Historical routes for diversification of domesticated chickpea inferred from landrace genomics

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.

Corrigendum: How could the use of crop wild relatives in breeding increase the adaptation of crops to marginal environments?

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How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments?

Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.

Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well-Represented Collections

The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-most-important cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein. L. culinaris was domesticated in the Fertile Crescent, and six additional wild taxa (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) are recognized. Numerous genetic diversity studies have shown that wild relatives present high levels of genetic variation and provide a reservoir of alleles that can be used for breeding programs. Furthermore, the integration of genetics/genomics and breeding techniques has resulted in identification of quantitative trait loci and genes related to attributes of interest. Genetic maps, massive genotyping, marker-assisted selection, and genomic selection are some of the genetic resources generated and applied in lentil. In addition, despite its size (∼4 Gbp) and complexity, the L. culinaris genome has been assembled, allowing a deeper understanding of its architecture. Still, major knowledge gaps exist in lentil, and a deeper understanding and characterization of germplasm resources, including wild relatives, is critical to lentil breeding and improvement. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Recording of lentil seed descriptors Basic Protocol 2: Lentil seed imaging Basic Protocol 3: Lentil seed increase Basic Protocol 4: Recording of primary lentil seed INCREASE descriptors.

Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism

Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, Medicago polymorpha, and its nitrogen-fixing rhizobium symbiont, Ensifer medicae, which have coinvaded North America. We find that mutualism benefits for plants are indistinguishable between invaded- and native-range symbioses. However, rhizobia gain greater fitness from invaded-range mutualisms than from native-range mutualisms, and this enhancement of symbiont fecundity could increase the mutualism's spread by increasing symbiont availability during plant colonization. Furthermore, mutualism traits in invaded-range symbioses show lower genetic variance and a simpler partitioning of genetic variance between host and symbiont sources, compared to native-range symbioses. This suggests that biological invasion has reduced mutualists' potential to respond to coevolutionary selection. Additionally, rhizobia bearing a locus (hrrP) that can enhance symbiotic fitness have more exploitative phenotypes in invaded-range than in native-range symbioses. These findings highlight the impacts of biological invasion on the evolution of mutualistic interactions.

Corrigendum: Editorial: Wild Plants as Source of New Crops

[This corrects the article DOI: 10.3389/fpls.2020.591554.].

The Impact of Domestication on Aboveground and Belowground Trait Responses to Nitrogen Fertilization in Wild and Cultivated Genotypes of Chickpea (Cicer sp.)

Despite the importance of crop responses to low fertility conditions, few studies have examined the extent to which domestication may have limited crop responses to low-fertility environments in aboveground and belowground traits. Moreover, studies that have addressed this topic have used a limited number of wild accessions, therefore overlooking the genotypic and phenotypic diversity of wild relatives. To examine how domestication has affected the response of aboveground and belowground agronomic traits, we measured root and leaf functional traits in an extensive set of wild and domesticated chickpea accessions grown in low and high nitrogen soil environments. Unlike previous studies, the wild accessions used in this study broadly capture the genetic and phenotypic diversity of domesticated chickpea’s (Cicer arietinum) closest compatible wild relative (C. reticulatum). Our results suggest that the domestication of chickpea led to greater capacities for plasticity in morphological and biomass related traits but may have lowered the capacity to modify physiological traits related to gas exchange. Wild chickpea displayed greater phenotypic plasticity for physiological traits including stomatal conductance, canopy level photosynthesis, leaf level photosynthesis, and leaf C/N ratio. In contrast to domesticated chickpea, wild chickpea displayed phenotypes consistent with water loss prevention, by exhibiting lower specific leaf area, stomatal conductance and maintaining efficient water-use. In addition to these general patterns, our results indicate that the domestication dampened the variation in response type to higher nitrogen environments for belowground and aboveground traits, which suggests reduced genetic diversity in current crop germplasm collections.

Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)

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.

The impact of salinity on mycorrhizal colonization of a rare legume, Galactia smallii, in South Florida pine rocklands

Objectives

The success of restoration plantings depends on the capacity of transplanted individuals or seeds to establish and reproduce. It is increasingly recognized that restoration success depends quite heavily upon biotic interactions and belowground processes. Under stressful abiotic conditions, such as soils salinized by storm surge and sea level rise, symbiotic interactions with soil microbes such as mycorrhizae may be critically important. In this study, we investigate the impact of salinity on percent colonization of roots by arbuscular mycorrhizal fungi, in addition to the impacts of this colonization on plant fitness under saline conditions. Fifty Galactia smallii plants from an ex situ collection were subjected to a salinity treatment for 6 weeks, and 50 plants were untreated. Plants were harvested and assessed for percent colonization by arbuscular mycorrhizal fungi, nodule number, shoot and root dry biomass, and micronutrient content.

Results

Colonization by arbuscular mycorrhizae was higher in plants in the salinity treatment than in untreated plants; plants in the salinity treatment were also found to have a lower root:shoot ratio, and higher phosphorus and nitrogen levels. These results support the importance of arbuscular mycorrhizal fungi in restoration efforts of endangered plants in fragmented and threatened ecosystems, such as pine rocklands.

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy.

Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.