Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.

The Call of the Wild: Rethinking Food Production in Ancient Amazonia

The Amazon basin is accepted as an independent center of plant domestication in the world. A variety of important plants were domesticated in the Amazon and its surroundings; however, the majority of plants cultivated today in the Amazon are not domesticated, if this descriptor is understood to convey substantial genetic and phenotypic divergence from wild varieties or species. Rather, many domesticates are trees and tubers that occupy an intermediate stage between wild and domesticated, which seems to be a prevailing pattern since at least the middle Holocene, 6,000 years ago. Likewise, basin-wide inventories of trees show a remarkable pattern where a few species, called hyperdominant, are overrepresented in the record, including many varieties that are economically and symbolically important to traditional societies. Cultivation practices among indigenous groups in the Amazon are embedded in other dimensions of meaning that go beyond subsistence, and such entanglement between nature and culture has long been noticed at the conceptual level by anthropologists. This principle manifests itself in ancient and dynamic practices of landscape construction and transformation, which are seriously threatened today by the risks posed by economic development and climate change to Amazonian traditional societies and biomes.

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

Especially in low-income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low-input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop 'rewildings'.

Revolutions in agriculture chart a course for targeted breeding of old and new crops

The dominance of the major crops that feed humans and their livestock arose from agricultural revolutions that increased productivity and adapted plants to large-scale farming practices. Two hormone systems that universally control flowering and plant architecture, florigen and gibberellin, were the source of multiple revolutions that modified reproductive transitions and proportional growth among plant parts. Although step changes based on serendipitous mutations in these hormone systems laid the foundation, genetic and agronomic tuning were required for broad agricultural benefits. We propose that generating targeted genetic variation in core components of both systems would elicit a wider range of phenotypic variation. Incorporating this enhanced diversity into breeding programs of conventional and underutilized crops could help to meet the future needs of the human diet and promote sustainable agriculture.

Plant domestication disrupts biodiversity effects across major crop types

Plant diversity fosters productivity in natural ecosystems. Biodiversity effects might increase agricultural yields at no cost in additional inputs. However, the effects of diversity on crop assemblages are inconsistent, probably because crops and wild plants differ in a range of traits relevant to plant-plant interactions. We tested whether domestication has changed the potential of crop mixtures to over-yield by comparing the performance and traits of major crop species and those of their wild progenitors under varying levels of diversity. We found stronger biodiversity effects in mixtures of wild progenitors, due to larger selection effects. Variation in selection effects was partly explained by within-mixture differences in leaf size. Our results indicate that domestication might disrupt the ability of crops to benefit from diverse neighbourhoods via reduced trait variance. These results highlight potential limitations of current crop mixtures to over-yield and the potential of breeding to re-establish variance and increase mixture performance.

Genome-Wide Association Study of Yield Component Traits in Intermediate Wheatgrass and Implications in Genomic Selection and Breeding

Intermediate wheatgrass (Thinopyrum intermedium, IWG) is a perennial grain crop with high biomass and grain yield, long seeds, and resistance to pests and diseases. It also reduces soil erosion, nitrate and mineral leaching into underground water tables, and sequesters carbon in its roots. The domestication timeline of IWG as a grain crop spans only 3 decades, hence it lags annual grain crops in yield and seed characteristics. One approach to improve its agronomic traits is by using molecular markers to uncover marker-trait associations. In this study, we performed association mapping on IWG breeding germplasm from the third recurrent selection cycle at the University of Minnesota. The IWG population was phenotyped in St Paul, MN in 2017 and 2018, and in Crookston, MN in 2018 for grain yield, seed length, width and weight, spike length and weight, and number of spikelets per spike. Strong positive correlations were observed among most trait pairs, with correlations as high as 0.76. Genotyping using high throughput sequencing identified 8,899 high-quality genome-wide SNPs which were combined with phenotypic data in association mapping to discover regions associated with the yield component traits. We detected 154 genetic loci associated with these traits of which 19 were shared between at least two traits. Prediction of breeding values using significant loci as fixed effects in genomic selection model improved predictive abilities by up to 14%. Genetic mapping of agronomic traits followed by using genomic selection to predict breeding values can assist breeders in selecting superior genotypes to accelerate IWG domestication.

Resource allocation trade-offs and the loss of chemical defences during apple domestication

BACKGROUND AND AIMS

Most crops have been dramatically altered from their wild ancestors with the primary goal of increasing harvestable yield. A long-held hypothesis is that increased allocation to yield has reduced plant investment in defence and resulted in crops that are highly susceptible to pests. However, clear demonstrations of these trade-offs have been elusive due to the many selective pressures that occur concurrently during crop domestication.

METHODS

To provide a robust test of whether increased allocation to yield can alter plant investment in defence, this study examined fruit chemical defence traits and herbivore resistance across 52 wild and 56 domesticated genotypes of apples that vary >26-fold in fruit size. Ninety-six phenolic metabolites were quantified in apple skin, pulp and seeds, and resistance to the codling moth was assessed with a series of bioassays.

KEY RESULTS

The results show that wild apples have higher total phenolic concentrations and a higher diversity of metabolites than domesticated apples in skin, pulp and seeds. A negative phenotypic relationship between fruit size and phenolics indicates that this pattern is driven in part by allocation-based trade-offs between yield and defence. There were no clear differences in codling moth performance between wild and domesticated apples and no overall effects of total phenolic concentration on codling moth performance, but the results did show that codling moth resistance was increased in apples with higher phenolic diversity. The concentrations of a few individual compounds (primarily flavan-3-ols) also correlated with increased resistance, primarily driven by a reduction in pupal mass of female moths.

CONCLUSIONS

The negative phenotypic relationship between fruit size and phenolic content, observed across a large number of wild and domesticated genotypes, supports the hypothesis of yield-defence trade-offs in crops. However, the limited effects of phenolics on codling moth highlight the complexity of consequences that domestication has for plant-herbivore interactions. Continued studies of crop domestication can further our understanding of the multiple trade-offs involved in plant defence, while simultaneously leading to novel discoveries that can improve the sustainability of crop production.

Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication

Humans have domesticated diverse species from across the plant kingdom, yet much of our foundational knowledge of domestication has come from studies investigating relatively few of the most important annual food crops. Here, we examine the impacts of domestication on genetic diversity in a tropical perennial fruit species, mango (Mangifera indica). We used restriction site associated DNA sequencing to generate genomic single nucleotide polymorphism (SNP) data from 106 mango cultivars from seven geographical regions along with 52 samples of closely related species and unidentified cultivars to identify centers of mango genetic diversity and examine how post-domestication dispersal shaped the geographical distribution of diversity. We identify two gene pools of cultivated mango, representing Indian and Southeast Asian germplasm. We found no significant genetic bottleneck associated with the introduction of mango into new regions of the world. By contrast, we show that mango populations in introduced regions have elevated levels of diversity. Our results suggest that mango has a more complex history of domestication than previously supposed, perhaps including multiple domestication events, hybridization and regional selection. Our work has direct implications for mango breeding and genebank management, and also builds on recent efforts to understand how woody perennial crops respond to domestication.

Genetic insights into morphometric inflorescence traits of wheat

KEY MESSAGE

Modifying morphometric inflorescence traits is important for increasing grain yield in wheat. Mapping revealed nine QTL, including new QTL and a new allele for the q locus, controlling wheat spike morphometric traits. To identify loci controlling spike morphometric traits, namely spike length (SL), internode length (IL), node number per spike (NPS), and node density (ND), we studied 146 Recombinant Inbred Lines of tetraploid wheat (Triticum turgidum L.) derived from standard spike and spike-branching mutant parents. Phenotypic analyses of spike morphometric traits showed low genetic coefficients of variation, resulting in high heritabilities. The phenotypic correlation between NPS with growing degree days (GDD) suggested the importance of GDD in the determination of node number in wheat. The major effect QTL for GDD or heading date was mapped to chromosome 7BS carrying the flowering time gene, Vrn3-B1. Mapping also identified nine QTL controlling spike morphometric traits. Most of these loci controlled more than a single trait, suggesting a close genetic interrelationship among spike morphometric traits. For example, this study identified a new QTL, QND.ipk-4AL, controlling ND (up to 17.6% of the phenotypic variance), IL (up to 11% of the phenotypic variance), and SL (up to 20.8% of the phenotypic variance). Similarly, the major effect QTL for IL was mapped to the q locus. Sequencing of the Q/q gene further revealed a new q allele, qdel-5A, in spike-branching accessions possessing a six base pair deletion close to the miR172 target site. The identification of qdel-5A suggested that the spike-branching tetraploid wheats are double mutants for the spikelet meristem (SM) identity gene, i.e., branched headt (TtBHt), and the q gene, which is believed to be involved in the SM indeterminacy complex in wheat.

Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees

The apple (Malus domestica [Suckow] Borkh.) is one of the most economically and culturally significant fruits in the world today, and it is grown in all temperate zones. With over a thousand landraces recognized, the modern apple provides a unique case study for understanding plant evolution under human cultivation. Recent genomic and archaeobotanical studies have illuminated parts of the process of domestication in the Rosaceae family. Interestingly, these data seem to suggest that rosaceous arboreal crops did not follow the same pathway toward domestication as other domesticated, especially annual, plants. Unlike in cereal crops, tree domestication appears to have been rapid and driven by hybridization. Apple domestication also calls into question the concept of centers of domestication and human intentionality. Studies of arboreal domestication also illustrate the importance of fully understanding the seed dispersal processes in the wild progenitors when studying crop origins. Large fruits in Rosaceae evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene. Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers. Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning. Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

De Novo Domestication: An Alternative Route toward New Crops for the Future

Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.

Rapid functional divergence after small-scale gene duplication in grasses

BACKGROUND

Gene duplication has played an important role in the evolution and domestication of flowering plants. Yet little is known about how plant duplicate genes evolve and are retained over long timescales, particularly those arising from small-scale duplication (SSD) rather than whole-genome duplication (WGD) events.

RESULTS

We address this question in the Poaceae (grass) family by analyzing gene expression data from nine tissues of Brachypodium distachyon, Oryza sativa japonica (rice), and Sorghum bicolor (sorghum). Consistent with theoretical predictions, expression profiles of most grass genes are conserved after SSD, suggesting that functional conservation is the primary outcome of SSD in grasses. However, we also uncover support for widespread functional divergence, much of which occurs asymmetrically via the process of neofunctionalization. Moreover, neofunctionalization preferentially targets younger (child) duplicate gene copies, is associated with RNA-mediated duplication, and occurs quickly after duplication. Further analysis reveals that functional divergence of SSD-derived genes is positively correlated with both sequence divergence and tissue specificity in all three grass species, and particularly with anther expression in B. distachyon.

CONCLUSIONS

Our results suggest that SSD-derived grass genes often undergo rapid functional divergence that may be driven by natural selection on male-specific phenotypes. These observations are consistent with those in several animal species, suggesting that duplicate genes take similar evolutionary trajectories in plants and animals.

Crop Biodiversity: An Unfinished Magnum Opus of Nature

Crop biodiversity is one of the major inventions of humanity through the process of domestication. It is also an essential resource for crop improvement to adapt agriculture to ever-changing conditions like global climate change and consumer preferences. Domestication and the subsequent evolution under cultivation have profoundly shaped the genetic architecture of this biodiversity. In this review, we highlight recent advances in our understanding of crop biodiversity. Topics include the reduction of genetic diversity during domestication and counteracting factors, a discussion of the relationship between parallel phenotypic and genotypic evolution, the role of plasticity in genotype × environment interactions, and the important role subsistence farmers play in actively maintaining crop biodiversity and in participatory breeding. Linking genotype and phenotype remains the holy grail of crop biodiversity studies.

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing

The combination of advanced genomics, genome editing and plant transformation biology presents a powerful platform for basic plant research and crop improvement. Together these advances provide the tools to identify genes as targets for direct editing as single base pair changes, deletions, insertions and site specific homologous recombination. Recent breakthrough technologies using morphogenic regulators in plant transformation creates the ability to introduce reagents specific toward their identified targets and recover stably transformed and/or edited plants which are genotype independent. These technologies enable the possibility to alter a trait in any variety, without genetic disruption which would require subsequent extensive breeding, but rather to deliver the same variety with one trait changed. Regulatory issues regarding this technology will predicate how broadly these technologies will be implemented. In addition, education will play a crucial role for positive public acceptance. Taken together these technologies comprise a platform for advanced breeding which is an imperative for future world food security.

The nectar report: quantitative review of nectar sugar concentrations offered by bee visited flowers in agricultural and non-agricultural landscapes

There is growing concern that some bee populations are in decline, potentially threatening pollination security in agricultural and non-agricultural landscapes. Among the numerous causes associated with this trend, nutritional stress resulting from a mismatch between bee nutritional needs and plant community provisioning has been suggested as one potential driver. To ease nutritional stress on bee populations in agricultural habitats, agri-environmental protection schemes aim to provide alternative nutritional resources for bee populations during times of need. However, such efforts have focused mainly on quantity (providing flowering plants) and timing (during flower-scarce periods), while largely ignoring the quality of the offered flower resources. In a first step to start addressing this information gap, we have used literature data to compile a comprehensive geographically explicit dataset on nectar quality (i.e., total sugar concentration), offered to bees both within fields (crop and weed species) as well as outside fields (wild species) around the globe. Social bees are particularly sensitive to nectar sugar concentrations, which directly impact calorie influx into the colony and consequently their fitness making it an important resource quality marker. We find that the total nectar sugar concentrations in general do not differ between the three plant communities studied. In contrast we find increased variability in nectar quality in the wild plant community compared to crop and weed community, which is likely explained by the increased phylogenetic diversity in this category of plants. In a second step we explore the influence of local habitat on nectar quality and its variability utilizing a detailed sunflower (Helianthus annuus L.) data set and find that geography has a small, but significant influence on these parameters. In a third step we identify crop groups (genera), which provide sub-optimal nectar resources for bees and suggest high quality alternatives as potential nectar supplements. In the long term this data set could serve as a starting point to systematically collect more quality characteristics of plant provided resources to bees, which ultimately can be utilized by scientist, regulators, NGOs and farmers to improve the flower resources offered to bees. We hope that ultimately this data will help to ease nutritional stress for bee populations and foster a data informed discussion about pollinator conservation in modern agricultural landscapes.

