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According to archaeological records, chickpea (Cicer arietinum) was first domesticated in the Fertile Crescent about 10k years BP. Its subsequent diversification in Middle East, South Asia, Ethiopia, and the Western Mediterranean, however, remains obscure and cannot be resolved using only archeological and historical evidence. Moreover, chickpea has two market types: ‘desi’ and ‘kabuli’, for which the geographic origin is a matter of debate. To decipher chickpea history, we took the genetic data from 421 chickpea landraces unaffected by the green revolution and tested complex historical hypotheses of chickpea migration and admixture on two hierarchical spatial levels: within and between major regions of cultivation. For chickpea migration within regions, we developed popdisp, a Bayesian model of population dispersal from a regional representative center towards the sampling sites, that considers geographical proximities between sites. This method confirmed that chickpea spreads within each geographical region along optimal geographical routes rather than by simple diffusion and estimated representative allele frequencies for each region. For chickpea migration between regions, we developed another model, migadmi, that takes allele frequencies of populations and evaluates multiple and nested admixture events. Applying this model to desi populations, we found both Indian and Middle Eastern traces in Ethiopian chickpea, suggesting the presence of a seaway from South Asia to Ethiopia. As for the origin of kabuli chickpeas, we found significant evidence for its origin from Turkey rather than Central Asia.

JCJ-L acknowledges financial support from the Spanish Government grant ref. RYC-2014-16536 (Ramon y Cajal research program of MINECO), and by the European Research Program MARIE CURIE (FP7-PEOPLE-2011-IOF) grant ref. number PIOF-GA-2011-301550. AC acknowledges the financial support of AGL2017-83772-R (AEI/FEDER, UE) and P20_00242 (PAIDI 2020) funded by the Spanish Ministry of Science and Innovation, and Junta de Andalucía, respectively. MV acknowledges the support of Fundação para a Ciência e Tecnologia, Portugal through the R&D research Unit GREEN-IT – Bioresources for Sustainability (UID/04551/2020, UIDP/04551/2020), and the LS4FUTURE Associated Laboratory (LA/P/0087/2020). EV's contribution to this work was supported by the Ministry of Science and Higher Education of the Russian Federation as part of the World-class Research Center program: Advanced Digital Technologies (contract No. 075-15-2022-311 dated 20.04.2022).

The spread of invasive species can be limited or promoted by the distributions of mutualists, which presents an opportunity for managing biological invasions. However, the ways in which the geographical distributions of mutualists shape the range limits and invasion dynamics of introduced species remains unclear. Legumes include noxious invaders whose success is tied to their mutualism with nitrogen-fixing rhizobium bacteria. We examine whether the availability of compatible rhizobia limits the spread of an invasive legume at both small (50 m) and large (United States) spatial scales across natural invasion fronts. Using greenhouse experiments we simulated the dispersal of Medicago polymorpha into soils at increasing distances from a host patch. We find that rhizobial mutualist availability rapidly declines to almost zero within 20 m of established legume patches and legume fitness and the percentage of leaf nitrogen derived from symbiotic nitrogen fixation show a concomitant decline. The decline of fitness due to the lack of rhizobium mutualists differs among M. polymorpha genotypes. Our findings support the missed mutualist hypothesis whereby mutualist limitation reduces invasiveness. As M. polymorpha colonizes novel areas, seeds following either short- (50 m) or long-range seed dispersal will be mutualist-limited and exhibit low fitness and nitrogen fixation. Without co-introduction via transport of soil containing both mutualists, the patchy distribution of E. medicae may limit M. polymorpha invasion. Plant lineages exhibit genetic variation upon which selection could act to reduce dependence on rhizobia, thus a scarcity of symbionts could cause plant symbiosis traits to evolve during invasion.

Students often struggle to connect concepts with evidence, sometimes because development of research skills has not been emphasized in their science courses. We developed a strategy and protocol to train high school students in research and experimental investigation of questions related to course material on legume biology. The richness of this subject matter allows for adaptations of our framework to address diverse areas of science, including principles in ecology, environmental science, agriculture, microbiology, and evolution. Our framework includes a hands-on classroom inquiry that investigates the symbiotic relationship between nitrogen-fixing rhizobial bacteria and legumes. This student-led, inquiry-based project employs an intellectually demanding, hands-on method of education to build critical research skills using an adaptable model and inexpensive materials. We also report positive student feedback from a post hoc survey to gauge student attitudes toward the activity and the effectiveness of this framework.

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.

