A pangenome reference of wild and cultivated rice

The wild rice <i>Oryza rufipogon</i>, progenitor of Asian cultivated rice <i>O. sativa</i>, is an important resource for rice breeding. Here we presented a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse <i>O. rufipogon</i> accessions and 16 diverse <i>O. sativa</i> varieties. This pangenome contains 3.87 Gb novel sequences absent in the <i>japonica </i>Nipponbare reference genome. We captured alternate assemblies that included heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes with 28,907 core-genes and 13,728 wild rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance gene analogs in wild rice compared to that in cultivars. Our analysis indicated that two cultivated subpopulations, intro-<i>indica </i>and <i>basmati</i> were generated through gene flows among cultivars in South Asia. We also provided strong evidence to support the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 SNPs and 13,853 PAVs differentiated between <i>indica</i> and <i>japonica</i>, which mainly be traced back to the divergence of their respective ancestors and a larger genetic bottleneck in <i>japonica</i>. This study provides reference resource for enhancing rice improvements and enriches our understanding of the origin and domestication process of rice.<br>

普通野生稻（Oryza rufipogon）是亚洲栽培稻（Oryza sativa）的祖先物种，亦是水稻遗传育种领域的重要种质资源。本研究构建了基于145份染色体级基因组组装体的野生稻与栽培稻泛基因组（pangenome），其中包含129份遗传多样性丰富的普通野生稻种质资源（accessions），以及16份多样性各异的亚洲栽培稻品种。该泛基因组包含3.87 Gb的新增序列，此类序列在粳稻（japonica）参考基因组日本晴（Nipponbare）中并未被收录。研究团队还获取了包含初级组装体中缺失的杂合信息的替代组装体，共鉴定得到69531个泛基因（pan-genes），其中包括28907个核心基因（core-genes）以及13728个野生稻特异性基因。相较于栽培稻，野生稻中的抗病基因类似物（resistance gene analogs）丰度更高、多样性也显著更强。分析结果显示，两个栽培稻亚群——籼稻（intro-indica）与巴斯马蒂稻（basmati）——均由南亚地区的栽培稻种群间的基因交流演化而来。本研究还提供了强有力的证据，支持所有亚洲栽培稻仅经历过一次独立驯化起源事件。此外，本研究共鉴定得到855122个单核苷酸多态性（Single Nucleotide Polymorphism，简称SNPs）以及13853个存在/缺失变异（Presence/Absence Variants，简称PAVs），此类变异可有效区分籼稻与粳稻，其成因主要可追溯至二者祖先类群的分化以及粳稻群体中更为严重的遗传瓶颈效应。本研究为水稻遗传改良提供了关键参考资源，同时也深化了我们对水稻起源与驯化过程的认知。