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Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation

Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes...

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Autores principales: Songsomboon, Kittikun, Brenton, Zachary, Heuser, James, Kresovich, Stephen, Shakoor, Nadia, Mockler, Todd, Cooper, Elizabeth A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8495935/
https://www.ncbi.nlm.nih.gov/pubmed/33950177
http://dx.doi.org/10.1093/g3journal/jkab154
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author Songsomboon, Kittikun
Brenton, Zachary
Heuser, James
Kresovich, Stephen
Shakoor, Nadia
Mockler, Todd
Cooper, Elizabeth A
author_facet Songsomboon, Kittikun
Brenton, Zachary
Heuser, James
Kresovich, Stephen
Shakoor, Nadia
Mockler, Todd
Cooper, Elizabeth A
author_sort Songsomboon, Kittikun
collection PubMed
description Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.
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spelling pubmed-84959352021-10-07 Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation Songsomboon, Kittikun Brenton, Zachary Heuser, James Kresovich, Stephen Shakoor, Nadia Mockler, Todd Cooper, Elizabeth A G3 (Bethesda) Genome Report Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum. Oxford University Press 2021-05-05 /pmc/articles/PMC8495935/ /pubmed/33950177 http://dx.doi.org/10.1093/g3journal/jkab154 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Songsomboon, Kittikun
Brenton, Zachary
Heuser, James
Kresovich, Stephen
Shakoor, Nadia
Mockler, Todd
Cooper, Elizabeth A
Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
title Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
title_full Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
title_fullStr Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
title_full_unstemmed Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
title_short Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
title_sort genomic patterns of structural variation among diverse genotypes of sorghum bicolor and a potential role for deletions in local adaptation
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8495935/
https://www.ncbi.nlm.nih.gov/pubmed/33950177
http://dx.doi.org/10.1093/g3journal/jkab154
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