Strangely enough, they were not cut in such a way to take advantage of the direction of the lumina. To prevent air from coming into the amphora or moisture leaking out of it, the lumina should be at right angles to the neck of the bottle or amphora. They were oriented in the longitudinal direction of the bottleneck instead. An explanation is that the stoppers were of a reasonable size making it almost impossible to cut them in the proper way from a cork layer, which is limited in thickness. No other examples of cork stoppers are known from such an early period. Before filling the vessels, the inside could have been daubed with pitch, as is described by, for example, Columella for the storage of figs , pears , and vinegar . Apicius recommends the same treatment for the storage of pot herbs . Like present-day coating of cans with tin, this daubing with pitch prevents the exchange of air and microorganisms, too. But such a treatment could not be performed in a sterile environment, and therefore the storage life of the content remained limited. Special attention has to be paid to fruits such as pomegranates, grapes, apples, and pears that produce the gas ethylene, a natural end product of respiration. This gas effects fruit maturation, which is disadvantageous if the fruit has to be stored for a good while. Today, special precautionary measures are taken against this undesired maturation by influencing the atmosphere of storage rooms and by not reusing the same packaging material. The storage life of such fruit is benefited by removing specimens that have already started to decay, as is frequently mentioned in classical sources dealing with food preservation . Of special interest is Columella’s statement of “a general rule that above all things apples and grapes should not be laid up in the same place or near one another that the odor of the apples can reach the grapes. For exhalations of this kind quickly spoil the grapes.” . In fact, this empirical advice almost expresses present-day knowledge on this particular maturation process.Alcohol is a waste product of fermentation processes and is typical of anaerobic yeasts.

Food and fruit juices can be preserved by encouraging the growth of such microorganisms because the alcohol can reach a lethal concentration for all kinds of microorganisms. Alcoholic drinks can be used to preserve fruit, cut flower transport bucket although they will lose color unless they are sterilized. Lactic fermentation is another useful means of food preservation. Incomplete fermentation of sugar results in the production of lactic acid. As a result, the food acidity is lowered. Most enzymes are proteins, which are especially sensitive to relatively mild changes in pH. As both molecules are main components of organisms, their inactivity or destruction is vitally important. Enzyme activity increases the rate of all kinds of chemical reactions in a cell; the enzymes are highly specific in the reactions they catalyze. Enzymes are only active in a certain range of acidity with a specific optimum. Outside this temperature range the enzyme takes on a different three-dimensional form and loses its biological activity. A similar damage to enzymes is caused by changes in temperature. Wine, vinegar, and most fruits have low pH values at which most microorganisms will not grow. The normal storage life of fruits is one to two weeks. Changing the acidity of food can be achieved by adding sour mediums, such as sour milk, wine vinegar, beer vinegar, and even fig vinegar. Vegetables and fruits are the major foods that are preserved in this way. Lactic acid not only delays the growth of microorganisms, but it also improves the taste of the food. Adding salt is not essential, and aromatic herbs are added to improve the flavor. Columella enumerates a number of vegetables that can be preserved in a mixture of vinegar and brine. The use of spices is also effective in the preservation of food. Billing and Sherman , who studied the use of spices in relation to meat-based recipes, could demonstrate that spices inhibit or even kill food spoiling microorganisms. Spices that proved to be very effective were, among others, garlic , onion , cinnamon , cumin , and lemongrass .

