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.

doi:10.1093/g3journal/jkab154

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

Journal Article · Wed May 05 00:00:00 EDT 2021 · G3

DOI:https://doi.org/10.1093/g3journal/jkab154· OSTI ID:1848215

Songsomboon, Kittikun ^[1];

^[2]; Heuser, James ^[1]; Kresovich, Stephen ^[2]; Shakoor, Nadia ^[3];

^[3]; Cooper, Elizabeth A. ^[1]

Univ. of North Carolina, Charlotte, NC (United States). Dept. of Bioinformatics and Genomics; North Carolina Research Campus, Kannapolis, NC (United States)
Clemson Univ., SC (United States). Dept. of Plant and Environmental Sciences
Donald Danforth Plant Science Center, St. Louis, MO (United States)

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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Research Organization:: Clemson Univ., SC (United States)

Sponsoring Organization:: USDOE Advanced Research Projects Agency - Energy (ARPA-E)

Grant/Contract Number:: AR0000595

OSTI ID:: 1848215

Journal Information:: G3, Vol. 11, Issue 7; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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structural variation
Sorghum
k-mean clustering
local adaptation

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

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