title: A high-density SNP genotyping array for rice biology and molecular breeding.
abstract: A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecular breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the development of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for different objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.
authors.affiliation: Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Haodong
authors.initials: H
authors.lastname: Chen
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Huihui
authors.initials: H
authors.lastname: Yu
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Renbo
authors.initials: R
authors.lastname: Yu
authors.forename: Yue
authors.initials: Y
authors.lastname: Yao
authors.forename: Wenhui
authors.initials: W
authors.lastname: Zhang
authors.forename: Yuqing
authors.initials: Y
authors.lastname: He
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Tang
authors.forename: Fasong
authors.initials: F
authors.lastname: Zhou
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
keywords: array; molecular breeding.; rice; single nucleotide polymorphisms (SNPs)