These authors contributed equally to this work.
A whole-genome SNP array (RICE6K) for genomic breeding in rice
Article first published online: 13 SEP 2013
© 2013 China National Seed Group Co. Ltd. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
Plant Biotechnology Journal
Volume 12, Issue 1, pages 28–37, January 2014
How to Cite
2013) A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol. J., doi: 10.1111/pbi.12113, , , and (
The authors H. Yu, J. Li and F. Zhou have commercial interest in RICE6K as employees of China National Seed Group Co., Ltd.
- Issue published online: 26 DEC 2013
- Article first published online: 13 SEP 2013
- Manuscript Accepted: 30 JUL 2013
- Manuscript Revised: 25 JUL 2013
- Manuscript Received: 26 JUN 2013
- Introduction of International Advanced Agricultural Science and Technology Program of China. Grant Number: 2012-G2
- National High Technology Research and Development Program of China. Grant Number: 2012AA10A304
- National Natural Science Foundation of China. Grant Number: 31100962
- Doctoral Program of Higher Education of China. Grant Number: 20110146120013
- SNP chip;
- genomic breeding;
- functional markers;
- rice (Oryza sativa L.)
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, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K 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 RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs 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 RICE6K 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 RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding.