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Epistatic Association Mapping in Homozygous Crop Cultivars

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  • Hai-Yan Lü
  • Xiao-Fen Liu
  • Shi-Ping Wei
  • Yuan-Ming Zhang

Abstract

The genetic dissection of complex traits plays a crucial role in crop breeding. However, genetic analysis and crop breeding have heretofore been performed separately. In this study, we designed a new approach that integrates epistatic association analysis in crop cultivars with breeding by design. First, we proposed an epistatic association mapping (EAM) approach in homozygous crop cultivars. The phenotypic values of complex traits, along with molecular marker information, were used to perform EAM. In our EAM, all the main-effect quantitative trait loci (QTLs), environmental effects, QTL-by-environment interactions and QTL-by-QTL interactions were included in a full model and estimated by empirical Bayes approach. A series of Monte Carlo simulations was performed to confirm the reliability of the new method. Next, the information from all detected QTLs was used to mine novel alleles for each locus and to design elite cross combination. Finally, the new approach was adopted to dissect the genetic basis of seed length in 215 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 19 main-effect QTLs and 3 epistatic QTLs were identified, more than 10 novel alleles were mined and 3 elite parental combinations, such as Daqingdou and Zhengzhou790034, were predicted.

Suggested Citation

  • Hai-Yan Lü & Xiao-Fen Liu & Shi-Ping Wei & Yuan-Ming Zhang, 2011. "Epistatic Association Mapping in Homozygous Crop Cultivars," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-10, March.
    • Handle: RePEc:plo:pone00:0017773
    DOI: 10.1371/journal.pone.0017773
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    References listed on IDEAS

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    1. Clive J Hoggart & John C Whittaker & Maria De Iorio & David J Balding, 2008. "Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies," PLOS Genetics, Public Library of Science, vol. 4(7), pages 1-8, July.
    2. Shizhong Xu, 2007. "An Empirical Bayes Method for Estimating Epistatic Effects of Quantitative Trait Loci," Biometrics, The International Biometric Society, vol. 63(2), pages 513-521, June.
    3. A. Sasaki & M. Ashikari & M. Ueguchi-Tanaka & H. Itoh & A. Nishimura & D. Swapan & K. Ishiyama & T. Saito & M. Kobayashi & G. S. Khush & H. Kitano & M. Matsuoka, 2002. "A mutant gibberellin-synthesis gene in rice," Nature, Nature, vol. 416(6882), pages 701-702, April.
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    Cited by:

    1. Cox Lwaka Tamba & Yuan-Li Ni & Yuan-Ming Zhang, 2017. "Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-20, January.
    2. Su Hong Bu & Zhao Xinwang & Can Yi & Jia Wen & Tu Jinxing & Yuan Ming Zhang, 2015. "Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-18, March.

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