Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines.
Mapping chromosome regions responsible for quantitative phenotypic variation in recombinant populations provides an effective means to characterize the genetic basis of complex traits. We conducted a quantitative trait loci (QTL) analysis of 150 rice recombinant inbred lines (RILs) derived from a cross between two cultivars, Oryza sativa ssp. indica cv. 93-11 and Oryza sativa ssp. japonica cv. Nipponbare. The RILs were genotyped through next-generation sequencing, which accurately determined the recombination breakpoints and provided a new type of genetic markers, recombination bins, for QTL analysis. We detected 49 QTL with phenotypic effect ranging from 3.2 to 46.0% for 14 agronomics traits. Five QTL of relatively large effect (14.6-46.0%) were located on small genomic regions, where strong candidate genes were found. The analysis using sequencing-based genotyping thus offers a powerful solution to map QTL with high resolution. Moreover, the RILs developed in this study serve as an excellent system for mapping and studying genetic basis of agricultural and biological traits of rice.
Wang
Lu
L
National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.
Wang
Ahong
A
Huang
Xuehui
X
Zhao
Qiang
Q
Dong
Guojun
G
Qian
Qian
Q
Sang
Tao
T
Han
Bin
B
D002681:China; D002874:Chromosome Mapping / Q000379:methods*; D018556:Crops, Agricultural / Q000235:genetics; D003433:Crosses, Genetic; D017343:Genes, Plant; D005819:Genetic Markers; D056626:Inflorescence / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D018520:Plant Shoots / Q000235:genetics; D040641:Quantitative Trait Loci; D011995:Recombination, Genetic; D012639:Seeds / Q000235:genetics
D005819:Genetic Markers