The most effective one was garlic, a plant that is well represented in the Berenike record. Black pepper, on the other hand, was among the least effective bacteriocides: it inhibited only 38 percent of the bacteria studied. The use of spices as preservatives as well as for improving the flavor is mentioned, for example, in the cookery book of Apicius.Cooling and heating are methods that block the biological activity of the enzymes by exceeding the temperature range. In temperate regions one could take advantage of the cold winters and food could be preserved in snow. According to Columella , vessels containing food should not be exposed to the sun, but stored as cold and dry as possible to prevent food from becoming moldy and decaying. In the distant past, food was stored in icehouses, whereas today refrigerators and deep freezers are used instead. The dolium with peppercorns found in Berenike was, probably for similar reasons, buried in the ground. Although lowering the temperature of food is a most effective way of slowing down the process of aging without affecting the characteristic features such as taste and color, it is not realistic for most of the year in Berenike. Therefore, other treatments that prolonged the storage life must have been applied to especially perishable fruits. Heating food is only effective in combination with preservation methods that void recontamination. Boiling food for some time will not make it germ free, and as the food cools down, microorganisms will duplicate again as the temperature nears the optimum for microorganisms.By selecting only perfect specimens, a quick decomposition resulting from contagious diseases is prevented. Further contamination with microorganisms is prevented by using rainwater that has been boiled for a considerable time and by sealing the storage vessel. A cool place obviously slows down the increase of the microorganisms. With respect to apples, pears, quinces, plums, cherries, and figs, Apicius states that the fruit should be picked with stems . A similar procedure is recommended by Columella for every fruit that has to be stored for a long time . He states that grapes may remain green for as much as a year if the pedicels are treated immediately with hot, hard pitch . In this way there is no opening through which air could penetrate that would initiate the fermentation process. Pliny describes the plucking of apples together with the branches, the ends of which were thrust into elder pitch and then buried. The pedicels of figs, however, were removed, after which they were sun-dried and mixed with condiments and then made into a paste by trampling . Ripe apples, pears, quinces, plums, cherries, and figs can be preserved in honey or, as far as quinces are concerned, in a mixture of honey and boiled wine. Whole bunches of grapes were carefully placed in vessels that were compartmentalized with pieces of wood so that the grapes could not touch each other or the vessel itself.

Sawdust or chaff was used for covering the bunches of grapes. The large fruits of the pomegranate and quince even facilitate the embedding in a thick layer of well-kneaded potter’s clay, which can be removed later on by plunging it in water so that the clay dissolves to release the perfectly preserved fruits . The drying of grapes is also combined with dipping them into a solution of alkali and olive oil as is, for example, described from Syria . The alkali is extracted from the ashes of salt wort , a desert plant gathered by uprooting it when it is still green. After burning the salt wort, the ashes are soaked in water and exposed for an extended period to the sun. Then the water is strained and some olive oil is added to it. According to Jabbur, the mixture should contain the right proportions of both ingredients. The use of a preserving mixture for grapes, consisting of a balanced combination of salt, oil, and cinder lye, is also described by Columella . The solution serves a dual purpose: it cleans the grapes and by softening and cracking the peel of the grapes, procona flower transport containers water more easily evaporates so that they dry and turn into raisins. There does not seem to be a general rule with respect to stoning fruits as part of the preservation procedure. According to Columella it was the practice of many people to cut up quinces and take out the seeds, because it was thought that the seeds were harmful. But very often, whole fruits were dried or pickled. This may be partly due to the difficulty of removing the stones from the flesh.The storage life of products that reached Berenike, either commodities, provisions for ships, or food products meant for their inhabitants, must have being given special attention as most were imported over long distances and were exposed to high temperatures. Markets that could offer perishables such as fruits and vegetables were not present, but some of these products could be grown in kitchen gardens. At Berenike itself, preservation conditions can be considered modest. The temperatures that allow microorganisms to grow are present during most part of the year. The aridity and the salty air, on the other hand, act as severe limiting factors for microbiological activity. This can be deduced from the present-day conservation conditions of archaeobotanical food remains. Much of the desiccated plant material, also erroneously mentioned as mummified, is still in an excellent condition, including pulses that tend to disappear in moister environments. But the atmospheric humidity, resulting from the presence of the Red Sea, is responsible for the morning dew during the winter and early spring and might have been problematic for optimizing storage facilities. This is especially true for dried food as it easily absorbs moisture.The transport of grain to Berenike would not have been problematic. Wheat and barley could have been obtained from the Nile Valley, a short trip as such. Rice and Job’s tears were transported over large distances as they were obtained from Indian harbors. Rice is well known for its good preservation conditions. Contrary to wheat, it is not susceptible to insect damage, can be kept for several years, and will even improve in taste . Storage of grain for a long period certainly requires special conditions, but the turnover at Berenike would have been relatively quick. Pulses consumed or transshipped in Berenike would have been more problematic. A valuable feature of domestic pulses is that pods do not open quickly, which means that dispersal is prevented. Nevertheless, seed loss is still experienced during harvesting, and this can be limited by harvesting pods when they are still not completely ripe. A consequence of this is that the seeds are not completely dry, a condition not optimal for storage, as is mentioned by Theophrastus . But special treatments of individual fruits or their individual characteristics could perhaps cope with this early harvesting. Cato , for example, describes a method for treating lentils. First, the lentils have to be soaked in silphium vinegar. Next they are exposed to the sun, rubbed with oil, and finally dried. Some members of the pea family, including pea , contain phytoalexines in their seeds, which have an antimicrobial activity . Other members of the pea family, namely, Abrus, twisted acacia , Nile acacia , carob , tamarind , and senna , have hard seeds or well-dried fruits that may only suffer from insect damage. For storing oil containing seeds, such as fl ax and safflower , it is important that the seeds remain intact during harvesting. Otherwise the oil will be liberated, causing rancidity in storage . Vegetables grown for their leaves are vulnerable in an arid climate. Garlic, which was available on a regular scale, could easily be transported in a dried condition. Eventually, brine and vinegar could be added to the sun-dried garlic, as is mentioned by Columella . Spices and condiments can be kept as long as they contain flavorings. These flavorings not only improve the taste of the food, but also protect the food against vermin.

Classical writers use the word myrobalan only in connection with oil-producing plants, such as sugar date and bentree . The use of myrobalan in connection with the cherry plum is of more recent date. It was first applied by the botanist Carolus Clusius . As is expressed in the epithet of one of the synonyms , the fruits of the cherry plum bear resemblance in both size and color, as far as the red-colored specimens are concerned, to those of the cherries and the mirabelle . Today, this name is especially used for cherry plums used as stocks for grafting plums, apricots , and peach . That the Romans did cultivate the cherry plum could be evidenced, however, from archaeobotanical records. So far, three Roman sites have revealed the diagnostic endocarps: Bad Homburg, Ellingen, and Köngen, all located in southern Germany . Other records concern much earlier periods and include charred endocarp fragments from the Middle Palaeolithic Douara Cave in Syria, identified as wild cherry plum by means of chemical analysis and Neolithic remains from Russia, Moldavia, and Slovakia. More recent records are unearthed from medieval contexts such as those from Poland, Czechoslovakia, Hungary, Italy, and Germany . Because the fruits are not adapted to the arid conditions of Egypt, their presence in Berenike certainly points to import from the Mediterranean area or beyond.The taxonomy as well as the domestication of plums are still in discussion owing to their vegetative reproduction and hybridization. The vegetative reproduction of plums has a long tradition in its domestication history. Domestic plum varieties can be propagated from root suckers and by grafting, 25 liter pot plastic in which grafts of the desired species are unifi ed with the stock of a host species called scion. This kind of reproduction, in addition to cross-pollination and hybridization, has resulted in a highly varied polyploid complex of plum taxa.

