Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype–phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.

中文翻译：

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广泛的结构变异对高粱的主要影响

遗传多样性对于作物育种和改良至关重要，对农艺性状背后的基因组变异的剖析既可以帮助育种，又可以深入了解基本的生物学机制。尽管最近的植物基因组分析揭示了许多结构变异（SV），但目前大多数作物遗传变异的研究仍以单核苷酸多态性（SNP）为主。 SV 对整体性状变异的影响程度以及它们在全基因组选择中的效用尚不清楚。在本研究中，我们基于不同高粱品系（n = 363）的全基因组重测序构建了SV数据集，验证了光周期敏感性与品种类型的相关性，并确定了纤维素高粱和甜高粱趋异进化背后的SV热点。此外，我们还展示了 SV 对高粱适应相关性状遗传力的互补贡献。重要的是，将 SV 多态性纳入关联研究揭示了单独使用 SNP 时未观察到的基因型-表型关联。基于全基因组 SNP、SV 和整合的 SNP + SV 数据集的三向全基因组关联研究 (GWAS) 显示 SV 与高粱性状之间存在显着关联。将 SV 添加到 GWAS 中大大增加了某些性状的遗传力估计，表明它们对基因组水平的功能等位基因变异的重要贡献。我们发现 SV 对可遗传基因表达变异的广泛影响可能为它们对表型变异的不成比例的影响提供一个合理的机制。这项研究扩展了我们对高粱的认识，并强调了高粱对高粱的广泛影响。