A general framework for statistical linkage analysis in multivalent tetraploids

Rongling Wu, Chang Xing Ma

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

In multivalent polyploids, simultaneous pairings among homologous chromosomes at meiosis result in a unique cytological phenomenon-double reduction. Double reduction casts an impact on chromosome evolution in higher plants, but because of its confounded effect on the pattern of gene cosegregation, it complicates linkage analysis and map construction with polymorphic molecular markers. In this article, we have proposed a general statistical model for simultaneously estimating the frequencies of double reduction, the recombination fraction, and optimal parental linkage phases between any types of markers, both fully and partially informative, or dominant and codominant, for a tetraploid species that undergoes only multivalent pairing. This model provides an in-depth extension of our earlier linkage model that was built upon Fisher's classifications for different gamete formation modes during the polysomic inheritance of a multivalent polyploid. By implementing a two-stage hierarchical EM algorithm, we derived a closed-form solution for estimating the frequencies of double reduction through the estimation of gamete mode frequencies and the recombination fraction. We performed different settings of simulation studies to demonstrate the statistical properties of our model for estimating and testing double reduction and the linkage in multivalent tetraploids. As shown by a comparative analysis, our model provides a general framework that covers existing statistical approaches for linkage mapping in polyploids that are predominantly multivalent. The model will have great implications for understanding the genome structure and organization of polyploid species.

Original languageEnglish (US)
Pages (from-to)899-907
Number of pages9
JournalGenetics
Volume170
Issue number2
DOIs
StatePublished - Jun 1 2005

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Polyploidy
Tetraploidy
Germ Cells
Genetic Recombination
Chromosomes
Chromosome Mapping
Meiosis
Statistical Models
Genome
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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A general framework for statistical linkage analysis in multivalent tetraploids. / Wu, Rongling; Ma, Chang Xing.

In: Genetics, Vol. 170, No. 2, 01.06.2005, p. 899-907.

Research output: Contribution to journalArticle

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