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According to archaeological records, chickpea (Cicer arietinum) was first domesticated in the Fertile Crescent about 10,000 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 toward 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.

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain 'genetic gems' with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.

In pea (Pisum sativum L.), alleles of the Sym2 gene determine the specificity of the interaction with nodule bacteria (rhizobia). The Sym2A allele present in landraces from Afghanistan provides higher selectiveness toward rhizobia than the Sym2E allele present in European cultivars. Rhizobial strains possessing the nodX gene can interact with both Sym2A and Sym2E peas, while strains lacking nodX can interact only with Sym2E peas. Here, we studied the previously obtained introgression line A33.18 bearing Sym2A in a homozygous state in the genome of the European pea cultivar 'Rondo'. A33.18 has proved its high selectiveness in pot experiments. Genome sequencing has shown that A33.18 possesses an 18.2 Mb region inherited from Afghanistan pea with 63 genes, including 5 receptor kinase genes, among which was the Sym2 candidate gene LykX. In a field experiment, under inoculation with the nodX+ strain TOM, over 95% of nodules of A33.18 contained TOM, as opposed to less than 8% of nodules containing TOM in the parental European cultivar 'Rondo'. Thus, introgression of Sym2A enabled peas to interact specifically with the nodX+ strain, favoring the formation of nodules by the strain from the inoculum and protecting peas from the indigenous soil microbiota. [ABSTRACT FROM AUTHOR]

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.

Vavilovia (Vavilovia formosa (Stev.) Fed.) belongs to the tribe Fabeae along with peas, vetchlings, vetches and lentils. It prefers high mountain areas in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia, Syria and Turkey. A true success in the ex situ conservation has recently been achieved, within the display plot Flora and Vegetation of Armenia in the Yerevan Botanic Garden. The hybridization between vavilovia and other Fabeae was done in the N. I. Vavilov Institute of Plant Industry with F1 seeds and F1 plants that did not produce the next generation. The recent molecular research showed that vavilovia belongs to a Lathyrus-Pisum-Vavilovia clade with a clearly distinct status.

Adaptability and stable pod per plant productivity of 20 varieties of vegetable common bean from the collection of the Vavilov Institute (VIR) were investigated. The accessions were grown on 8 selective backgrounds: four different patterns and density of planting during two years. The most adaptive accessions, i.e. most tolerant to the different density, having the stable productivity, were identified. The level of affection of accessions with bacterial diseases depending on the density of planting was also determined. The optimal pattern and sowing density had been proposed for breeding nurseries as a selective background for breeding of genotypes with stable productivity.