Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences
Zhen-Yu Gao, Shan-Cen Zhao, Wei-Ming He, Long-Biao Guo, You-Lin Peng, Jin-Jin Wang, Xiao-Sen Guo, Xue-Mei Zhang, Yu-Chun Rao, Chi Zhang, Guo-Jun Dong, Feng-Ya Zheng, Chang-Xin Lu, Jiang Hu, Qing Zhou, Hui-Juan Liu, Hai-Yang Wu, Jie Xu, Pei-Xiang Ni, Da-Li Zeng, Deng-Hui Liu, Peng Tian, Li-Hui Gong, Chen Ye, Guang-Heng Zhang, Jian Wang, Fu-Kuan Tian, Da-Wei Xue, Yi Liao, Li Zhu, Ming-Sheng Chen, Jia-Yang Li, Shi-Hua Cheng, Geng-Yun Zhang, Jun Wang, and Qian Qian
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang Province,China
Abstract: The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang-You-Pei-Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93-11 and maternal cultivar PA64s of Liang-You-Pei-Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice.
Keywords: Oryza sativa;QTL dissection;genome sequence update