Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

Abstract

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F₂ females were produced by full-sib mating of F₁ birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

Keywords: Japanese quail; QTL; RAD-seq; SNP marker; egg-related traits.

Figure 1

Genetic map of SNP markers distributed on 13 linkage groups. The abscissa shows the chromosome number. The ordinate presents the marker position based on cM.

Figure 2

Genome-wide LOD plot of detected QTL for age at first egg (blue) and yolk color-yellowness₂ (black) on chromosome 2. The horizontal lines show the genome-wide significance at 5% (straight line) and suggestive threshold at 10% (dotted line) levels.

Figure 3

Genome-wide LOD plot of detected QTL for egg long axis₁ (black) on chromosome 4, yolk weight₁ (red) on chromosomes 6 and 10, and egg shell strength₁ (blue) on chromosome 6. The horizontal lines show the genome-wide significance at 5% (straight line) and suggestive threshold at 10% (dotted line) levels.

Figure 4

Genome-wide LOD plot of detected QTL for egg weight₁ (black) and albumen weight₁ (red) on chromosome 10, and egg short axis₁ (blue) on chromosomes 10 and Z1. The horizontal lines show the genome-wide significance threshold at 1% (dashed line) and 5% (straight line) and suggestive threshold at 10% (dotted line) levels.

Figure 5

Genome-wide LOD plot of detected QTL for egg shell weight₁ (blue) on chromosome 12 and yolk diameter₁ (black) on chromosome Z1. The horizontal lines show the genome-wide significance threshold at 1% (dashed line) and 5% (straight line) and suggestive threshold at 10% (dotted line) levels.

Figure 6

Detected QTL presented in the genetic map. The abscissa shows the chromosome number. The ordinate represents the position of the markers based on cM. Q stands for the QTL number.