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.

Regional and global shifts in crop diversity through the Anthropocene

The Anthropocene epoch is partly defined by anthropogenic spread of crops beyond their centres of origin. At global scales, evidence indicates that species-level taxonomic diversity of crops being cultivated on large-scale agricultural lands has increased linearly over the past 50 years. Yet environmental and socio-economic differences support expectations that temporal changes in crop diversity vary across regions. Ecological theory also suggests that changes in crop taxonomic diversity may not necessarily reflect changes in the evolutionary diversity of crops. We used data from the Food and Agricultural Organization (FAO) of the United Nations to assess changes in crop taxonomic- and phylogenetic diversity across 22 subcontinental-scale regions from 1961–2014. We document certain broad consistencies across nearly all regions: i) little change in crop diversity from 1961 through to the late 1970s; followed by ii) a 10-year period of sharp diversification through the early 1980s; followed by iii) a “levelling-off” of crop diversification beginning in the early 1990s. However, the specific onset and duration of these distinct periods differs significantly across regions and are unrelated to agricultural expansion, indicating that unique policy or environmental conditions influence the crops being grown within a given region. Additionally, while the 1970s and 1980s are defined by region-scale increases in crop diversity this period marks the increasing dominance of a small number of crop species and lineages; a trend resulting in detectable increases in the similarity of crops being grown across regions. Broad similarities in the species-level taxonomic and phylogenetic diversity of crops being grown across regions, primarily at large industrial scales captured by FAO data, represent a unique feature of the Anthropocene epoch. Yet nuanced asymmetries in regional-scale trends suggest that environmental and socio-economic factors play a key role in shaping observed macro-ecological changes in the plant diversity on agricultural lands.

The global biogeography of polyploid plants

Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the uneven distribution of polyploid plants across the globe. Nevertheless, the lack of large comparative datasets has restricted such studies to local floras and to narrow taxonomical scopes, limiting our understanding of the underlying drivers of polyploid plant distribution. We present a map portraying the worldwide polyploid frequencies, based on extensive spatial data coupled with phylogeny-based polyploidy inference for tens of thousands of species. This allowed us to assess the potential global drivers affecting polyploid distribution. Our data reveal a clear latitudinal trend, with polyploid frequency increasing away from the equator. Climate, especially temperature, appears to be the most influential predictor of polyploid distribution. However, we find this effect to be mostly indirect, mediated predominantly by variation in plant lifeforms and, to a lesser extent, by taxonomical composition and species richness. Thus, our study presents an emerging view of polyploid distribution that highlights attributes that facilitate the establishment of new polyploid lineages by providing polyploids with sufficient time (that is, perenniality) and space (low species richness) to compete with pre-adapted diploid relatives.

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing

Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia-M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia. Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.

Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication?

Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more prone to harbor within-species differentiation due to genomic features, suppressed recombination, smaller effective population size or increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure produced by multiple independent domestications each especially in Andean and Mesoamerican / Middle American geographies. We genotyped 22,531 GBS-derived SNP markers in 209 individuals of wild and cultivated Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepool comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, genomic regions with overall high relative differentiation (measured by FST) coincided with regions of low SNP density and regions of elevated delta divergence between-genepools (ΔDiv), independent of the scale of divergence. The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggest that shared variants are being recurrently fixed at replicated regions of the genome, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation and within-species divergence. In summary, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue to fortuitously shape genomic differentiation at various others scales of divergence.

Differential Susceptibility of Wild and Cultivated Blueberries to an Invasive Frugivorous Pest

Highbush blueberry is a crop native to the northeast USA that has been domesticated for about 100 years. This study compared the susceptibility of wild and domesticated/cultivated highbush blueberries to an invasive frugivorous pest, the spotted wing drosophila (Drosophila suzukii). We hypothesized that: 1) cultivated fruits are preferred by D. suzukii for oviposition and better hosts for its offspring than wild fruits; and, 2) wild and cultivated fruits differ in physico-chemical traits. Fruits from wild and cultivated blueberries were collected from June through August of 2015 and 2016 from 10 to 12 sites in New Jersey (USA); with each site having wild and cultivated blueberries growing in close proximity. The preference and performance of D. suzukii on wild and cultivated blueberries were studied in choice and no-choice bioassays. In addition, we compared size, firmness, acidity (pH), total soluble solids (°Brix), and nutrient, phenolic, and anthocyanin content between wild and cultivated berries. In choice and no-choice bioassays, more eggs were oviposited in, and more flies emerged from, cultivated than wild blueberries. Cultivated fruits were 2x bigger, 47% firmer, 14% less acidic, and had lower °Brix, phenolic, and anthocyanin amounts per mass than wild fruits. Levels of potassium and boron were higher in cultivated fruits, while calcium, magnesium, and copper were higher in wild fruits. These results show that domestication and/or agronomic practices have made blueberries more susceptible to D. suzukii, which was associated with several physico-chemical changes in fruits. Our study documents the positive effects of crop domestication/cultivation on an invasive insect pest.

The cotton HD-Zip transcription factor GhHB12 regulates flowering time and plant architecture via the GhmiR157-GhSPL pathway

Domestication converts perennial and photoperiodic ancestral cotton to day-neutral cotton varieties, and the selection of short-season cotton varieties is one of the major objectives of cotton breeding. However, little is known about the mechanism of flowering time in cotton. Here, we report a cotton HD-ZIP I-class transcription factor (GhHB12) specifically expressed in axillary buds, which antagonisticlly interacts with GhSPL10/13 to repress the expression of GhFT, GhFUL, and GhSOC1, resulting in bushy architecture and delayed flowering under long-day conditions. We found that GhHB12-mediated ancestral upland cotton phenotypes (bushy architecture and delayed flowering) could be rescued under short-day conditions. We showed that overexpressing of GhrSPL10 partially rescues the bushy architecture and delayed flowering phenotypes, while overexpression of GhmiR157 reinforced these phenotypes in GhHB12-overexpressing plants. This study defines a regulatory module which regulates cotton architecture, phase transition and could be applied in the breeding of early maturing cotton varieties.

Xin He et al. present a characterization of GhHB12, a HD-ZIP family transcription factor expressed in upland cotton axillary buds. They show that GhHB12 regulates flowering time, plant architecture and phase transition via a regulatory module that could be harnessed to improve cotton for mechanical harvesting.

Seed characteristic variations and genetic structure of wild Zizania latifolia along a latitudinal gradient in China: implications for neo-domestication as a grain crop

Crop wild relatives are not only important genetic resources for crop improvement, but also domestication candidates for selecting new crops. As a close relative of American wild rice Zizania palustris, Z. latifolia is a perennial aquatic grass widely distributed in China. Although Z. latifolia has been domesticated and cultivated as an aquatic vegetable for >1000 years, a neo-domestication for grain production needs to be soundly evaluated. In this study, we investigated the seed characteristic variations and genetic structure of 15 Z. latifolia wild populations along a latitudinal gradient in China. Our results showed that Z. latifolia tended to produce relatively larger seeds with lower moisture content and lower investments in seed pericarp at lower latitudes. The width, size, shape, seed-pericarp ratio and relative water content of seeds were significantly associated with climatic variables. The seeds of Z. latifolia showed a relatively low germination percentage and strong dormancy, which might hinder the neo-domestication. In addition, high genetic differentiation had been found among Z. latifolia populations, which could be attributed to isolation by distance. This study offered preliminary information for the utilization and conservation of wild Z. latifolia. It suggested that the wild populations in the middle and lower reaches of the Yangtze River could be good candidates for grain crop domestication due to appropriate seed traits and high genetic diversity. The neo-domestication of wild Z. latifolia requires further researches on the genetic mechanism of the Domestication Syndrome and more works on artificial breeding.

Identification of candidate domestication-related genes with a systematic survey of loss-of-function mutations

Domestication is an important key co-evolutionary process through which humans have extensively altered the genomic make-up and appearance of both plants and animals. The identification of domestication-related genes remains very arduous. In this study, we present a systematic analytical approach that harnesses two recent advances in genomics, whole-genome sequencing (WGS) and prediction of loss-of-function (LOF) mutations, to greatly facilitate the assembly of an enriched catalogue of domestication-related candidate genes. Using WGS data for 296 cultivated (Glycine max) and 64 wild soybean accessions, we identified 8699 LOF variants, and 116 genes that are uniquely fixed for one or more LOF allele(s) in domesticated soybeans. Existing soybean transcriptomic data led us to overcome analytical challenges associated with whole-genome duplications and to identify neo- or subfunctionalized genes. This systematic approach allowed us to identify 110 candidate domestication-related genes in an efficient and rapid way. This catalogue contains previously well characterized domestication genes in soybean, as well as some orthologs from other domesticated crop species. In addition, it comprises many promising candidate domestication genes. Overall, this collection of candidate domestication-related genes in soybean is almost twice as large as the sum of all previously reported candidate genes in all other crops. We believe this systematic approach could readily be used in wide range of species.

