A Major Locus for Quantitatively Measured Shank Skin Color Traits in Korean Native Chicken

Abstract

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [L*], redness [a*], and yellowness [b*]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects b* value (logarithm of odds [LOD] = 47.5, p = 1.60×10^-49) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences a* value (LOD = 14.2, p = 6.14×10^-16). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and a* (P_MGA = 1.69×10^-28; P_QTDT = 2.40×10^-25). The strongest associations were between BCDO2 g.9367 A>C and b* (P_MGA = 3.56×10^-66; P_QTDT = 1.68×10^-65). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

Keywords: BCDO2; Korean Native Chicken; Linkage and Association; Quantitative Trait Locus; Shank Skin Color.

Figure 1

The phenotypic variations of shank skin color in Korean native chicken. The range and median values of L^*, a^*, and b^* are presented.

Figure 2

The marginal and conditional logarithm of odds (LOD) scores for b* (A) and a* (B) in Korean native chicken (KNC). The conditional LOD score means that beta-carotene dioxygenase 2 (BCDO2) g.9367 A>C variant was added when the LOD score was computed. The marker map with distances between genetic markers in Kosambi centimorgans (cM) is shown on the x-axis. The y-axis represents LOD scores. The horizontal lines represents 5% genome-wide significance.