title: Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing.
abstract: A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing. Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 "high quality" SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.
authors.affiliation: Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Haodong
authors.initials: H
authors.lastname: Chen
authors.forename: Tianqing
authors.initials: T
authors.lastname: Zheng
authors.forename: Renbo
authors.initials: R
authors.lastname: Yu
authors.forename: William Bryan
authors.initials: WB
authors.lastname: Terzaghi
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
authors.forename: Jianlong
authors.initials: J
authors.lastname: Xu
authors.forename: Hang
authors.initials: H
authors.lastname: He
mesh_terms: D017343:Genes, Plant; D008040:Genetic Linkage; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci