Lou Qiaojun, Chen Yunyu, Wang Xin, Zhang Yulu, Gao Tingting, Shi Jiawei, Yan Ming, Feng Fangjun, Xu Kai, Lin Feng, Xie Shangyuan, Xi Xiaoyan, Nie Yuanyuan, Gao Huan, Xia Hui, Wang Lei, Li Tiemei, Chen Shoujun, Zhu Ying, Zhang Jianwei, Mei Hanwei, Chen Liang, Yang Wanneng, Luo Lijun
Shanghai Agrobiological Gene Center, Shanghai 201106, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China.
National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
Plant Commun. 2025 Mar 10;6(3):101218. doi: 10.1016/j.xplc.2024.101218. Epub 2024 Dec 6.
Dissecting the mechanism of drought resistance (DR) and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change. Here, we selected a typical drought-avoidant (DA) variety, IRAT109, and a drought-tolerant (DT) variety, Hanhui15, as parents to develop a stable recombinant inbred line (RIL) population (F, 1262 lines). The de novo assembled genomes of both parents were released. By resequencing of the RIL population, a set of 1 189 216 reliable SNPs were obtained and used to construct a dense genetic map. Using above- and belowground phenomic platforms and multimodal cameras, we captured 139 040 image-based traits (i-traits) of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32 586 drought-responsive quantitative trait loci (QTLs), including 2097 unique QTLs. QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8, and QTLs associated with leaf i-traits occurred more than 800 times on the 5' end of chromosome 3, indicating the potential effects of these QTLs on plant phenotypes. We selected three candidate genes (OsMADS50, OsGhd8, OsSAUR11) related to leaf, panicle, and root traits, respectively, and verified their functions in DR. OsMADS50 was found to negatively regulate DR by modulating leaf dehydration, grain size, and downward root growth. A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments, and the composite QTL regions showed substantial overlap (76.9%) with known DR gene regions. Based on three candidate DR genes, we proposed a haplotype design suitable for different environments and breeding objectives. This study provides a valuable reference for multimodal and time-series phenomic analyses, deciphers the genetic mechanisms of DA and DT rice varieties, and offers a molecular navigation map for breeding of DR varieties.
剖析水稻抗旱机制并设计抗旱品种是应对气候变化挑战的有效策略。在此，我们选择了典型的避旱品种IRAT109和耐旱品种旱恢15作为亲本，构建了一个稳定的重组自交系群体（F，1262个株系）。公布了两个亲本的从头组装基因组。通过对重组自交系群体进行重测序，获得了一组1189216个可靠的单核苷酸多态性（SNP），并用于构建高密度遗传图谱。利用地上和地下表型平台以及多模态相机，我们在水稻整个生育期捕获了139040个基于图像的全株表型性状（i-性状），以响应干旱胁迫，并鉴定出32586个干旱响应数量性状位点（QTL），其中包括2097个独特的QTL。与穗部i-性状相关的QTL在第8号染色体中部出现超过600次，与叶片i-性状相关的QTL在第3号染色体5'端出现超过800次，表明这些QTL对植物表型具有潜在影响。我们分别选择了与叶片、穗部和根系性状相关的三个候选基因（OsMADS50、OsGhd8、OsSAUR11），并验证了它们在抗旱中的功能。发现OsMADS50通过调节叶片脱水、粒型和根系向下生长来负调控抗旱性。在田间试验干旱条件下，还从重组自交系群体的597个株系中筛选出18个和21个分别与粒重和植株生物量显著相关的复合QTL，这些复合QTL区域与已知的抗旱基因区域有大量重叠（76.9%）。基于三个候选抗旱基因，我们提出了适合不同环境和育种目标的单倍型设计。本研究为多模态和时间序列表型分析提供了有价值的参考资料，解析了避旱和耐旱水稻品种的遗传机制，并为抗旱品种的选育提供了分子导航图。
