Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

Abstract

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.

Keywords: chickens; egg production trait; egg quality trait; epistasis; genotype-phenotype relationship; quantitative trait loci.

Fig. 1.

Resource population based on the Oh-Shamo and White Leghorn breeds of chickens for QTL mapping. (A) An Oh-Shamo male was crossed to three White Leghorn females to produce F₁ offspring. F₂ females (n=421) were produced by full-sib mating between four F₁ males and 19 F₁ females. Light and dark gray sections in the chromosomes of the F₂ females indicate the chromosomal fragments derived from the Oh-Shamo and White Leghorn breeds, respectively. S and W indicate the alleles derived from the Oh-Shamo and White Leghorn breeds, respectively. Segregating alleles in the F2 individuals were confirmed by DNA marker genotyping of individuals in P, F₁, and F₂ generations. (B) An Oh-Shamo male (left) and a White Leghorn female (right). Morphological differences are obvious between the two breeds.

Fig. 2.

Illustration of the egg laying stage and egg-related traits investigated. Chickens were reared over the course of a year from hatching. Eggs were inspected for external and internal traits at early (first egg age), middle (300-days-old), and late (400-days-old) egg laying stages. Egg production rates were calculated every four weeks for 22- to 62-week-old.

Fig. 3.

Conceptual diagram of the genetic control of quantitative traits. QTLs are classified into two groups; main-effect QTLs and epistatic QTLs. Main-effect QTLs affect a trait through individual alleles present at a single locus. On the other hand, epistatic QTLs affect a trait through allele combinations between two loci. Conceptually, it is thought that both types of QTLs affect phenotypic variation of egg traits.

Fig. 4.

Genetic network influencing phenotypic variation of egg-related traits found in the QTL studies with a single resource population. QTLs detected in our previous studies (Goto et al., 2011; 2014a; 2014b) are summarized in this figure. Detailed information including QTL position, flanking markers, and mode of inheritance is summarized in Table 1. Light gray vertical lines numbered 1–24, 26–28, and Z (above) indicate chromosomes. Dark gray ellipses and squares indicate QTL regions with main and epistatic effects on egg-related traits, respectively. Light gray lines between loci indicate epistatic interactions. Based on this figure, at least 30 QTL regions on 17 different chromosomes control phenotypic variation of egg-related traits, which clearly indicates a complex genetic basis of quantitative traits.