The variability of the plum species is also expressed in their endocarps and, therefore, hampers the identification of these mostly well-preserved fragments from archaeological contexts. Woldring suggests that the black fruited damson plum originates directly from sloe . The damson plum itself is considered to be the main progenitor of the domestic plum . Another possible domestication history is proposed by KörberGrohne , who is of the opinion that the hexaploid domestic plum is a hybrid of the tetraploid sloe and the diploid cherry plum . A third possibility is discussed by Zohary and Hopf , who state that the domesticated plum evolved directly from the variable cherry plum and consider both taxa therefore as a single species .Five endocarps have been unearthed in Berenike that belong to Prunus domestica, three of them bearing resemblance to the domestic plum ; the other two show more similarity to modern endocarps of the damson plum . The endocarps partly originate from trenches 33 and 48, which also revealed the cherry plum, suggesting that these two fruits belonged to the same assemblage of food supply. In point of fact, the endocarps of P. domestica in Berenike are the first evidence of its use as food in Egypt. The two other Egyptian records of plum concern its wood, originating from Thebes , and its leaves made into a garland, which was found in a Greco-Roman grave in Antinoë . This scanty Egyptian record contrasts with the sizeable archaeobotanical record of P. domestica from Europe in particular. Certain groups of plums of the subspecies domestica and insititia are easily dried and become prunes, which can be easily stored and transported. The import of plums as prunes from the Mediterranean area, where plums were cultivated in orchards, would have been easy and would have been a nourishing food supply in Berenike. That only a small number of fruit remains has been found might indicate that the supply was limited. But it is also possible that most of the delivered prunes had been already destoned, which is quite easily done with fruits of P. domestica.

If so, endocarps of plums would only occasionally have ended up in the dump areas of Berenike.The peach is a latecomer in the tradition of horticulture. Originating from the mountainous areas of Tibet and western China, it reached Greece through Persia about 300 BC. Dilphilus of Siphnos, who lived from 340–289 BC, is the first Greek author who undeniably mentions this tree . The only archaeobotanical record from Greece originates from Samos and is dated to the seventh century AD . The Romans did not cultivate the peach until the first century AD . Most varieties of peach require 500 to 1,000 hours of cold temperatures below 7°C to bloom naturally in the spring. So its distribution is restricted to temperate regions of the world with cold, but not severe, winters . The climatic conditions in most parts of Egypt are, therefore, not favorable for the cultivation of peaches. In present-day Egypt, peach cultivation is mainly confined to the Bahriya Oasis and the northern Sinai . The oldest Egyptian record of the peach originates from Ptolemaic el-Hibeh in the Nile Valley, some 60 km south of the Fayum . Other finds are dated to the Roman and early Byzantine periods and are recorded from the Fayum , the Dakhla Oasis , the Nile Valley , and the Red Sea coastal area . The concentration of finds in the Fayum supports the claim that peach was one of the new crops introduced to the Fayum . The find of just one single part of the inner fruit wall of a peach in Berenike may reflect that this luxury fruit was probably only sporadically available, although it may not be excluded that destoned peaches also were brought to Berenike. Peaches may have originated from Egyptian plantations or from a more remote distant area to the north of Egypt. The recovery from a late context argues for the import of peaches produced in Egypt. According to Pliny , the journey from Koptos to Berenike took 12 days, and the same period was necessary to travel from Alexandria to Koptos . Thus, imported either from Egyptian orchards or from the Mediterranean area, the long distance transport and storage of the perishable peaches would only have been feasible if the peaches were conserved as syrup or as pickles.

Although seeds of peaches contain a considerable amount of oil, it is unlikely that they were transported to Berenike especially for this nutriment only. If this was the case, one would expect to find only some spoiled seeds and not remnants of the relatively large fruit stones.The wild forms of the pomegranate are abundantly present in two areas: to the east in the south Caspian belt and northeastern Turkey and more to the west in the Balkan area, including Albania and Montenegro . Wood suggests that the tree might be native to Arabia as the only other member of the family, namely, P. protopunica Balf. f., is endemic in Socotra. Archaeobotanical evidence, however, points to the eastern Mediterranean area as the core area of its domestication. Textual records and wall paintings in Egyptian tombs that make reference of horticultural practices of the pomegranate are dated to the New Kingdom , whereas the first archaeobotanical records are dated to the preceding Second Intermediate Period . There is some doubt about the dating of small fruits of the pomegranate recorded from the Twelfth Dynasty at Dra Abu el-Naga, and it is suggested that they probably belong to the Eighteenth Dynasty . In addition to the archaeobotanical finds, 25 litre plant pot which include whole fruits, rinds, seeds, leaves, and flower , ceramic imitations and dinnerware designs based on the whole fruit, also express the appreciation of the highly prized tree. The main production area of pomegranates in present-day Egypt is the lagoon of Marash Matruh in the western Mediterranean coastal strip, about 170 km west of El-Alamein . Fruits of wild specimens are sour and relatively small; those of domesticated ones are large and more appetizing. The fleshy fruit consists of 8–12 carpels, each containing many seeds. The fruit is often called a “berry,” but this is incorrect because the juicy, edible part is in fact the seed coat. Pliny distinguishes five different tastes: sweet, sour, mixed, acid, and vinous. The fruits can be eaten fresh, and the somewhat bitter seeds are not swallowed, or their juice can be drunk as grenadine or used for fermentation into shedeh or rhoites wine .

