Raw genotyped total called structural variant (SV)
Genomic structural mutations especially deletion 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, including some crops, 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, and over the course of its history it has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity within the existing germplasm. In this study, we identified genome-wide deletions in the Biomass Association Panel (BAP), 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 22,359 deletions after filtering. The size of deletions ranged from 51 to 89,716 bp with a median size of 956 bp. The global site frequency spectrum of the deletions fit a model of neutral evolution, suggesting that the majority of deletions were not under any types of selection. Clustering results based on SNPs separated the deletions of the genotypes into eight clusters which largely corresponded with geographic origins. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic (plant defense and bacterial resistance) and abiotic stress (drought and temperature) responses, supporting the possibility that at least some deletions contribute to local adaptation in sorghum.
Heuser, James; Songsomboon, Kittikun; Shakoor, Nadia; Cooper, Elizabeth; Brenton, Zachary; Kresovich, Stephen (2021), "Raw genotyped total called structural variant (SV)", Zenodo, doi: 10.5061/dryad.9cnp5hqhc