Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice(Oryza sativa L.)  

作　　者：Chaopu Zhang Min Li Lunping Liang Jun Xiang Fan Zhang Chenyang Zhang Yizhen Li Jing Liang Tianqing Zheng Fanlin Zhang Hua Li Binying Fu Yingyao Shi Jianlong Xu Bingchuan Tian Zhikang Li Wensheng Wang 

机构地区：[1]College of Agronomy,Anhui Agricultural University,Hefei 230036,Anhui,China [2]Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China [3]National Nanfan Research Institute(Sanya),Chinese Academy of Agricultural Sciences,Sanya 572024,Hainan,China [4]Higentec Co.,Ltd.,Changsha 410000,Hunan,China

出　　处：《The Crop Journal》2023年第3期800-807,共8页作物学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(31971927 and U21A20214);the Science and Technology Major Project of Anhui Province(2021d06050002);the Improved Varieties Joint Research(Rice)Project of Anhui Province(the 14th five-year plan);the National Key Research and Development Program of China(2020YFE0202300);the CAAS Innovative Team Award;the Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City(B21HJ0215,B21HJ0223,and B21HJ0508);Nanfan Special Project,CAAS(YBXM04)。

摘　　要：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 highquality 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 Gene Titan 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.

关 键 词：Rice3K56 SNP array GENOTYPING Genetic analysis Molecular breeding 

分 类 号：S511[农业科学—作物学]