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QTL scanning for rice yield using a whole genome SNP array.

Cong Tan1, Zhongmin Han1, Huihui Yu2

  • 1National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.

Journal of Genetics and Genomics = Yi Chuan Xue Bao
|January 1, 2014
PubMed
Summary

High-throughput SNP genotyping using the RICE6K array identified 3324 markers and 23 yield QTLs in a rice recombinant inbred line (RIL) population. Favorable alleles for breeding are present in both parents, suggesting pyramiding can develop elite lines.

Keywords:
Bin mapQTLRICE6K SNP arrayRILsSegregation distortion

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Area of Science:

  • Plant genetics
  • Genomics
  • Molecular breeding

Background:

  • High-throughput SNP genotyping is crucial for plant genetic studies and breeding.
  • The RICE6K SNP array, utilizing Illumina Bead Array and Infinium technology, enables genome-wide allelic variation analysis.

Purpose of the Study:

  • To genotype a rice recombinant inbred line (RIL) population using the RICE6K SNP array.
  • To construct a high-density genetic map and identify quantitative trait loci (QTLs) for yield.

Main Methods:

  • Genotyping of a RIL population derived from an indica x japonica cross using the RICE6K SNP array.
  • Development of a high-density genetic map comprising 1495 recombination bins.
  • Identification of QTLs for yield using the high-throughput SNP genotyping data.

Main Results:

  • 3324 high-quality SNP markers were identified and grouped into 1495 bins.
  • A genetic map spanning 1591.2 cM was constructed with an average bin length of 1.1 cM.
  • 23 yield QTLs were identified, with 7 novel QTLs detected. Segregation distortion was observed in 24 regions.

Conclusions:

  • Favorable alleles for yield are distributed between the indica (Zhenshan 97) and japonica (Xizang 2) parents.
  • Pyramiding favorable alleles from both parents is a viable strategy for developing elite rice lines.
  • The study discusses the optimal mapping population size for QTL analysis with high-throughput SNP platforms.