Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
Nat Commun. 2023 Mar 21;14(1):1567. doi: 10.1038/s41467-023-37004-y.
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.
理解和利用遗传多样性是水稻高产稳产的关键因素。在这里，我们利用 73 个高质量的基因组，涵盖了亚洲稻（Oryza sativa）的亚种群结构，加上两个野生亲缘种（O. rufipogon 和 O. punctata）的基因组，构建了一个包含 1769 个非冗余倒位的泛基因组倒位指数，这些倒位跨越了 O. sativa cv. Nipponbare 参考基因组序列的平均约 29%。利用这个指数，我们估计亚洲稻的倒位率约为每百万年 700 个倒位，是先前估计的植物倒位率的 16 到 50 倍。对这些倒位的详细分析表明，它们对基因表达、重组率和连锁不平衡有影响。我们的研究揭示了亚洲稻泛基因组中大型倒位（≥100bp）的普遍性和规模，并暗示了它们在功能生物学和作物表现中尚未被充分探索的作用。
