Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

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 c...

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Autores principales:	Elena Plekhanova, Margarita A. Vishnyakova, Sergey Bulyntsev, Peter L. Chang, Noelia Carrasquilla-Garcia, Kassaye Negash, Eric von Wettberg, Nina Noujdina, Douglas R. Cook, Maria G. Samsonova, Sergey V. Nuzhdin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b0cfb215f57f4a96a11ff4744cdd895d
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spelling	oai:doaj.org-article:b0cfb215f57f4a96a11ff4744cdd895d2021-12-02T12:32:57ZGenomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits10.1038/s41598-017-05087-52045-2322https://doaj.org/article/b0cfb215f57f4a96a11ff4744cdd895d2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05087-5https://doaj.org/toc/2045-2322Abstract 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.Elena PlekhanovaMargarita A. VishnyakovaSergey BulyntsevPeter L. ChangNoelia Carrasquilla-GarciaKassaye NegashEric von WettbergNina NoujdinaDouglas R. CookMaria G. SamsonovaSergey V. NuzhdinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Elena Plekhanova Margarita A. Vishnyakova Sergey Bulyntsev Peter L. Chang Noelia Carrasquilla-Garcia Kassaye Negash Eric von Wettberg Nina Noujdina Douglas R. Cook Maria G. Samsonova Sergey V. Nuzhdin Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
description	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.
format	article
author	Elena Plekhanova Margarita A. Vishnyakova Sergey Bulyntsev Peter L. Chang Noelia Carrasquilla-Garcia Kassaye Negash Eric von Wettberg Nina Noujdina Douglas R. Cook Maria G. Samsonova Sergey V. Nuzhdin
author_facet	Elena Plekhanova Margarita A. Vishnyakova Sergey Bulyntsev Peter L. Chang Noelia Carrasquilla-Garcia Kassaye Negash Eric von Wettberg Nina Noujdina Douglas R. Cook Maria G. Samsonova Sergey V. Nuzhdin
author_sort	Elena Plekhanova
title	Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
title_short	Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
title_full	Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
title_fullStr	Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
title_full_unstemmed	Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
title_sort	genomic and phenotypic analysis of vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b0cfb215f57f4a96a11ff4744cdd895d
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Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

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