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

Abstract

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.

GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces

“…Previous studies based on climatic data have revealed gene expressed regions that might be involved in the answer to different environments [ 123 , 124 , 125 , 126 , 127 , 128 ]. They also suggest a role for the target genes in responses to environmental effects during plant development, such as those involved in regulation of the circadian clock, DNA methylation or flowering delay.…”

“…Three additional MTAs were also private alleles of the exotic landrace population and all were associated to bioclimatic variables, which suggest that these variants might be a signal of adaptation. Previous studies, performed on sorghum landraces have evidenced that the environment of origin have had a significant role in shaping SNP allele variation and suggested that these genomic signatures of adaptation might be used for crop improvement [ 126 , 127 , 128 , 131 ].…”

Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single‐Seed‐Descent Genetic Resources for Chickpea

“…Genetic analyses demonstrate that the desi‐vs‐kabuli dichotomy arose multiple times independently, correlated with loss of function in a key transcriptional regulator (Penmetsa et al., 2016). Population structure analysis of diverse chickpea collections has shown that the identification of these groups is largely correlated with geographic distribution rather than desi and kabuli differentiation (De Giovanni et al., 2017; Penmetsa et al., 2016; Sokolkova et al., 2020; Varshney et al., 2021).…”

“…The VIR chickpea collection is unique in its preponderance of historic landraces, sampled prior to the advent of intensive modern breeding. Thus, the VIR collection is likely to capture genetic adaptations and functional diversity that reflect historic local and regional practices (Plekhanova et al., 2017), providing opportunities to study post‐domestication and diversification processes prior to the Green Revolution (Sokolkova et al., 2020).…”

“…Several studies that have used chickpea core collections are also available, based on genotyping by sequencing (GBS) data (Pavan et al, 2017;Roorkiwal et al, 2018). Sokolkova et al (2020) used GBS to genotype a set of 407 landraces sampled from the chickpea VIR collections, which included the domestication and secondary diversity centers. Von Wettberg et al (2018) collected a wide set of wild chickpea materials (about 1,000 accessions) and characterized these using GBS.…”