Mungbean (Vigna radiata) (L.) R.Wilczek and urdbean (V. mungo) (L.) Hepper are two warm-season legumes that are nutritionally dense and contribute to food security. Despite their value, they have historically been underutilized. The N. I. Vavilov’s All-Russian Institute of Plant Genetic Resources Vigna germplasm collection is particularly critical for these crops because it includes accessions acquired over a century, from before 1920 into the twenty-first century. Here we evaluate 986 accessions of V. radiata (822) and V. mungo (164) from the VIR collection to assess historical shifts before and after the Green Revolution in three of the most important traits for breeding: the maturity period, seed productivity per plant, and the weight of 1000 seeds. In addition, for the subset of 200 accessions collected in 1910–1926, another 23 morphological and agronomic traits have been evaluated. This examination allows us to assess differences among these two closely related species, reveals the differences in germplasm from different regions, and trace changes in phenotypic characters in accessions acquired at different times. Indian landraces, in the region of primary domestication and diversification of both crops, are the most phenotypically diverse. It is evident that phenotypic diversity has decayed over time, with shifts towards medium time to maturation and large-seeded types in more recently acquired accessions bred after the start of the Green Revolution. The substantial phenotypic variation in the collection indicates that a number of breeder-desired traits are present in the VIR collection, particularly in the older material pre-dating the advent of Green Revolution breeding.

According to archaeological records, chickpea (Cicer arietinum) was first domesticated in the Fertile Crescent 10 thousand years ago. Its subsequent diversification in South Asia, Ethiopia, and the Western Mediterranean, however, remains obscure and cannot be resolved using only archeological and historical evidence. In particular, chickpea has two market types: ‘desi’, which has a similar flower and seed coat color to chickpea’s wild relatives; and ‘kabuli’, which has light-colored seed, and is linguistically tied to Central Asia but has an unknown geographic origin.Based on the genetic data from 421 chickpea landraces from six geographic regions, we tested complex historical hypotheses of chickpea migration and admixture on two levels: within and between major regions of cultivation. For the former, we developed popdisp, a Bayesian model of population dispersal from a regional center towards sample locations, and confirmed that chickpea spread within each region along trade routes rather than by simple diffusion.For the latter, migration between regions, we developed another model, migadmi, that evaluates multiple and nested admixture events. Applying this model to desi populations, we found both Indian and Middle Eastern traces in Ethiopian chickpea, suggesting presence of a seaway from South Asia to Ethiopia — and the cultural legacy of the Queen of Sheba. As for the origin of kabuli chickpeas, we found significant evidence for an origin from Turkey rather than Central Asia.

A major agronomic challenge for chickpea (Cicer arietinum L.) production is temperatures above 35 °C, which causes reduced fertility and seed development. This study was aimed at assessing the phenotypic variation of chickpea genotypes under variable heat stress conditions. Chickpea genotypes were grown in heat‐stressed locations in both Ethiopia and India to assess phenotypic variation for heat tolerance. In addition, genomic relationships among the genotypes were assessed using genome‐wide single nucleotide polymorphism (SNP) markers. A total of 121 genotypes were assessed at three field sites in Ethiopia, under heat stress and nonstress conditions, and 57 genotypes were assessed under high‐heat‐stress conditions at the International Crops Research Institute for the Semiarid Tropics (ICRISAT) in Hyderabad, India. Data for five phenological and seven agromorphological traits were recorded. The results showed that the chickpea genotypes were severely affected by excessive heat at Hyderabad as compared with those planted under non‐heat‐stress conditions in Debre Zeit, Ethiopia. At extremely high temperatures, chickpea plants exhibited reduced floral initiation, arrested seed and pod development, shortened life cycles, and reduced plant height, seed size, grain yield, and yield‐related traits. Across stressed and nonstressed environments, there were highly significant differences among the genotypes for most of the traits (ANOVA, P ≤ .001). Under heat‐stressed environments, DZ‐Cr‐0034 was found to be a highly tolerant, whereas DZ‐Cr‐0026 was found to be a highly sensitive genotype. Genetic relationships among the genotypes were determined using 5,722 SNPs, revealing a single group of Ethiopian genotypes with small number of cultivars showing introgression from Middle Eastern germplasm. This study clearly demonstrated that there is genetic variability in chickpea for heat tolerance that can be harnessed to meet expected shifts towards warmer climatic conditions.

Background Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. Results We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein. Conclusions The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts.

Over the past 70 years, the world has witnessed extraordinary growth in crop productivity, enabled by a suite of technological advances, including higher yielding crop varieties, improved farm management, synthetic agrochemicals, and agricultural mechanization. While this “Green Revolution” intensified crop production, and is credited with reducing famine and malnutrition, its benefits were accompanied by several undesirable collateral effects (Pingali, 2012). These include a narrowing of agricultural biodiversity, stemming from increased monoculture and greater reliance on a smaller number of crops and crop varieties for the majority of our calories. This reduction in diversity has created vulnerabilities to pest and disease epidemics, climate variation, and ultimately to human health (Harlan, 1972). The value of crop diversity has long been recognized (Vavilov, 1992). A global system of genebanks (e.g., www.genebanks.org/genebanks/) was established in the 1970s to conserve the abundant genetic variation found in traditional “landrace” varieties of crops and in crop wild relatives (Harlan, 1972). While preserving crop variation is a critical first step, the time has come to make use of this variation to breed more resilient crops. The DivSeek International Network (https://divseekintl.org/) is a scientific, not-for-profit organization that aims to accelerate such efforts.

