Phenomics-assisted genetic dissection and molecular design of drought resistance in rice

Qiaojun Lou; Yunyu Chen; Xin Wang; Yulu Zhang; Tingting Gao; Jiawei Shi; Ming Yan; Fangjun Feng; Kai Xu; Feng Lin; Shangyuan Xie; Xiaoyan Xi; Weikun Li; Yuanyuan Nie; Huan Gao; Hui Xia; Lei Wang; Tiemei Li; Shoujun Chen; Ying Zhu; Jianwei Zhang; Hanwei Mei; Liang Chen; Wanneng Yang; Lijun Luo

doi:10.1016/j.xplc.2024.101218

Phenomics-assisted genetic dissection and molecular design of drought resistance in rice

Plant Commun. 2024 Dec 6:101218. doi: 10.1016/j.xplc.2024.101218. Online ahead of print.

Authors

Qiaojun Lou¹, Yunyu Chen², Xin Wang³, Yulu Zhang², Tingting Gao², Jiawei Shi², Ming Yan⁴, Fangjun Feng⁴, Kai Xu⁴, Feng Lin⁵, Shangyuan Xie², Xiaoyan Xi², Weikun Li², Yuanyuan Nie⁶, Huan Gao⁴, Hui Xia⁴, Lei Wang⁴, Tiemei Li⁴, Shoujun Chen⁴, Ying Zhu⁷, Jianwei Zhang², Hanwei Mei⁴, Liang Chen⁸, Wanneng Yang⁹, Lijun Luo¹⁰

Affiliations

¹ 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.
² National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
³ Shanghai Agrobiological Gene Center, 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.
⁴ Shanghai Agrobiological Gene Center, Shanghai 201106, China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China.
⁵ Zhejiang University, Hangzhou 310058, China.
⁶ Jiangxi Research and Development Center of Super Rice, Nanchang Branch of Chinese National Center for Rice Improvement, Nanchang 330200, China.
⁷ 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.
⁸ Shanghai Agrobiological Gene Center, Shanghai 201106, China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China. Electronic address: cl@sagc.org.cn.
⁹ National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: ywn@mail.hzau.edu.cn.
¹⁰ Shanghai Agrobiological Gene Center, Shanghai 201106, China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China. Electronic address: lijun@sagc.org.cn.

PMID: 39645582
DOI: 10.1016/j.xplc.2024.101218

Abstract

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 (F₈, 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.

Keywords: QTLs; de novo drought-resistant rice genomes; drought resistance; high-throughput phenomics; molecular design; multimodal camera; quantitative trait loci; whole-plant image traits.