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Open Access Methodology article

A new mapping method for quantitative trait loci of silkworm

Hai-Ming Xu1, Chang-Shuai Wei1, Yun-Ting Tang2, Zhi-Hong Zhu1, Yang-Fu Sima3 and Xiang-Yang Lou14*

Author Affiliations

1 Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China

2 Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China

3 College of Agriculture Science and Technology, Soochow University, Suzhou 215006, China

4 Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA

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BMC Genetics 2011, 12:19  doi:10.1186/1471-2156-12-19

Published: 28 January 2011

Abstract

Background

Silkworm is the basis of sericultural industry and the model organism in insect genetics study. Mapping quantitative trait loci (QTLs) underlying economically important traits of silkworm is of high significance for promoting the silkworm molecular breeding and advancing our knowledge on genetic architecture of the Lepidoptera. Yet, the currently used mapping methods are not well suitable for silkworm, because of ignoring the recombination difference in meiosis between two sexes.

Results

A mixed linear model including QTL main effects, epistatic effects, and QTL × sex interaction effects was proposed for mapping QTLs in an F2 population of silkworm. The number and positions of QTLs were determined by F-test and model selection. The Markov chain Monte Carlo (MCMC) algorithm was employed to estimate and test genetic effects of QTLs and QTL × sex interaction effects. The effectiveness of the model and statistical method was validated by a series of simulations. The results indicate that when markers are distributed sparsely on chromosomes, our method will substantially improve estimation accuracy as compared to the normal chiasmate F2 model. We also found that a sample size of hundreds was sufficiently large to unbiasedly estimate all the four types of epistases (i.e., additive-additive, additive-dominance, dominance-additive, and dominance-dominance) when the paired QTLs reside on different chromosomes in silkworm.

Conclusion

The proposed method could accurately estimate not only the additive, dominance and digenic epistatic effects but also their interaction effects with sex, correcting the potential bias and precision loss in the current QTL mapping practice of silkworm and thus representing an important addition to the arsenal of QTL mapping tools.