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Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.


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.

SUBMITTER: Gao ZY 

PROVIDER: S-EPMC3761582 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.

Gao Zhen-Yu ZY   Zhao Shan-Cen SC   He Wei-Ming WM   Guo Long-Biao LB   Peng You-Lin YL   Wang Jin-Jin JJ   Guo Xiao-Sen XS   Zhang Xue-Mei XM   Rao Yu-Chun YC   Zhang Chi C   Dong Guo-Jun GJ   Zheng Feng-Ya FY   Lu Chang-Xin CX   Hu Jiang J   Zhou Qing Q   Liu Hui-Juan HJ   Wu Hai-Yang HY   Xu Jie J   Ni Pei-Xiang PX   Zeng Da-Li DL   Liu Deng-Hui DH   Tian Peng P   Gong Li-Hui LH   Ye Chen C   Zhang Guang-Heng GH   Wang Jian J   Tian Fu-Kuan FK   Xue Da-Wei DW   Liao Yi Y   Zhu Li L   Chen Ming-Sheng MS   Li Jia-Yang JY   Cheng Shi-Hua SH   Zhang Geng-Yun GY   Wang Jun J   Qian Qian Q  

Proceedings of the National Academy of Sciences of the United States of America 20130812 35


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 gen  ...[more]

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