QTL Scanning for Rice Yield Using a Whole Genome SNP Array

Cong Tan; Zhongmin Han; Huihui Yu; Wei Zhan; Weibo Xie; Xun Chen; Hu Zhao; Fasong Zhou; Yongzhong Xing

doi:10.1016/j.jgg.2013.06.009

Volume 40 Issue 12

Dec. 2013

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QTL Scanning for Rice Yield Using a Whole Genome SNP Array

doi: 10.1016/j.jgg.2013.06.009

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

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Corresponding author: E-mail address: yzhxing@hotmail.com (Yongzhong Xing)
Received Date: 2013-01-15
Accepted Date: 2013-06-20
Rev Recd Date: 2013-05-29

Available Online: 2013-08-20

Publish Date: 2013-12-20

Abstract

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 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.
- RILs,
- RICE6K SNP array,
- Bin map,
- Segregation distortion,
- QTL

These authors contribute equally to the work.

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References(67)

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