Legumes represent the second most important family of crop plants after grasses, accounting for approximately 27% of the world's crop production. Past domestication processes resulted in a high degree of relatedness between modern varieties of crops, leading to a narrower genetic base of cultivated germplasm prone to pests and diseases. Crop wild relatives (CWRs) harbor genetic diversity tested by natural selection in a range of environments. To fully understand and exploit local adaptation in CWR, studies in geographical centers of origin combining ecology, physiology, and genetics are needed. With the advent of modern genomics and computation, combined with systematic phenotyping, it is feasible to revisit wild accessions and landraces and prioritize their use for breeding, providing sources of disease resistances; tolerances of drought, heat, frost, and salinity abiotic stresses; nutrient densities across major and minor elements; and food quality traits. Establishment of hybrid populations with CWRs gives breeders a considerable benefit of a prebreeding tool for identifying and harnessing wild alleles and provides extremely valuable long‐term resources. There is a need of further collecting and both ex situ and in situ conservation of CWR diversity of these taxa in the face of habitat loss and degradation and climate change. In this review, we focus on three legume crops domesticated in the Fertile Crescent, pea, chickpea, and lentil, and summarize the current state and potential of their respective CWR taxa for crop improvement.

Background Phenology data collected recently for about 300 accessions of Vigna radiata (mungbean) is an invaluable resource for investigation of impacts of climatic factors on plant development. Results We developed a new mathematical model that describes the dynamic control of time to flowering by daily values of maximal and minimal temperature, precipitation, day length and solar radiation. We obtained model parameters by adaptation to the available experimental data. The models were validated by cross-validation and used to demonstrate that the phenology of adaptive traits, like flowering time, is strongly predicted not only by local environmental factors but also by plant geographic origin and genotype. Conclusions Of local environmental factors maximal temperature appeared to be the most critical factor determining how faithfully the model describes the data. The models were applied to forecast time to flowering of accessions grown in Taiwan in future years 2020-2030.

To establish and spread in a new location, an invasive species must be able to carry out its life cycle in novel environmental conditions. A key trait underlying fitness is the shift from vegetative to reproductive growth through floral development. In this study, we used a common garden experiment and genotyping-by-sequencing to test whether the latitudinal flowering cline of the North American invasive plant Medicago polymorpha was translocated from its European native range through multiple introductions, or whether the cline rapidly established due to evolution following a genetic bottleneck. Analysis of flowering time in 736 common garden plants showed a latitudinal flowering time cline in both the native and invaded ranges where genotypes from lower latitudes flowered earlier. Genotyping-by-sequencing of 9,658 SNPs in 446 individuals revealed two major subpopulations of M. polymorpha in the native range, only one of which is present in the invaded range. Additionally, native range populations have higher genetic diversity than invaded range populations, suggesting that a genetic bottleneck occurred during invasion. All invaded range individuals are closely related to plants collected from native range populations in Portugal and southern Spain, and population assignment tests assigned invaded range individuals to this same narrow source region. Taken together, our results suggest that latitudinal clinal variation in flowering time has rapidly evolved across the invaded range despite a genetic bottleneck following introduction.

Vicia ocalensis Godfrey & Kral (Ocala vetch) is a declining endemic plant that is state-listed as endangered in Florida and as critically imperiled globally. This perennial vine is historically known from only three populations along the shorelines of separate spring systems within the Ocala National Forest. One of these populations recently rejuvenated after being absent for 15 years. All populations have experienced great annual fluctuations in size, and are increasingly threatened by recreational use of the springs, herbicide treatment, and other habitat disturbances. The aims of this study are to assess genetic diversity within and between the three historical populations of V. ocalensis and characterize habitat supporting the two extant populations of V. ocalensis to inform conservation strategies. We analyzed 743 amplified fragment length polymorphism (AFLP) markers. Our AFLP results show evidence of high inbreeding and weak genetic differentiation among populations. Genetic diversity within Population 1 and Population 3 was lower than Population 2. Complementary monitoring data over the last 10 yr shows population size declines in these three populations. The low genetic diversity and inbreeding is a concern for this species, especially coupled with habitat loss, degradation, and fragmentation. Our analysis of habitat suggests that germination substrate is a key component in determining suitable habitat for V. ocalensis, but understory and overstory plants may also influence habitat suitability. Habitat protection, restoration of similar habitats, population introductions, and ex situ preservation are all recommended for this species.

