A quantitative trait locus on chromosome 2 was identified that accounts for a substantial proportion of phenotypic variance of the yellow plumage color in chicken

Abstract

Chicken plumage color is an important economical trait in poultry breeding, as triple-yellow indigenous broilers are preferred over western commercial broilers in the Chinese market. However, the studies on the pigmentation of plumage coloration are relatively rare at present. Here, we performed a genome-wide mapping study on an F₂ intercross, whose 2 founders were one hybrid commercial line "High Quality chicken Line A" that originated from the Anak red chicken and one indigenous line "Huiyang Beard" chicken that is a classical "triple-yellow" Chinese indigenous breed. Moreover, we used an automatic colorimeter that can quantitatively assess the colorations in L∗, a∗, and b∗ values. One major quantitative trait locus (QTL) on chromosome 2 was thus identified by both genome-wide association and linkage analyses, which could explain 10 to 20% of the total phenotypic variance of the b∗ measurements of the back plumage color. Using linkage analysis, 2 additional QTL on chromosome 1 and 20 were also found to be significantly associated with the plumage coloration in this cross. With additional samples from Anak red and Huiyang Beard chickens as well as pooled resequencing data from the 2 founders of this cross, we then further narrowed down the QTL regions and identified several candidate genes, such as CABLES1, CHST11, BCL2L1, and CHD22. As the effects of QTL found in this study were substantial, quantitatively measuring the coloration rather than the descriptive measurements provides stronger statistical power for the analyses. In addition, this major QTL on chromosome 2 that was associated with feather pigmentation at the genome-wide level will facilitate the future chicken breeding for yellow plumage color. In conclusions, we mapped 3 associated QTL on chromosome 1, 2, and 20. The candidate genes identified in this study shed light in the genetic basis of yellow plumage color in chicken.

Keywords: genome-wide association; linkage analysis; yellow plumage color.

Figure 1

Genome-wide association and linkage analysis for LBPC10 and BBPC10 traits. (A) Manhattan plot for the genome-wide association study for LBPC10 traits. (B) The identification of QTL related with LBPC10 trait by linkage analysis. (C) Manhattan plot for the genome-wide association study for BBPC10 traits. (D) The identification of QTLs related with BBPC10 trait by linkage analysis. The Manhattan plot indicates the −log10 (observed P values) for genome-wide SNP (y-axis) plotted against the irrespective positions on each chromosome (x-axis).

Figure 2

The distribution of LBPC10 measurements on the different core haplotypes. “AGG” and “GAA” were the 2 main haplotypes. Letters in yellow mean the corresponding haplotypes have an effect to increase L∗ values, while letters in blue denote their effects in decreasing the L∗ values.

Figure 3

The distribution of the whole-genome F_ST clusters within the QTL. The arrows represent F_ST clusters in the core haplotypes. 1% top F_ST clusters across the genome was defined as the threshold set to 0.43.