Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
Open Access
- 5 May 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 11 (7)
- https://doi.org/10.1093/g3journal/jkab154
Abstract
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.Keywords
Funding Information
- Department of Energy’s Advanced Research Project Agency (DE-AR0000595)
This publication has 79 references indexed in Scilit:
- The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatusGenome Biology and Evolution, 2013
- Population genomic and genome-wide association studies of agroclimatic traits in sorghumProceedings of the National Academy of Sciences of the United States of America, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- The variant call format and VCFtoolsBioinformatics, 2011
- CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencingGenome Research, 2011
- Pervasive gene content variation and copy number variation in maize and its undomesticated progenitorGenome Research, 2010
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing dataGenome Research, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- Structural variation in the human genomeNature Reviews Genetics, 2006