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A model for linkage analysis with apomixis

Theoretical and Applied Genetics volume 123, pages 681–691 (2011)Cite this article

Abstract

Apomixis, or asexual reproduction through seeds, occurs in over 400 species of angiosperms. Although apomixis can favorably perpetuate desired genotypes through successive seed generation, it may also bring about some difficulty for linkage analysis and quantitative trait locus mapping. In this article, we explore the issue of how apomixis affects the precision and power of linkage analysis with molecular markers. We derive a statistical model for estimating the linkage between different markers when some progeny are derived from apomixis. The model was constructed within the maximum likelihood framework and implemented with the EM algorithm. A series of procedures are formulated to test the linkage of markers, the rate of apomixis, and the degree of genetic interference during meiosis. The model was examined and validated through simulation studies. The model will provide a tool for linkage mapping and evolutionary studies for plant species that undergo apomixis.

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Acknowledgments

This work is partially supported by an Open Fund 200602 from former Zhejiang Forestry University, a grant 30771752 from the NSF of China, NSF/IOS-0923975, Changjiang Scholars Award, and “Thousand-person Plan” Award.

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Affiliations

  1. Department of Biostatistics, University of Florida, Gainesville, FL, 32611, USA

    Wei Hou

  2. The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Lin’an, 311300, Zhejiang, China

    Shen Lin & Yanru Zeng

  3. Department of Statistics, West Virginia University, Morgantown, WV, 26506, USA

    Yao Li

  4. Center for Computational Biology, Beijing Forestry University, Beijing, 100083, China

    Xiaoming Pang & Rongling Wu

  5. National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, China

    Xiaoming Pang & Rongling Wu

  6. Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, 100083, China

    Xiaoming Pang & Rongling Wu

Authors
  1. Wei Hou
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  2. Shen Lin
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  3. Yao Li
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  4. Xiaoming Pang
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  5. Yanru Zeng
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  6. Rongling Wu
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Corresponding authors

Correspondence to Yanru Zeng or Rongling Wu.

Additional information

W. Hou and S. Lin contributed equally to this work.

Communicated by M. Sillanpaa.

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Hou, W., Lin, S., Li, Y. et al. A model for linkage analysis with apomixis. Theor Appl Genet 123, 681–691 (2011). https://doi.org/10.1007/s00122-011-1618-4

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  • DOI: https://doi.org/10.1007/s00122-011-1618-4

Keywords

  • Linkage Analysis
  • Recombination Fraction
  • Progeny Genotype
  • Genetic Interference
  • Linkage Detection