Multilocus genomics of outcrossing plant populations

Wei Hou, Tian Liu, Yao Li, Qin Li, Jiahan Li, Kiranmoy Das, Arthur Berg and Rongling Wu

Theoretical Population Biology, 2009, vol. 76, issue 1, 68-76

Abstract: The structure and organization of natural plant populations can be understood by estimating the genetic parameters related to mating behavior, recombination frequency, and gene associations with DNA-based markers typed throughout the genome. We developed a statistical and computational model for estimating and testing these parameters from multilocus data collected in a natural population. This model, constructed by a maximum likelihood approach and implemented within the EM algorithm, is shown to be robust for simultaneously estimating the outcrossing rate, recombination frequencies and linkage disequilibria. The algorithm built with three or more markers allows the characterization of crossover interference in meiosis and high-order disequilibria among different genes, thus providing a powerful tool for illustrating a detailed picture of genetic diversity and organization in natural populations. Computer simulations demonstrate the statistical properties of the proposed model. This multilocus model will be useful for studying the pattern and amount of genetic variation within and among populations to further infer the evolutionary history of a plant species.

Keywords: Recombination frequency; Linkage disequilibrium; Outcrossing rate; Open-pollinated population; EM algorithm (search for similar items in EconPapers)
Date: 2009
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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:76:y:2009:i:1:p:68-76

DOI: 10.1016/j.tpb.2009.04.005

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