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,Xing Wang Deng,Qifa Zhang

doi:10.1093/mp/sst135

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.

Highlights

Rice (Oryza sativa L.) is one of the most important crops, supplying food for over half of the world’s population
For each selected candidate single nucleotide polymorphism (SNP), we analyzed its location and Minor Allele Frequencies (MAFs) to ensure that the final array was of high quality and could be widely used in diverse research and breeding programs
We generated a histogram of the inter-SNP spacing distribution for the RiceSNP50 array by mapping the SNPs onto the rice MSU6.1 genome assembly (Figure 1B), which shows that the average distance between adjacent SNPs is 7 kb, and the gaps between 76.6% of the SNPs are less than 10 kb

Summary

Introduction

Rice (Oryza sativa L.) is one of the most important crops, supplying food for over half of the world’s population. A genome-wide comparative study of intermediate-sized structural variation (SV) among rice (O. sativa) and three of its closest relatives in the Oryza genus uncovered many structural differences among the genomes of O. sativa and the wild relatives (Hurwitz et al, 2010). Several re-sequencing projects have provided a great deal of information about rice genomic structure and genetic diversity (Huang et al, 2010, 2012a, 2012b; Xu et al, 2012a). These sequencing projects found millions of polymorphisms along the entire rice genome, including several million SNPs

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Conclusion