Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
Open Access
- 6 July 2017
- journal article
- research article
- Published by Springer Science and Business Media LLC in Scientific Reports
- Vol. 7 (1), 4816
- https://doi.org/10.1038/s41598-017-05087-5
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.Keywords
This publication has 73 references indexed in Scilit:
- Complex Patterns of Local Adaptation in TeosinteGenome Biology and Evolution, 2013
- Genomic rearrangements and the evolution of clusters of locally adaptive lociProceedings of the National Academy of Sciences of the United States of America, 2013
- A map of rice genome variation reveals the origin of cultivated riceNature, 2012
- STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno methodConservation Genetics Resources, 2011
- A framework for variation discovery and genotyping using next-generation DNA sequencing dataNature Genetics, 2011
- Structure-Function Similarities between a Plant Receptor-like Kinase and the Human Interleukin-1 Receptor-associated Kinase-4Online Journal of Public Health Informatics, 2011
- GCTA: A Tool for Genome-wide Complex Trait AnalysisAmerican Journal of Human Genetics, 2011
- Genetic perspectives on crop domesticationTrends in Plant Science, 2010
- Fast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics, 2010
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007