Computationally efficient map construction in the presence of segregation distortion

Shah, Rohan, Cavanagh, Colin R. and Huang, B. Emma (2014) Computationally efficient map construction in the presence of segregation distortion. Theoretical and Applied Genetics, 127 12: 2585-2597. doi:10.1007/s00122-014-2401-0


Author Shah, Rohan
Cavanagh, Colin R.
Huang, B. Emma
Title Computationally efficient map construction in the presence of segregation distortion
Journal name Theoretical and Applied Genetics   Check publisher's open access policy
ISSN 0040-5752
1432-2242
Publication date 2014-09-27
Year available 2014
Sub-type Article (original research)
DOI 10.1007/s00122-014-2401-0
Open Access Status
Volume 127
Issue 12
Start page 2585
End page 2597
Total pages 13
Place of publication Heidelberg Germany
Publisher Springer
Collection year 2015
Language eng
Formatted abstract
Key message

We present a novel estimator for map construction in the presence of segregation distortion which is highly computationally efficient. For multi-parental designs this estimator outperforms methods that do not account for segregation distortion, at no extra computational cost.

Abstract

Inclusion of genetic markers exhibiting segregation distortion in a linkage map can result in biased estimates of genetic distance and distortion of map positions. Removal of distorted markers is hence a typical filtering criterion; however, this may result in exclusion of biologically interesting regions of the genome such as introgressions and translocations. Estimation of additional parameters characterizing the distortion is computationally slow, as it relies on estimation via the Expectation Maximization algorithm or a higher dimensional numerical optimisation. We propose a robust M-estimator (RM) capable of handling tens of thousands of distorted markers from a single linkage group. We show via simulation that for multi-parental designs the RM estimator can perform much better than uncorrected estimation, at no extra computational cost. We then apply the RM estimator to chromosome 2B in wheat in a multi-parent population segregating for the Sr36 introgression, a known transmission distorter. The resulting map contains over 700 markers, and is consistent with maps constructed from crosses which do not exhibit segregation distortion.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Mathematics and Physics
Official 2015 Collection
 
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