WOS: 000412877000020, Crop wild relatives are a reservoir of phenotypic variation not present in the germplasm of cultivated species and thus have great potential for crop improvement. However, issues of genetic compatibility often interfere with effective utilization of crop wild relative taxa. Among chickpea (Cicer arietinum L.) crop wild relatives, Cicer echinospermum P.H. Davis is the sole species in the secondary genepool, being partially compatible with the primary genepool that is composed of the cultigen and its progenitor wild species Cicer reticulatum Ladizinksy. We report results from genetic studies among interspecific hybrids between cultivated chickpea and accessions from six recently identified wild C. echinospermum sites in southeastern Turkey, encompassing the known genetic diversity of the secondary genepool. Our studies indicate that both hybrid sterility and hybrid breakdown occur and are associated with distinct subgroups of C. echinospermum. Analysis of early-generation progenies suggests that both hybrid sterility and hybrid breakdown are conditioned by one to few genetic loci. These results clarify ambiguity in the nature of the hybridization barriers of reduced fertility in interspecific crossing of cultivated chickpea with C. echinospermum and should foster a more systematic and wider use of C. echinospermum for base broadening of cultivated chickpea., US National Science Foundation Plant Genome ProgramNational Science Foundation (NSF) [NSF-PGRP 1339346]; Agriculture Development Fund of the Saskatchewan Ministry of Agriculture; Saskatchewan Pulse Growers; Western Grains Research Foundation; United States Agency for International Development under the Feed the Future ProgramUnited States Agency for International Development (USAID) [AID-OAA-A-14-00008], We thank Dr. T.H. Noel Ellis for helpful comments on an earlier draft of this manuscript. This research was supported by grants from US National Science Foundation Plant Genome Program NSF-PGRP 1339346 to D.R. Cook, E.J.B. von Wettberg, and R.V. Penmetsa; by a cooperative agreement from the United States Agency for International Development under the Feed the Future Program AID-OAA-A-14-00008 to D.R. Cook, E.J.B. von Wettberg, A. Kahraman, and R.V Penmetsa; and by grants to B. Tar'an from the Agriculture Development Fund of the Saskatchewan Ministry of Agriculture, The Saskatchewan Pulse Growers, and The Western Grains Research Foundation.

There are 69 species of edible Mangifera recognized in Southeast Asia. Most of these species have not been characterized for nutritional properties. This paper describes the nutritional quality of the pulp of several Mangifera species - Mangifera casturi, Mangifera lalijiwa, Mangifera odorata, Mangifera zeylanica and two cultivars of Mangifera indica, 'Tommy-Kent' and 'Tommy Atkins' - at two maturity stages.; Results: The results showed that nutritional quality varied with maturity stage and among species. The immature pulp of all species had higher content of total dietary fibre, vitamin C, vitamin E, total soluble polyphenols and antioxidant capacity. In mature pulp, the protein, ash, fat, soluble carbohydrate and B vitamin values were higher in all species. The species with the best nutritional quality were, in order from highest to lowest, M. casturi, M. odorata, M. zeylanica, M. indica cultivars and M. lalijiwa.; Conclusion: The fruit pulp of three species had higher nutritional quality at both maturity stages in comparison with M. indica cultivars. These other Mangifera species can be nutritionally important in communities facing food insecurity and have potential as emerging crops. The decline of these valuable species in their natural habitats is an increasing concern, and their nutritional properties justify greater efforts to protect them. © 2017 Society of Chemical Industry.; © 2017 Society of Chemical Industry.

Wild Cicer species are considered as useful genetic resources for resistance to biotic and abiotic stresses due to limited resistance in cultivated chickpeas. As a wild perennial species in the genus Cicer L., Cicer isauricum P.H. Davis is an endemic species to Turkey and endangered status according to the International Union for Conservation of Nature criteria. Here we report on its eco-geographic distribution and environmental stresses that affect the species, and advocate for its in situ and ex situ conservation. A new population of the species was discovered in Geyikbayiri, Gulluk Mountains in Antalya, Turkey. Cicer isauricum not only suffers from significant biotic stresses such as ascochyta blight [Ascochyta rabiei (Pass.) Labr.], pod borer (Helicoverpa armigera Hubner) and broomrape (Orobanche sp.), but is also subjected to drought and heat stress in its habitat. Infection with ascochyta blight in natural habitats was diagnosed by molecular techniques, and pod borer and broomrape were observed only phenotypically. PCR amplification of the internal transcribed spacer region of genomic DNA from cultured fungal isolates, yielded sequences with 100% nucleotide identity with the corresponding sequence in GeneBank for Didymella rabiei Kovachevski (anamorph: A. rabiei). The pathogen may have co-evolved with C. isauricum in the newly discovered site. Because C. isauricum is exposed to drought and accompanying heat stress in its natural habitat, it appears able to tolerate heat stress up to 45 °C during podding stage and terminal drought in late summer from its woody, deep rooting. C. isauricum bears multiple flowers per axil, a potentially useful trait in cultivated chickpea. In conclusion, C. isauricum is a potential genetic source for resistance to biotic and abiotic stresses, in need of greater protection due to its endangered status.

