Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.
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.
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang Province, China.
Zhen-Yu
ZY
Gao
Shan-Cen
SC
Zhao
Wei-Ming
WM
He
Long-Biao
LB
Guo
You-Lin
YL
Peng
Jin-Jin
JJ
Wang
Xiao-Sen
XS
Guo
Xue-Mei
XM
Zhang
Yu-Chun
YC
Rao
Chi
C
Zhang
Guo-Jun
GJ
Dong
Feng-Ya
FY
Zheng
Chang-Xin
CX
Lu
Jiang
J
Hu
Qing
Q
Zhou
Hui-Juan
HJ
Liu
Hai-Yang
HY
Wu
Jie
J
Xu
Pei-Xiang
PX
Ni
Da-Li
DL
Zeng
Deng-Hui
DH
Liu
Peng
P
Tian
Li-Hui
LH
Gong
Chen
C
Ye
Guang-Heng
GH
Zhang
Jian
J
Wang
Fu-Kuan
FK
Tian
Da-Wei
DW
Xue
Yi
Y
Liao
Li
L
Zhu
Ming-Sheng
MS
Chen
Jia-Yang
JY
Li
Shi-Hua
SH
Cheng
Geng-Yun
GY
Zhang
Jun
J
Wang
Qian
Q
Qian
D008040:Genetic Linkage; D018745:Genome, Plant; D006824:Hybridization, Genetic; D012275:Oryza / Q000235:genetics*; D040641:Quantitative Trait Loci; D011995:Recombination, Genetic
Oryza sativa; QTL dissection; genome sequence update