A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

Haodong Chen, Weibo Xie, Hang He, Huihui Yu, Wei Chen, Jing Li, Renbo Yu, Yue Yao, Wenhui Zhang, Yuqing He, Xiaoyan Tang, Fasong Zhou (+2 others)
2014 Molecular Plant  
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
more » ... ata 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. . (2012). SNP discovery and development of a high-density genotyping array for sunflower. PLoS One. 7, e29814.
doi:10.1093/mp/sst135 pmid:24121292 fatcat:v532l6lbyjanhojyshlxubg7mi