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

International Journal of Molecular Sciences

AnnaA. Igolkina¹  Alena Sokolkova¹  NinaV. Noujdina¹  MariaG. Samsonova¹  SergeyV. Nuzhdin¹  Noelia Carrasquilla-Garcia²  DouglasR. Cook²  Eric von Wettberg³  PeterL. Chang⁴  SergeyV. Bulyntsev⁵  MargaritaA. Vishnyakova⁵ 

[1] Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;Department of Plant Pathology, University of California Davis, Davis, CA 95616, USA;Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA;Dornsife College of Letters Arts & Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA;Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia;

关键词: bioclimatic analysis;    chickpea;    GBS;    GWAS;    haploblock;    SNP;   

DOI  :  10.3390/ijms21113952

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown