Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

Hua Zhang; Qiang Zhao; Zhi-Zhong Sun; Chang-Quan Zhang; Qi Feng; Shu-Zhu Tang; Guo-Hua Liang; Ming-Hong Gu; Bin Han; Qiao-Quan Liu

doi:10.1016/j.jgg.2011.11.004

Volume 38 Issue 12

Dec. 2011

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Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

doi: 10.1016/j.jgg.2011.11.004

Hua Zhang^{a, #},
Qiang Zhao^{b, #},
Zhi-Zhong Sun^a,
Chang-Quan Zhang^a,
Qi Feng^{b, c},
Shu-Zhu Tang^{a, c},
Guo-Hua Liang^{a, c},
Ming-Hong Gu^{a, c},
Bin Han^{b, c},
Qiao-Quan Liu^{a, c}

a
Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou 225009, China
b
National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
c
National Center for Plant Gene Research (Shanghai), Shanghai 200032, China

More Information

Corresponding author: E-mail address: qqliu@yzu.edu.cn (Qiao-Quan Liu)
Received Date: 2011-07-30
Accepted Date: 2011-11-15
Rev Recd Date: 2011-11-06

Available Online: 2011-11-26

Publish Date: 2011-12-20

Abstract

Abstract

Chromosome segment substitution lines (CSSLs) are useful for the precise mapping of quantitative trait loci (QTLs) and dissection of the genetic basis of complex traits. In this study, two whole-genome sequenced rice cultivars, the japonica Nipponbare and indica 9311 were used as recipient and donor, respectively. A population with 57 CSSLs was developed after crossing and back-crossing assisted by molecular markers, and genotypes were identified using a high-throughput resequencing strategy. Detailed graphical genotypes of 38 lines were constructed based on resequencing data. These CSSLs had a total of 95 substituted segments derived fromindica 9311, with an average of about 2.5 segments per CSSL and eight segments per chromosome, and covered about 87.4% of the rice whole genome. A multiple linear regression QTL analysis mapped four QTLs for 1000-grain weight. The largest-effect QTL was located in a region on chromosome 5 that contained a cloned major QTL GW5/qSW5 for grain size in rice. These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice, and offer ideal materials and foundations for japonica breeding.
- Chromosome segment substitution lines (CSSLs),
- Molecular marker-assisted selection,
- High-throughput resequencing

These authors contributed equally to this work.

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References(33)

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