Association analysis of CHRDL1 gene polymorphism and skin color traits in Chishui black-bone chicken

【Objective】 The purpose of the study was to analyze the association between tendon protein-like protein 1 gene(CHRDL1) polymorphism and skin color traits in Chishui black-bone chicken, and to screen out the key SNP loci of CHRDL1 gene that regulated the skin color of Chishui black-bone chicken, so as to provide theoretical basis for revealing the regulation mechanism of black-bone chicken melanin depositionand promoting the breeding of skin color trait in Chishui black-bone chicken.【Method】 Chishui black-bone chicken were used as the research object, and SNP loci were screened by determining the exon sequence of Chishui black-bone chicken CHRDL1 gene, which were analyzed bioinformatically using online softwares such as ProtParam, TargetP, PSORT II, NetPhos 2.0, TMHMM, SMART, and STRING, etc. The association of polymorphism in the ChRDL1 gene with skin color traits was analyzed.【Result】 Three SNPs lociwere found in exons 2, 4 and 5 of the CHRDL1 gene of Chishui black-bone chicken, which were g.2752T→C (nonsense mutations), g.8459G→T (Ser→ILe) and g.27148T→C(nonsense mutations), which belonged to the moderate polymorphisms(0.25P_HWE>0.05). Among these loci, g.8459G→T and g.27148T→C loci showed weak linkage disequilibrium. The theoretical isoelectric point(pI) of Chishui black-bone chicken CHRDL1 protein was 8.17, which belonged to hydrophobic unstable protein with phosphorylation and glycosylation sites. It was mainly localized inextracellular(44.4%), nuclear(22.2%) and mitochondria(22.2%). There was no transmembrane structure, but there were 3 conserved von Willebrand disease C type repeat sequence(VWC structural domains). The transmembrane structure, the functional structural domain and the interacting protein were unchanged before and after the mutation. The results of association analysis showed that the differences in chest skin color parameters among individuals with different genotypes at the SNP loci were not significant(P>0.05), except that the ΔL of individuals with the TT genotype at the g.2752T→C locus was significantly higher than that of individuals with the CC genotype and the CT genotype(P<0.05, the same below), and that the ΔL of individuals with the TT genotype at the g.8459G→ T locus was significantly higher than that of individuals with the GG genotype and the GT genotype.【Conclusion】 Three SNPs loci were found in exons 2, 4 and 5 of the CHRDL1 gene of Chishui black-bone chicken, which are g.2752T→C, g.8459G→T and g.27148T→C, respectively. Among them, the loci of g.2752T→C and g.8459G→T show skin color variability, which may be the marker loci for skin color trait in Chishui black-bone chicken.