Goto Tatsuhiko, Tsudzuki Masaoki
Genetics, Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.
J Poult Sci. 2017 Jan 25;54(1):1-12. doi: 10.2141/jpsa.0160121.
Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.
鸡在诸如与产蛋相关的数量性状上表现出广泛的表型变异。数量性状基因座（QTL）分析是一种用于理解表型（性状测量值）与基因型数据（分子标记）之间关系的统计方法。我们利用基于日本大型斗鸡（大斗鸡）和白来航鸡品种的原始资源群体，对与产蛋相关的性状进行了QTL分析。在本文中，我们分别总结了对产蛋量的11个性状和蛋品质的66个性状进行广泛QTL分析的结果。我们发现，17条不同染色体上至少30个QTL区域影响与产蛋相关性状的表型变异。每个基因座对性状都有年龄特异性效应，效应的多样性也很明显，如加性、显性和上位性互作效应。虽然全基因组关联研究（GWAS）适用于对具有加性效应的GWAS基因座进行基因水平的精细定位，但QTL定位研究使我们能够全面了解遗传控制，如染色体区域、对表型变异的遗传贡献、遗传方式以及常见和罕见等位基因的年龄特异性。QTL分析还描述了实验群体中基因型与表型之间的关系。积累包括GWAS基因座在内的QTL信息，对于在没有表型数据的情况下进行群体基因组学研究以验证已识别的正选择基因组特征也很有用。将QTL研究与下一代测序技术与未表征的遗传资源相结合，将增进目前对家畜基因型与表型之间关系的理解。