The early twenty-first century has seen a rapid development of new high-throughput DNA sequencing technologies and related “-omics” approaches that are rapidly revolutionizing many areas of biology. These developments have made it possible to perform previously impossible studies of the genetic basis of abiotic stress tolerance in a range of organisms. Here, we explore some of these developments with regards to previously understudied or “orphan” legume crops, many of which have a long history of providing food and nutritional security to people living in semiarid regions with limited soil fertility.

Although microorganisms are known to dominate Earth’s biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome—tripartite and monopartite—with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.

Background Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by introgression of wild alleles. Results We built a novel model for flowering time of wild chickpeas collected at 21 different sites in Turkey and grown in 4 distinct environmental conditions over several different years and seasons. We propose a general approach, in which the analytic forms of dependence of flowering time on climatic parameters, their regression coefficients, and a set of predictors are inferred automatically by stochastic minimization of the deviation of the model output from data. By using a combination of Grammatical Evolution and Differential Evolution Entirely Parallel method, we have identified a model that reflects the influence of effects of day length, temperature, humidity and precipitation and has a coefficient of determination of R2=0.97. Conclusions We used our model to test two important hypotheses. We propose that chickpea phenology may be strongly predicted by accession geographic origin, as well as local environmental conditions at the site of growth. Indeed, the site of origin-by-growth environment interaction accounts for about 14.7% of variation in time period from sowing to flowering. Secondly, as the adaptation to specific environments is blueprinted in genomes, the effects of genes on flowering time may be conditioned on environmental factors. Genotype-by-environment interaction accounts for about 17.2% of overall variation in flowering time. We also identified several genomic markers associated with different reactions to climatic factor changes. Our methodology is general and can be further applied to extend existing crop models, especially when phenological information is limited. Electronic supplementary material The online version of this article (10.1186/s12870-019-1685-2) contains supplementary material, which is available to authorized users.

Summary Extrafloral nectar (EFN) provides plants with indirect defence against herbivores by attracting predatory insects, predominantly ants. Decades of research have supported the role of EFN as an effective plant defence, dating back to Thomas Belt's description of ants on acacia in 1874. Despite this extensive body of literature, knowledge of the ecological role of EFN has rarely been applied in the field of pest management. We review the existing literature on the use of EFN in agriculture and consider the obstacles that have hindered this transition. Chief among these obstacles is the influence of ecological context on the outcome of EFN-mediated interactions. As such, we consider the options for various agricultural systems in the light of the growth habit of EFN-producing species, focusing first on orchard species and then on herbaceous crops. In each case, we highlight the benefits and difficulties of utilizing EFN as a pest management tool and of measuring its efficacy. Synthesis and applications. We argue that it is time for a shift in extrafloral nectar (EFN) research towards applied settings and seek to address the question: How can a context-dependent and often inducible plant trait be utilized as a reliable tool in agricultural pest management? Breeding crops for increased EFN production, and intercropping with EFN-producing plants, can enhance assemblages of beneficial insects in many agricultural settings. Orchard systems, in particular, provide an ecological context in which the attraction of ants can contribute to cost-effective and sustainable pest management programmes over a broad geographic range.

Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.

Objective Chamaecrista fasciculata is a widespread annual legume across Eastern North America, with potential as a restoration planting, biofuel crop, and genetic model for non-papillinoid legumes. As a non-Papilinoid, C. fasciculata, belongs to the Caesalpiniod group in which nodulation likely arose independently of the nodulation in Papilinoid and Mimosoid legumes. Thus, C. fasciculata is an attractive model system for legume evolution. In this study, we describe population structure and genetic diversity among 32 USDA germplasm accessions of C. fasciculata using 317 AFLP markers developed from 12 primer pairs, to assess where geographically there is the most genetic variation. Results We found that the C. fasciculata germplasm collection fall into four clusters with admixture among them. After correcting for outliers, our analysis shows two primary groups across Eastern and Central North America. To better understand the population biology of this species, further sampling of the full range of this widespread species is needed across North America, as well as the development of a larger set of markers providing denser coverage of the genome. Further sampling will help clarify geographical relationships in this widespread temperate species. Electronic supplementary material The online version of this article (10.1186/s13104-019-4152-0) contains supplementary material, which is available to authorized users.

In wild habitats, fruit dehiscence is a critical strategy for seed dispersal; however, in cultivated crops it is one of the major sources of yield loss. Therefore, indehiscence of fruits, pods, etc., was likely to be one of the first traits strongly selected in crop domestication. Even with the historical selection against dehiscence in early domesticates, it is a trait still targeted in many breeding programs, particularly in minor or underutilized crops. Here, we review dehiscence in pulse (grain legume) crops, which are of growing importance as a source of protein in human and livestock diets, and which have received less attention than cereal crops and the model plant Arabidopsis thaliana. We specifically focus on the (i) history of indehiscence in domestication across legumes, (ii) structures and the mechanisms involved in shattering, (iii) the molecular pathways underlying this important trait, (iv) an overview of the extent of crop losses due to shattering, and the effects of environmental factors on shattering, and, (v) efforts to reduce shattering in crops. While our focus is mainly pulse crops, we also included comparisons to crucifers and cereals because there is extensive research on shattering in these taxa.

