Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.
Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and 0-diversity genes during breeding. Using pedigree information, we also traced SNP transmission patterns and observed breeding signatures in pedigree. These regions included the larger number of key well-known functional genes. Besides, 35 regions spanning 0.16% of the rice gnome had been differentially selected between conventional and restorer pedigrees. These genes identified here will be useful to the further pedigree breeding. Our study provides insights into the genetic basis of backbone varieties and will have immediate implications for performing genome-wide breeding by design.
State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, P.R. China.
Xingfei
X
Zheng
Hunan Provincial Key Laboratory for Biology and Control of Plant Disease and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, P.R. China.
Lanzhi
L
Li
Nextomics Biosciences, Wuhan, 430075, P.R. China.
Fan
F
Liang
State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, P.R. China.
Changjun
C
Tan
Agricultural College of Yangzhou University, Yangzhou, 225009, P.R. China.
Shuzhu
S
Tang
College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
Sibin
S
Yu
State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, P.R. China.
Ying
Y
Diao
Rice Institute, Sichuan Agricultural University, Chengdou, 611130, China. lisc926105@163.com.
Shuangcheng
S
Li
State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, P.R. China. huzhongli@whu.edu.cn.
Zhongli
Z
Hu
D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D012275:Oryza / Q000145:classification* / Q000235:genetics*; D010375:Pedigree; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA