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.
Highlights
Landraces dominated agriculture for millennia, until the advent of intensive modern breeding in the mid 20th century, when reduced sets of elite cultivated varieties largely displaced the wider diversity of local genotypes [1]
The grouping of traits and ancestral bioclimatic variables does not necessarily imply co-selection during domestication (e.g., [26]), these clusters may represent genetic complexes co-adapted to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation
Phenotyping of the 407 chickpea genotype collection was conducted at the Vavilov Institute of Plant Genetic Resources (VIR) Kuban experimental station with climatic conditions well suited for chickpea cultivation
Summary
Landraces dominated agriculture for millennia, until the advent of intensive modern breeding in the mid 20th century, when reduced sets of elite cultivated varieties largely displaced the wider diversity of local genotypes [1]. In the early 20th century (1911–1940), N.I. Vavilov led a systematic effort to collect and preserve crop diversity, maintained within the Vavilov Institute of Plant Genetic Resources (VIR) collection in St. Petersburg, Russia [3]. The geographic distribution and genetic diversity of most crops collected during this time frame are likely to reflect their historic patterns of cultivation established over the preceding millennia. Exploring these unique genetic resources provides an opportunity to revisit hypotheses about the radiation and secondary diversification of crops, not possible using later collections. The expanded diversity of these early collections likely contains ‘genetic gems’ with the potential to enhance modern breeding efforts [4]
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