Leaf economics spectrum in rice: leaf anatomical, biochemical, and physiological trait trade-offs

The leaf economics spectrum (LES) is an ecophysiological concept describing the trade-offs of leaf structural and physiological traits, and has been widely investigated on multiple scales. However, the effects of the breeding process on the LES in crops, as well as the mechanisms of the trait trade-offs underlying the LES, have not been thoroughly elucidated to date. In this study, a dataset that included leaf anatomical, biochemical, and functional traits was constructed to evaluate the trait covariations and trade-offs in domesticated species, namely rice (Oryza species). The slopes and intercepts of the major bivariate correlations of the leaf traits in rice were significantly different from the global LES dataset (Glopnet), which is based on multiple non-crop species in natural ecosystems, although the general patterns were similar. The photosynthetic traits responded differently to leaf structural and biochemical changes, and mesophyll conductance was the most sensitive to leaf nitrogen (N) status. A further analysis revealed that the relative limitation of mesophyll conductance declined with leaf N content; however, the limitation of the biochemistry increased relative to leaf N content. These findings indicate that breeding selection and high-resource agricultural environments lead crops to deviate from the leaf trait covariation in wild species, and future breeding to increase the photosynthesis of rice should primarily focus on improvement of the efficiency of photosynthetic enzymes.

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.

Molecular Evidence for Two Domestication Events in the Pea Crop

Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.

Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food

The origins of agriculture were key events in human history, during which people came to depend for their food on small numbers of animal and plant species. However, the biological traits determining which species were domesticated for food provision, and which were not, are unclear. Here, we investigate the phylogenetic distribution of livestock and crops, and compare their phenotypic traits with those of wild species. Our results indicate that phylogenetic clustering is modest for crop species but more intense for livestock. Domesticated species explore a reduced portion of the phenotypic space occupied by their wild counterparts and have particular traits in common. For example, herbaceous crops are globally characterized by traits including high leaf nitrogen concentration and tall canopies, which make them fast-growing species and proficient competitors. Livestock species are relatively large mammals with low basal metabolic rates, which indicate moderate to slow life histories. Our study therefore reveals ecological differences in domestication potential between plants and mammals. Domesticated plants belong to clades with traits that are advantageous in intensively managed high-resource habitats, whereas domesticated mammals are from clades adapted to moderately productive environments. Combining comparative phylogenetic methods with ecologically relevant traits has proven useful to unravel the causes and consequences of domestication.

Crop domestication: anthropogenic effects on insect-plant interactions in agroecosystems

Although crop domestication is considered a model system for understanding evolution, the eco-evolutionary effects of domesticated crops on higher trophic levels have rarely been discussed. Changes in size, shape, quality, or timing of plant traits during domestication can influence entire arthropod communities. The plant traits specific to crop plants can be rare in nature. In the face of such novelty, it is important to understand how species and trophic levels vary in their responses. Although the evidence is still limited, crop domestication can influence the ecology, genetics, and evolution of plants, insect herbivores, natural enemies, and pollinators. We call for more study on how eco-evolutionary processes operate under domestication to provide new insight on the sustainability of species interactions within agroecosystems.

Crop Domestication Alters Floral Reward Chemistry With Potential Consequences for Pollinator Health

Crop domestication can lead to weakened expression of plant defences, with repercussions for herbivore and pathogen susceptibility. However, little is known about how domestication alters traits that mediate other important ecological interactions in crops, such as pollination. Secondary metabolites, which underpin many defence responses in plants, also occur widely in nectar and pollen and influence plant-pollinator interactions. Thus, domestication may also affect secondary compounds in floral rewards, with potential consequences for pollinators. To test this hypothesis, we chemically analysed nectar and pollen from wild and cultivated plants of highbush blueberry (Vaccinium corymbosum L.), before conducting an artificial diet bioassay to examine pollinator-pathogen interactions. Our results indicated that domestication has significantly altered the chemical composition of V. corymbosum nectar and pollen, and reduced pollen chemical diversity in cultivated plants. Of 20 plant metabolites identified in floral rewards, 13 differed significantly between wild and cultivated plants, with a majority showing positive associations with wild compared to cultivated plants. These included the amino acid phenylalanine (4.5 times higher in wild nectar, 11 times higher in wild pollen), a known bee phagostimulant and essential nutrient; and the antimicrobial caffeic acid ester 4-O-caffeoylshikimic acid (two times higher in wild nectar). We assessed the possible biological relevance of variation in caffeic acid esters in bioassays, using the commercially available 3-O-caffeoylquinic acid. This compound reduced Bombus impatiens infection by a prominent gut pathogen (Crithidia) at concentrations that occurred in wild but not cultivated plants, suggesting that domestication may influence floral traits with consequences for bee health. Appreciable levels of genetic variation and heritability were found for most floral reward chemical traits, indicating good potential for selective breeding. Our study provides the first assessment of plant domestication effects on floral reward chemistry and its potential repercussions for pollinator health. Given the central importance of pollinators for agriculture, we discuss the need to extend such investigations to pollinator-dependent crops more generally and elaborate on future research directions to ascertain wider trends, consequences for pollinators, mechanisms, and breeding solutions.

