State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
Plant J. 2022 Aug;111(4):1032-1051. doi: 10.1111/tpj.15870. Epub 2022 Jun 30.
Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long-term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra-Geng subspecies remain largely unknown. Here, we identified MITOGEN-ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome-wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3 ) directly evolved from Chinese Oryza rufipogon III and was largely retained in high-latitude and high-altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP-776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9 ) promoter originated from novel variation of intra-Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3 to colder climatic conditions in high-latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3 and OsLEA9 enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold-adaptive differentiation of intra-Geng, but also provides new genetic resources for rice molecular breeding in low-temperature areas.
低温胁迫会严重影响水稻的生殖阶段和地理分布。在栽培稻的长期驯化过程中，粳/亚种逐渐比籼/亚种形成了更强的耐寒性。然而，粳亚种内的耐寒性的进化路径和自然等位基因在很大程度上仍然未知。在这里，我们通过转录组分析和全基因组关联研究，鉴定出 MITOGEN-ACTIVATED PROTEIN KINASE 3（OsMAPK3）和 LATE EMBRYOGENESIS ABUNDANT PROTEIN 9（OsLEA9）是粳亚种适应低温的两个重要调节因子。转基因验证表明，OsMAPK3 和 OsLEA9 在生殖阶段赋予了水稻耐寒性。选择和进化分析表明，粳稻的 OsMAPK3 （OsMAPK3）版本直接从中国普通野生稻 III 进化而来，并在驯化过程中主要保留在低温的高纬度和高海拔地区。后来，昆明小白谷和丽江小黑谷版本的 OsLEA9（OsLEA9）启动子中的功能核苷酸多态性（FNP-776）起源于粳亚种内的新变异，被选择并主要保留在温带粳亚种中，以与 OsMAPK3 一起提高粳亚种对高纬度地区较冷气候条件的适应能力。育种潜力分析表明，OsMAPK3 和 OsLEA9 的聚合增强了粳稻的耐寒性，并促进了栽培稻向寒冷地区的扩展。本研究不仅突出了粳亚种内耐寒性分化的进化路径，而且为低温地区水稻分子育种提供了新的遗传资源。
