Multilocus tetrasomic linkage analysis using hidden Markov chain model

The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically import...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2010-03, Vol.107 (9), p.4270-4274
Main Authors: Leach, Lindsey J, Wang, Lin, Kearsey, Michael J, Luo, Zewei
Format: Article
Language:English
Subjects:
Algorithms
Biological Evolution
Biological Sciences
Cell division
Chromosomes
Deoxyribonucleic acid
Diploidy
DNA
Genetic Linkage
Genetic loci
Genetic mapping
Genetic Markers
Genomics
Genotype
Genotypes
Human genetics
Likelihood Functions
Markov analysis
Markov Chains
Modeling
Models, Theoretical
Parametric models
Phenotypes
Ploidies
Potatoes
Tetrasomics
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Summary:The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically important species are autopolyploids, with autotetraploidy being a typical example. These species undergo much more complicated chromosomal segregation and recombination at meiosis than diploids. In addition, there is evidence of polyploidy-induced and highly dynamic changes in the structure of the genome. These polysomic characteristics indicate the inappropriateness of the theory and methods of linkage analysis in diploids for use in these species and a gap in the theory and methodology of tetraploid map construction. This paper presents a theoretical model and statistical framework for multilocus linkage analysis in autotetraploids for use with dominant and/or codominant DNA molecular markers. The theory and methods incorporate the essential features of allele segregation and recombination under tetrasomic inheritance and the major challenges in statistical modeling and marker data analysis. We validated the method and explored its statistical properties by intensive simulation study and demonstrated its utility by analysis of AFLP and SSR marker data from an outbred autotetraploid potato population.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0908477107