The male sterility (MS) line is a prerequisite for efficient production of hybrid seeds in rice, a self-pollinating species. MS line breeding is pivotal for hybrid rice improvement. Understanding the historical breeding trajectory will help to improve hybrid rice breeding strategies. Maternally inherited cytoplasm is an appropriate tool for phylogenetic reconstruction and pedigree tracing in rice hybrids. In this study, we analyzed the cytoplasmic genomes of 1495 elite hybrid rice varieties and identified five major types of cytoplasm, which correspond to different hybrid production systems. As the cytoplasm donors for hybrids, 461 MS lines were also divided into five major types based on cytoplasmic and nuclear genomic architecture. Specific core accessions cooperating with different fertility-associated genes drove the sequence divergence of MS lines. Dozens to hundreds of convergent and divergent selective sweeps spanning several agronomic trait-associated genes were identified among different types of MS lines. We further analyzed the cross patterns between different types of MS lines and their corresponding restorers. This study systematically analyzed the cytoplasmic genomes of rice hybrids revealed their relationships with nuclear genomes of MS lines, and illustrated the trajectory of hybrid rice breeding and the strategies for breeding different types of MS lines providing new insights for future improvement of hybrid rice.

雄性不育 (MS) 系是在自花授粉物种水稻中高效生产杂交种子的先决条件。MS系选育是杂交水稻改良的关键。了解历史育种轨迹将有助于改进杂交水稻育种策略。母系遗传的细胞质是水稻杂交种系统发育重建和谱系追踪的合适工具。在这项研究中，我们分析了 1495 个杂交水稻优良品种的细胞质基因组，并确定了五种主要类型的细胞质，它们对应于不同的杂交生产系统。作为杂种的细胞质供体，461个MS系也根据细胞质和核基因组结构分为五种主要类型。与不同生育力相关基因合作的特定核心加入推动了 MS 系的序列分歧。在不同类型的 MS 品系中鉴定了数十到数百个跨越几个农艺性状相关基因的收敛和发散选择性扫描。我们进一步分析了不同类型的 MS 系及其相应的恢复系之间的交叉模式。本研究系统分析了水稻杂交种的细胞质基因组，揭示了它们与MS系核基因组的关系，阐明了杂交水稻育种的轨迹和培育不同类型MS系的策略，为未来杂交水稻的改良提供了新的思路。在不同类型的 MS 品系中鉴定了数十到数百个跨越几个农艺性状相关基因的收敛和发散选择性扫描。我们进一步分析了不同类型的 MS 系及其相应的恢复系之间的交叉模式。本研究系统分析了水稻杂交种的细胞质基因组，揭示了它们与MS系核基因组的关系，阐明了杂交水稻育种的轨迹和培育不同类型MS系的策略，为未来杂交水稻的改良提供了新的思路。在不同类型的 MS 品系中鉴定了数十到数百个跨越几个农艺性状相关基因的收敛和发散选择性扫描。我们进一步分析了不同类型的 MS 系及其相应的恢复系之间的交叉模式。本研究系统分析了水稻杂交种的细胞质基因组，揭示了它们与MS系核基因组的关系，阐明了杂交水稻育种的轨迹和培育不同类型MS系的策略，为未来杂交水稻的改良提供了新的思路。