Chemometric Analysis of Cannabinoids: Chemotaxonomy and Domestication Syndrome

Cannabis is an interesting domesticated crop with a long history of cultivation and use. Strains have been selected through informal breeding programs with undisclosed parentage and criteria. The term "strain" refers to minor morphological differences and grower branding rather than distinct cultivated varieties. We hypothesized that strains sold by different licensed producers are chemotaxonomically indistinguishable and that the commercial practice of identifying strains by the ratio of total THC and CBD is insufficient to account for the reported human health outcomes. We used targeted metabolomics to analyze 11 known cannabinoids and an untargeted metabolomics approach to identify 21 unknown cannabinoids. Five clusters of chemotaxonomically indistinguishable strains were identified from the 33 commercial products. Only 3 of the clusters produce CBDA in significant quantities while the other 2 clusters redirect metabolic resources toward the THCA production pathways. Six unknown metabolites were unique to CBD-rich strains and/or correlated to CBDA and 3 unknowns were found only in THC-rich strains. Together, these data indicate the domestication of the cannabis germplasm has resulted in a loss of the CBDA pathway in some strains and reallocation of resources between CBDA and THCA pathways in others. The impact of domestication is a lack of chemical diversity and loss of biodiversity in modern cannabis strains.

Plant domestication decreases both constitutive and induced chemical defences by direct selection against defensive traits

Studies reporting domestication effects on plant defences have focused on constitutive, but not on induced defences. However, theory predicts a trade-off between constitutive (CD) and induced defences (ID), which intrinsically links both defensive strategies and argues for their joint consideration in plant domestications studies. We measured constitutive and induced glucosinolates in wild cabbage (Brassica oleracea ssp. oleracea) and two domesticated varieties (B. oleracea var. acephala and B. oleracea var. capitata) in which the leaves have been selected to grow larger. We also estimated leaf area (proxy of leaf size) to assess size-defence trade-offs and whether domestication effects on defences are indirect via selection for larger leaves. Both CD and ID were lower in domesticated than in wild cabbage and they were negatively correlated (i.e. traded off) in all of the cabbage lines studied. Reductions in CD were similar in magnitude for leaves and stems, and CD and leaf size were uncorrelated. We conclude that domestication of cabbage has reduced levels not only constitutive defences but also their inducibility, and that reductions in CD may span organs not targeted by breeding. This reduction in defences in domesticated cabbage is presumably the result of direct selection rather than indirect effects via trade-offs between size and defences.

The Impact of Genetic Changes during Crop Domestication

Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.

Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia

Annatto (Bixa orellana L.) is a tropical American crop, commercially valuable due to its application in the food and cosmetics industries as a natural dye. The wild ancestor of cultivated annatto is B. orellana var. urucurana. Although never cultivated, this variety occurs in open forests and anthropogenic landscapes, and is always associated with riparian environments. In this study, we evaluated the genetic diversity and structure of B. orellana var. urucurana populations in Brazilian Amazonia using 16 microsatellite loci. We used Ecological Niche Modeling (ENM) to characterize the potential geographical range of this variety in northern South America. We analyzed 170 samples from 10 municipalities in the states of Rondônia, Pará and Roraima. A total of 194 alleles was observed, with an average of 12.1 alleles per locus. Higher levels of expected (H_E) than observed (H_O) heterozygosities were found for all populations. Bayesian analysis, Neighbor-Joining dendrograms and PCAs suggest the existence of three strongly structured groups of populations. A strong and positive correlation between genetic and geographic distances was found, suggesting that genetic differentiation might be caused by geographic isolation. From species distribution modelling, we detected that South Rondônia, Madre di Dios River basin, Llanos de Mojos, Llanos de Orinoco and eastern Ecuador are highly suitable areas for wild annatto to occur, providing additional targets for future exploration and conservation. Climatic adaptation analyses revealed strong differentiation among populations, suggesting that precipitation plays a key role in wild annatto’s current and potential distribution patterns.

To defend or to grow: lessons from Arabidopsis C24

The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterization of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding of how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) are a great asset to understand the mechanisms of multiple stress tolerances. One natural variant in Arabidopsis is the accession C24, and here we provide an overview of the increasing research interest in this accession. C24 is highlighted as a source of tolerance for multiple abiotic and biotic stresses, and a key accession to understand the basis of basal immunity to infection, high water use efficiency, and water productivity. Multiple biochemical, physiological, and phenological mechanisms have been attributed to these traits in C24, and none of them constrains productivity. Based on the uniqueness of C24, we postulate that the use of variation derived from natural selection in undomesticated species provides opportunities to better understand how complex environmental stress tolerances and resource use efficiency are co-ordinated.

