An EM algorithm for mapping segregation distortion loci.
BACKGROUND
Chromosomal region that causes distorted segregation ratios is referred to as segregation distortion locus (SDL). The distortion is caused either by differential representation of SDL genotypes in gametes before fertilization or by viability differences of SDL genotypes after fertilization but before genotype scoring. In both cases, observable phenotypes are distorted for marker loci in the chromosomal region close to the SDL. Under the quantitative genetics model for viability selection by proposing a continuous liability controlling the viability of individual, a simplex algorithm has been used to search for the solution in SDL mapping. However, they did not consider the effects of SDL on the construction of linkage maps.


RESULTS
We proposed a multipoint maximum-likelihood method to estimate the position and the effects of SDL under the liability model together with both selection coefficients of marker genotypes and recombination fractions. The method was implemented via an expectation and maximization (EM) algorithm. The superiority of the method proposed under the liability model over the previous methods was verified by a series of Monte Carlo simulation experiments, together with a working example derived from the MAPMAKER/QTL software.


CONCLUSIONS
Our results suggested that the new method can serve as a powerful alternative to existing methods for SDL mapping. Under the liability model, the new method can simultaneously estimate the position and the effects of SDL as well as the recombinant fractions between adjacent markers, and also be used to probe into the genetic mechanism for the bias of uncorrected map distance and to elucidate the relationship between the viability selection and genetic linkage.
Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China. cszhu@ksu.edu
Chengsong
C
Zhu
Yuan-Ming
YM
Zhang
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods* / Q000706:statistics & numerical data; D020090:Chromosome Segregation / Q000235:genetics*; D008040:Genetic Linkage; D005838:Genotype; D018551:Solanum lycopersicum / Q000235:genetics; D008957:Models, Genetic; D009010:Monte Carlo Method