College of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Corresponding authors.
Wensheng Wang
College of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; Corresponding authors.
Single nucleotide polymorphism (SNP) genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants. In this study, a high-quality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide, which was then tested extensively in 192 representative rice samples. Printed on the GeneTitan chips of Affymetrix Axiom each containing 56,606 SNP markers, the Rice3K56 array has a high genotyping reliability (99.6%), high and uniform genome coverage (an average of 6.7-kb between adjacent SNPs), abundant polymorphic information and easy automation, compared with previously developed rice SNP arrays. When applied in rice varietal differentiation, population diversity analysis, gene mapping of 13 complex traits by a genome-wide association study analysis (GWAS), and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations, these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.