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.

Rare plant reintroductions are designed to increase the number of individuals in the wild, but can also improve genetic diversity of populations, reducing both short-term and long-term extinction risks. We used microsatellites developed for the genus Pseudophoenix H. Wendl. ex Sarg. to determine how reintroduced plants of the endangered Pseudophoenix sargentii H. Wendl. ex Sarg. planted in the Florida Keys in the early 1990s contributes to the population genetic structure of the species. We sampled 108 individuals representing wild and reintroduced populations in the Florida Keys and from the ex situ collection at Fairchild Tropical Botanic Garden. The wild stand on Elliott Key and the reintroduced individuals on Long Key displayed evidence of genetic drift, inbreeding, and decreased gene flow. In contrast, the ex situ plants and reintroduced individuals on Elliott Key displayed low inbreeding and higher heterozygosity. All populations deviated significantly from Hardy-Weinberg equilibrium. All p...

Soil DNA profiling has potential as a forensic tool to establish a link between soil collected at a crime scene and soil recovered from a suspect. However, a quantitative measure is needed to investigate the spatial/temporal variability across multiple scales prior to their application in forensic science. In this study, soil DNA profiles across Miami-Dade, FL, were generated using length heterogeneity PCR to target four taxa. The objectives of this study were to (i) assess the biogeographical patterns of soils to determine whether soil biota is spatially correlated with geographic location and (ii) evaluate five machine learning algorithms for their predictive ability to recognize biotic patterns which could accurately classify soils at different spatial scales regardless of seasonal collection. Results demonstrate that soil communities have unique patterns and are spatially autocorrelated. Bioinformatic algorithms could accurately classify soils across all scales with Random Forest significantly outperforming all other algorithms regardless of spatial level.

The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings.

PREMISE OF THE STUDY Seedling establishment and survival are highly sensitive to soil salinity and plants that evolved in saline environments are likely to express traits that increase fitness in those environments. Such traits are of ecological interest and they may have practical value for improving salt tolerance in cultivated species. We examined responses to soil salinity and tested potential mechanisms of salt tolerance in Medicago truncatula, using genotypes that originated from natural populations occurring on saline and nonsaline soils. METHODS Germination and seedling responses were quantified and compared between saline and nonsaline origin genotypes. Germination treatments included a range of sodium chloride (NaCl) concentrations in both offspring and parental environments. Seedling treatments included NaCl, abscisic acid (ABA), and potassium chloride (KCl). KEY RESULTS Saline origin genotypes displayed greater salinity tolerance for germination and seedling traits relative to nonsaline origin genotypes. We observed population specific differences for the effects of salinity on time to germination and for the impact of parental environment on germination rates. ABA and NaCl treatments had similar negative effects on root growth, although relative sensitivities differed, with saline population less sensitive to NaCl and more sensitive to ABA compared to their nonsaline counterparts. CONCLUSIONS We report population differentiation for germination and seedling growth traits under saline conditions among populations derived from saline and nonsaline environments. These observations are consistent with a syndrome of adaptations for salinity tolerance during early plant development, including traits that are common among saline environments and those that are idiosyncratic to local populations.

Premise of the study Fine-scale variation in temperature and soil moisture contribute to microhabitats across the landscape, affecting plant phenology, distribution, and fitness. The recent availability of compact and inexpensive temperature and humidity data loggers such as iButtons has facilitated research on microclimates. Methods and results Here, we highlight the use of iButtons in three distinct settings: comparisons of empirical data to modeled climate data for rare rock ferns in the genus Asplenium in eastern North America; generation of fine-scale data to predict flowering time and vernalization responsiveness of crop wild relatives of chickpea from southeastern Anatolia; and measurements of extreme thermal variation of solar array installations in Vermont. Discussion We highlight a range of challenges with iButtons, including serious limitations of the Hygrochron function that affect their utility for measuring soil moisture, and methods for protecting them from the elements and from human interference. Finally, we provide MATLAB code to facilitate the processing of raw iButton data.

