QTL Scanning for Rice Yield Using a Whole Genome SNP Array》.pdf

Available online at ScienceDirect JGG Journal of Genetics and Genomics 40 (2013) 629e638 ORIGINAL RESEARCH QTL Scanning for Rice Yield Using a Whole Genome SNP Array Cong Tan a,1, Zhongmin Han a,1, Huihui Yu b, Wei Zhan a, Weibo Xie a, Xun Chen a, Hu Zhao a, Fasong Zhou b, Yongzhong Xing a,* a National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China b Life Science and Technology Center, China National Seed Group Co., Ltd., Wuhan 430075, China Received 15 January 2013; revised 29 May 2013; accepted 20 June 2013 Available online 20 August 2013 ABSTRACT High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length of 1.1 cM per bin. Segregation distortions were observed in 24 regio