Crooks Lucy, Guo Yuanmei
State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
PLoS One. 2017 Jan 6;12(1):e0162045. doi: 10.1371/journal.pone.0162045. eCollection 2017.
Epistasis describes an interaction between the effects of loci. We included epistasis in quantitative trait locus (QTL) mapping of growth at a series of ages in a cross of a Chinese pig breed, Erhualian, with a commercial line, White Duroc. Erhualian pigs have much lower growth rates than White Duroc. We improved a method for genomewide testing of epistasis and present a clear analysis workflow. We also suggest a new approach for interpreting epistasis results where significant additive and dominance effects of a locus in specific backgrounds are determined. In total, seventeen QTL were found and eleven showed epistasis. Loci on chromosomes 2, 3, 4 and 7 were highlighted as affecting growth at more than one age or forming an interaction network. Epistasis resulted in both the QTL on chromosomes 3 and 7 having effects in opposite directions. We believe it is the first time for the chromosome 7 locus that an allele from a Chinese breed has been found to decrease growth. The consequences of epistasis were diverse. Results were impacted by using growth rather than body weight as the phenotype and by correcting for an effect of mother. Epistasis made a considerable contribution to growth in this population and modelling epistasis was important for accurately determining QTL effects.
上位性描述了基因座效应之间的相互作用。我们在中国猪种二花脸与商业品系大白杜洛克的杂交后代中，对一系列年龄阶段的生长性状进行数量性状基因座（QTL）定位时纳入了上位性分析。二花脸猪的生长速度远低于大白杜洛克猪。我们改进了一种全基因组上位性检测方法，并给出了清晰的分析流程。我们还提出了一种新的解释上位性结果的方法，即确定特定背景下一个基因座的显著加性效应和显性效应。总共发现了17个QTL，其中11个表现出上位性。2号、3号、4号和7号染色体上的基因座被突出显示为影响多个年龄阶段的生长或形成一个相互作用网络。上位性导致3号和7号染色体上的QTL产生相反方向的效应。我们认为，这是首次发现来自中国猪种的一个等位基因在7号染色体基因座上会降低生长速度。上位性的影响是多样的。使用生长而非体重作为表型以及校正母体效应会对结果产生影响。上位性对该群体的生长有相当大的贡献，对上位性进行建模对于准确确定QTL效应很重要。