The root and bark are used for expelling tapeworm, and the rind is used as an astringent for the treatment of, for example, diarrhea and bleeding . Several parts of the plant are also used for tanning and dyeing. According to Pliny , the rinds of unripe fruits are especially used for tanning leather for clothing. This kind of use is recorded from North Africa, including Tunis and Morocco, and from the Near East . The rind provides a yellow dye, which can be used as ink and for dyeing textiles. Whole, desiccated fruits or particles of the leathery rind are still available in Near Eastern shops with a good assortment of herbal products. In addition, the fruit was also considered as a symbol of fertility, based on the large number of seeds in a single fruit. This number has been estimated by Kucˇan at 250 to 400 seeds per fruit. The specimens from Berenike would have been imported from the Nile Valley. Fully ripe fruits keep well and can be transported over considerable distances if bruising is prevented.Several trenches from Berenike yielded fruits that could be identified to either Italian senna , with a characteristic flap like crested vein on both sides of the fruit, or to Alexandrian senna and S. holosericea, whose fruits lack this pronounced vein. Although their leaves easily distinguish S. alexandrina and S. holosericea, an identification on the basis of their fruits is not possible. For that reason, the sub-fossil fruits from Berenike lacking the crested veins have been attributed to both these species. The fruits of coffee senna do not come into consideration, as they are small and narrow. The above-mentioned species were formerly classified within the genus Cassia and may not be confused with the cassia frequently mentioned by classical writers with respect to the bark of certain cinnamon species, which also bear the name “cassia” in some of their vernacular names, such as cassia , Indian cassia , and Padang cassia . Both S. alexandrina and S. holosericea are desert plants and are recorded from the Eastern Desert, including the Red Sea coastal strip. Only Italian senna grows in the near vicinity of Berenike, whereas S. holosericea has been found in the late Roman settlement Qariya Mustafa ’Amr Gama in Wadi Umm Athl, some 40 km south of Berenike. The fruits of these species must have been deliberately collected as it seems unlikely that they once grow at Berenike’s site proper or that their fruits were blown into the site from populations growing in the nearby wadis. Only Alexandrian senna has some economic value. It provides tannin, and both dried leaves and fruits are used as a purgative and are still sold by herbalists in the Near East. Other archaeobotanical evidence from Egypt of Cassia and Senna concern threaded seeds of Cassia cf. absus L. found in Gebelein and charcoal of S. alexandrina found at Nabta Playa, dated to the late Palaeolithic. The glossy, rhomboid seeds of C. absus are still available at bazaars in the Near East, including Egypt.Wild species of sesame occur in India and Africa. Referring to the large number of wild species in Africa, it has been frequently suggested that the cultivation of sesame started in the African continent . Inter specific hybridization and chemical studies now indicate that sesame was first brought into cultivation in India, in which Sesamum orientale var. malabaricum Nar. is proposed as the crop progenitor . Bedigian and Harlan and Bedigian summerized the archaebotanical, philological and historical evidence. From India, the crop would have been introduced both eastward to China and westward to the Near East and the Mediterranean region. Archaeobotanical remains are recorded from India, Pakistan, China, the Near East, Turkey, Yemen, and Egypt. So far, the oldest find of sesame is recorded from Harappa in Pakistan, which is dated to 3500–3050 BC. Sesame is cultivated for its edible, lightly aromatic seeds and its odorless oil.