Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
North Carolina Research Campus, Kannapolis, NC 28081, USA.
G3 (Bethesda). 2021 Jul 14;11(7). doi: 10.1093/g3journal/jkab154.
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.
基因组结构突变，尤其是缺失，是许多物种变异的一个重要来源，并且可以在表型多样化和进化中发挥关键作用。先前在许多植物物种中的研究已经确定了多个结构变异（SVs）发生在或靠近与应激反应和疾病抗性相关的基因，这表明 SVs 可能在局部适应中发挥作用。高粱 [高粱（L.）Moench] 是世界上种植最广泛的谷类作物之一。它已经适应了多种不同的气候，并为多种用途而培育，从而产生了引人注目的表型多样性。在这项研究中，我们在生物量关联小组中鉴定了全基因组 SVs，该小组由来自多个国家和大陆的 347 个不同高粱基因型组成。利用每个基因型的基于 Illumina 的短读长全基因组重测序数据，我们总共发现了 24648 个 SVs，包括 22359 个缺失。缺失和其他类型的 SVs 的全球位点频率谱符合中性进化模型，表明这些突变中的大多数不受任何类型的选择。基于单核苷酸多态性的聚类结果将基因型分为八个聚类，这与地理起源大致对应，我们发现的许多大缺失是单个聚类所特有的。尽管大多数缺失似乎是中性的，但在与生物和非生物胁迫反应相关的基因中发现了少数聚类特异性缺失，这支持了至少一些缺失有助于高粱的局部适应的可能性。
