Open AccessA whole‐genome SNP array ( RICE 6 K ) for genomic breeding in rice
Author(s) -
Yu Huihui,
Xie Weibo,
Li Jing,
Zhou Fasong,
Zhang Qifa
Publication year - 2014
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12113
Subject(s) - biology , indel , single nucleotide polymorphism , molecular breeding , germplasm , snp genotyping , genotyping , snp array , genetics , genome , snp , genomics , quantitative trait locus , genotype , microbiology and biotechnology , gene , botany
Summary The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics‐based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole‐genome single nucleotide polymorphism ( SNP ) array, RICE 6K, based on Infinium technology, using representative SNP s selected from more than four million SNP s identified from resequencing data of more than 500 rice landraces. RICE 6K contains 5102 SNP and insertion–deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty‐five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE 6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNP s per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE 6 K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE 6K provides an efficient and reliable genotyping tool for rice genomic breeding.