The Mating System of the Wild-to-Domesticated Complex of Gossypium hirsutum L. Is Mixed

The domestication syndrome of many plants includes changes in their mating systems. The evolution of the latter is shaped by ecological and genetic factors that are particular to an area. Thus, the reproductive biology of wild relatives must be studied in their natural distribution to understand the mating system of a crop species as a whole. Gossypium hirsutum (upland cotton) includes both domesticated varieties and wild populations of the same species. Most studies on mating systems describe cultivated cotton as self-pollinated, while studies on pollen dispersal report outcrossing; however, the mating system of upland cotton has not been described as mixed and little is known about its wild relatives. In this study we selected two wild metapopulations for comparison with domesticated plants and one metapopulation with evidence of recent gene flow between wild relatives and the crop to evaluate the mating system of cotton's wild-to-domesticated complex. Using classic reproductive biology methods, our data demonstrate that upland cotton presents a mixed mating system throughout the complex. Given cotton's capacity for outcrossing, differences caused by the domestication process in cultivated individuals can have consequences for its wild relatives. This characterization of the diversity of the wild relatives in their natural distribution, as well as their interactions with the crop, will be useful to design and implement adequate strategies for conservation and biosecurity.

Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation

Wheat streak mosaic virus (WSMV) causes streak mosaic disease in wheat (Triticum aestivum L.) and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of Wsm2 remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice (Oryza sativa) and Brachypodium distachyon. Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of Wsm2 and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while Brachypodium does not, which allowed us to hypothesize the presence of a Wsm2 ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. Given that Wsm2 is likely duplicated through an intrachromosomal illegitimate recombination and that Wsm2 is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Brachypodium. Taken together, we predicted a total of 93 good candidates for a Wsm2 ancestor locus. All of these 93 candidates are not tightly linked with Wsm2, indicative of the role of illegitimate recombination in the birth of Wsm2. Further sequence analysis suggests that the protein products of Wsm2 may combat WSMV disease through a molecular mechanism involving protein degradation and/or membrane trafficking. The 93 putative Wsm2 ancestor loci discovered in this study could serve as good candidates for future genetic isolation of the true Wsm2 locus.

The ecological footprint of Acca sellowiana domestication maintains the residual vertebrate diversity in threatened highlands of Atlantic Forest

Past and contemporary human actions are causing numerous changes in patterns and processes at various ecosystem scales and trophic levels, including unintended downstream changes, such as species interactions. In its native range Acca sellowiana (Feijoa) combines some characteristics of human interactions: incipient domestication, restricted to subtropical Atlantic Forest highlands, associated with the threatened conifer Araucaria angustifolia (Araucaria), within a domesticated landscape with anthropogenic forest patches, and provides fruit at a time of resource shortage (Araucaria seeds—pinhão). We quantify the trophic relationships between Feijoa and vertebrates, and evaluate the influences on interactions caused by environmental variations, Feijoa domestication evidences, spatial distance and fruit availability. In four sites within protected areas, we selected 28 focal individuals of Feijoa (seven/site) and collected three temporal replicas between 2015 and 2016, when we measured productivity and frugivory via 45-second videos taken with camera traps. Using ecological network, rarefaction curves and variation partitioning analyses, we evaluate the frugivory network topology, the spatiotemporal structure of communities in relation to fruit availability and the influence of predictive variables on frugivory. We found a large spatiotemporal variation in productivity of Feijoa and that 20 species consumed Feijoa fruits, with a species degree of 2.8 (±5.7) and average Feijoa degree of 14.4 (±10.1), in a modular network with intermediary connectance. Rarefaction curves showed that richness and the independent records are congruent with the fruit amount. Variation partitioning showed that, for the focal individuals, canopy area, green coverage, patch size and distance to water influenced frugivory, and the Feijoa domestication influenced significantly the mammalian frugivory. Feijoa is an important resource that provides food during the time of year when Pinhão is absent, and attracts frugivores, maintain the residual diversity of vertebrates contributing to the structure of communities in highlands. Our insights allowed us to evaluate the magnitude of the interactions between vertebrates and an incipient domesticated tree, in a cultural landscape and highly threatened environment, under a basal foodweb approach with implications for bottom-up and top-down forces. The results contribute to understanding animal-plant relationships, including concepts that can be replicated for other sessile prey and mobile predators in any region or habitat under different gradients of management. Thus, this work shows how human actions can change not only patterns of distribution and abundance but also the diversity and direction of interspecific interactions among species.