The Signatures of Ecological Adaptation in the Genomes of Chickpea Landraces

Sokolkova, Alena; Chang, Peter L.; Carrasquila-Garcia, Noelia; Noujdina, Nina; Cook, Douglas R.; Nuzhdin, Sergey V.; Samsonova, Maria

doi:10.1134/s0006350920020244

Cited by 7 publications

(7 citation statements)

References 7 publications

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“…SNP Ca6: 3024192, associated with beginning of flowering to the beginning of maturation phenotype, is located in the same haploblock Ca6_Block_3 (~87 kb upstream) as the previously detected SNP (Table S11), associated with days to 50% flowering [24]. Previously, we [25] published a study in which we were looking for associations between SNPs and bioclimatic covariates at collection sites. Two covariates, which include temperature characteristics, were jointly associated with one SNP on chromosome 8 (Ca8: 10314452).…”

Section: Discussionmentioning

confidence: 75%

Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

Sokolkova

Bulyntsev

Chang

et al. 2020

IJMS

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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.

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Section: Discussionmentioning

confidence: 75%

Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

Sokolkova

Bulyntsev

Chang

et al. 2020

IJMS

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“…In sub-Saharan Africa, chickpea (Cicer arietinum L.) is predominately cultivated in Ethiopia, Sudan, Eritrea, Kenya, Tanzania and Malawi (Bejiga & Van der Maesen, 2006). Chickpea was likely introduced into sub-Saharan Africa through Ethiopia, and indeed Vavilov designated Ethiopia as a secondary center of diversity for chickpea (Sokolkova et al, 2020). Ethiopian production accounts for 90% (Verkaar et al, 2017) of the total production in sub-Saharan Africa and 3% of the world's production (FAO, 2018) which makes Ethiopia sixth among the world's leading chickpea producers.…”

Section: Introductionmentioning

confidence: 99%

Screening of heat‐tolerant Ethiopian chickpea accessions: Assessment of phenological and agromorphological traits and genomic relationships

Getahun

Negash

Chang

et al. 2021

Agrosystems Geosci & Env

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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

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“…These SNPs were further filtered to meet requirements for minor allele frequency (MAF) >3% and genotype call-rate >90%. 2,579 SNPs in 421 accessions passed all filtering criteria and were retained for further analysis (Sokolkova et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

Historical trade routes for diversification of domesticated chickpea inferred from landrace genomics

Igolkina

Noujdina²,

Samsonova

et al. 2021

Preprint

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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.

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The Signatures of Ecological Adaptation in the Genomes of Chickpea Landraces

Cited by 7 publications

References 7 publications

Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

Screening of heat‐tolerant Ethiopian chickpea accessions: Assessment of phenological and agromorphological traits and genomic relationships

Historical trade routes for diversification of domesticated chickpea inferred from landrace genomics

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