Abstract
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.
Highlights
The Vavilov Institute of Plant Genetic Resources (VIR), in St
To start analysing the wealth of the VIR germplasm coupled with available phenotypic data, we have limited our scope to the oldest chickpea accessions collected nearly a hundred years ago from one centre of primary chickpea domestication (Turkey) and one centre of secondary diversification (Ethiopia)[11]
Genotyping-by-sequencing identified 14,059 segregating SNPs among 147 accessions originating from Turkey and Ethiopia
Summary
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. New paradigms are needed to increase sustainability in agricultural systems, including methods to explore the genetic potential of the vast but woefully underutilized germplasm resources available for most crop species. Crucial to this effort are the recent advent of low cost, high throughput DNA sequencing technologies and corresponding advances in computational genomics[2]. The Vavilov Institute of Plant Genetic Resources (VIR) in St. Petersburg is a uniquely valuable collection of crop germplasm because it captures the genetic and functional diversity of regionally stratified agriculture typical of one century ago. Landraces dominated agriculture from ~7 KYA until the advent of intensive modern breeding in the mid 20th century – when a few elite cultivated varieties largely displaced landraces
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