Summary 1. Based on expectations of the stress-gradient hypothesis for conspecific interactions, stress-sensitive genotypes may be able to persist in stressful environments when positive interactions between individuals occur under stressful environments. Additionally, we test how parental environmental effects alter responses to stress and outcomes of conspecific interactions in stress. While the stress-gradient hypothesis focuses on plant growth, earlier flowering may provide stress avoidance in short-lived organisms. 2. We studied responses to soil salinity and conspecific neighbour using genotypes of Medicago truncatula (Fabaceae) originating from saline or non-saline environments, utilizing seeds from parental plants grown in saline or non-saline environments. During the early stages of reproduction, we quantified leaf number, as a measure of vegetative growth, and number of flowers, as a measure of early reproduction potential. 3. Based on leaf counts, non-saline genotypes were better competitors than saline-origin genotypes and benefited from neighbouring plants in saline environments. This positive interaction was detected only when seeds were matured on parental plants grown in non-saline environments. Saline-origin genotypes displayed greater salinity tolerance in early flowering than non-saline genotypes. Plants with neighbours had greater early flowering, regardless of origin, consistent with facilitative interactions in stressful environments. 4. Transgenerational plastic responses influenced neighbouring plant interactions on plant growth, and results suggest that facilitative interactions may be transient only persisting for one generation. However, earlier flowering of non-saline genotypes when grown with a neighbouring plant is consistent with facilitative interactions resulting in reproductive benefits in saline environments, if earlier flowering is favoured in saline environments. 5. Synthesis. Adaptation to stressful environments allows tolerant genotypes to persist in these environments. Less appreciated is that stress-sensitive genotypes lacking such adaptations may persist in stressful environments via positive interactions with other individuals. Thus, positive interactions between individuals may explain the persistence of stress-sensitive genotypes within a population adapted to stressful environments.

Diverse germplasm is essential to breeding new pigeonpea varieties resilient against both abiotic and biotic challenges. In this chapter, we review the major abiotic and biotic challenges faced by pigeonpea, and trait assessment tools available to the breeding community to address these challenges. We place particular attention on drought tolerance, due to its widespread nature and large effect on yield. We emphasize the utility of wild material to expand the range of available genetic variation; as such material is generally underutilized in breeding programs. A complete genome brings great potential to the pigeonpea breeding community; to fulfill the promise of a genome for breeding for climate resilience, the full range of diversity available must be brought to bear. We hope that conditions in the future allow wild germplasm collections to expand, further capitalizing on the potential to increase pigeonpea yields and resilience against climate change.

Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.

Plants are rife with bacteria and fungi that colonize roots and shoots both externally and internally. By providing novel nutritional and defense pathways and influencing plant biochemical pathways, microbes can fundamentally alter plant phenotypes. Here we review the widespread nature of microbially mediated plant functional traits. We highlight that there is likely fitness conflict between hosts and symbionts and that fitness outcomes can depend on partner genotypes and ecological factors. Microbes may influence ecosystems through their effects on the functional trait values and population dynamics of their plant hosts. These effects may feed back on symbiont evolution by altering transmission rates of symbionts and scale up to ecosystem processes and services. We end by proposing new avenues of research in this emerging field.

Pseudophoenix ekmanii is a threatened palm species endemic to the Dominican Republic. Sap from trees is extracted to make a local drink; once they are tapped the individual usually dies. Plants are also illegally harvested for the nursery trade and destroyed by poachers hunting the endemic and threatened Hispaniolan parrot. We used 7 DNA microsatellite markers to assist land managers in developing conservation strategies for this palm. We sampled 4 populations along the known distribution range of this species (3 populations from the mainland and 1 from the small island of Isla Beata), for a total sample of n = 104. We found strong evidence for genetic drift, inbreeding, and moderate gene flow (i.e., all populations had at least 4 loci that were not in Hardy-Weinberg equilibrium, at least 9 loci pairs were in linkage disequilibrium, the pairwise F(ST) values ranged from 0.069 to 0.266, and had positive F(IS) values). Data supported an isolation-by-distance model, and cluster analyses based on genetic distances resolved 2 groups that match a north-south split. The population from Isla Beata had the lowest levels of genetic diversity and was the only one in which we found pairs of individuals with identical shared multilocus genotypes.

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.

Many mechanisms of invasive species success have been elucidated, but those driving cryptic invasions of non-native genotypes remain least understood. In one of the most successful cryptic plant invasions in North America, we investigate the mechanisms underlying the displacement of native Phragmites australis by its Eurasian counterpart. Since invasive Phragmites ’ populations have been especially prolifi c along eutrophic shorelines, we conducted a two-year fi eld experiment involving native and invasive genotypes that manipulated nutrient level and competitor identity (inter- and intra-genotypic competition) to assess their relative importance in driving the loss of native Phragmites . Inter-genotypic competition suppressed aboveground biomass of both native and invasive plants regardless of nutrient treatment ( ∼ 27%), while nutrient addition disproportionately enhanced the aboveground biomass (by 67%) and lateral expansion (by 3 farther) of invasive Phragmites . Excavation of experimental plots indicated that nutrient addition generates these diff erences in aboveground growth by diff erentially aff ecting rhizome production in invasive vs native plants; invasive rhizome biomass and rhizome length increased by 595% and 32% with nutrient addition, respectively, while natives increased by only 278% and 15%. Regardless of nutrient level, native rhizomes produced twice as many roots compared to invasives, which fi eld surveys revealed are heavily infected with mycorrhizal symbionts . Th ese results suggest that native Phragmites competes well under nutrient-limited conditions because its rhizomes are laden with nutrient-harvesting roots and mycorrhizae. Invasive Phragmites ’ vigorous aboveground response to nutrients and scarcity of lateral roots , in contrast, may refl ect its historic distribution in eutrophic Eurasian wetlands and correspond to its prevalence in New England marshes characterized by elevated nutrient availability and relaxed nutrient competition. Th ese fi ndings reveal that discrete diff erences in phenotype can interact with anthropogenic modifi cation of environmental conditions to help explain the success of cryptic invaders.

In the face of global change, agriculture increasingly requires germplasm with high yields on marginal lands. Identifying pathways that are adaptive under marginal conditions is increasingly possible with advances at the intersection of evolutionary ecology, population genetics, and functional genomics. Trait-based (reverse ecology) approaches have connected flowering time in Arabidopsis thaliana to single alleles with environment-specific effects. Similarly, genetic dissection of rice flooding tolerance enabled the production of near-isogenic lines exhibiting tolerance and high yields. An alternative gene-forward (forward ecology) approach identified candidate genes for local adaptation of Arabidopsis lyrata to heavy-metal rich soils. A global perspective on plant adaptation and trait correlations provides a foundation for breeding tolerant crops and suggests populations adapted to marginal habitats be conservation priorities.

A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions. Serpentine soils, characterized by high heavy-metal content and low calcium-to-magnesium ratios, are a classic context for studying adaptation of plants to local soil conditions. To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we pooled DNA from individuals from serpentine and nonserpentine soils and sequenced each 'gene pool' with the Illumina Genome Analyzer. The polymorphisms that are most strongly associated with soil type are enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation. Sequencing of three candidate loci in the European subspecies of A. lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution.

“Serpentinomics” is an emerging field of study which has the potential to greatly advance our understanding of serpentine ecology. Several newly developing —omic fields, often using high-throughput tools developed for molecular biology, will advance the field of serpentine ecology, or, “serpentinomics.” Using tools from the fields of ionomics, metabolomics, proteomics, transcriptomics and genomics, researchers will be able to address new (and old) ecological questions in powerful and creative ways. In particular, “serpentinomics” has the potential to uncover the mechanistic and genetic basis of the complexities of tolerance of and adaptation to serpentine soils, including the biochemistry of hyperaccumulation. Here we outline each of these —omic fields and describe possible applications to the field of serpentine ecology.

There are at least eight species of Impatiens (Jewelweeds) in the northeast, including native and non-native species, species of temperate and subtropical origins, and wild and planted species. The two native jewelweeds, I. capensis and I. pallida, are common in the region, and I. capensis has been introduced in Europe. Impatiens glandulifera is a non-native species that is locally well established and has the potential to become invasive in the region. The introduced I. balfourii and I. parviflora infrequently naturalize in the Northeast. Three Impatiens species of tropical origins, I. balsamina, I. walleriana, and I. hawkeri, may be able to establish in the Northeast with continued horticultural pressure. We review the descriptions and known distributions of these species, the direct experimental comparisons of their biological traits, and the histories of their introductions and horticultural uses. Such information is beneficial for assessing the invasive potential of these species in the nort...

Adaptation to different habitat types across a patchy landscape may either arise independently in each patch or occur due to repeated colonization of each patch by the same specialized genotype. We tested whether open- and closed-canopy forms of Impatiens capensis, an herbaceous annual plant of eastern North America, have evolved repeatedly by comparing hierarchical measures of F(ST) estimated from AFLPs to morphological differentiation measured by Q(ST) for five pairs of populations found in open and closed habitats in five New England regions. Morphological differentiation between habitats (Q(HT)) in elongation traits was greater than marker divergence (F(HT)), suggesting adaptive differentiation. Genotypes from open- and closed-canopy habitats differed in shade avoidance traits in several population pairs, whereas patterns of AFLP differentiation suggest this differentiation does not have a single origin. These results suggest that open- and closed-canopy habitats present different selective pressures, but that the outcome of diversifying selection may differ depending on specific closed- and open-canopy habitats and on starting genetic variation. Hierarchical partitioning of F(ST) and Q(ST) makes it possible to distinguish global stabilizing selection on traits across a landscape from diversifying selection between habitat types within regions.

Chickpea (Cicer arietinum) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so-called kabuli type, has white flowers and light-colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms (SNPs) and examined patterns of molecular diversity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic diversity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix-loop-helix (bHLH) transcription factor at chickpea's B locus that conditions flower and seed colors, orthologous to Mendel's A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic diversification after initial domestication of cultivated chickpea.