Abstract：CCAAT/enhancer binding protein alpha gene (CEBPA) plays an important role in lipogenesis, growth, and development, and sine oculis homeobox homolog 1 gene (Six1) plays a regulatory role in skeletal muscle development and muscle fiber type transformation, and both of the two genes are closely related to bone development. The single nucleotide polymorphisms (SNPs) of the exons of CEBPA gene and Six1 gene were detected by direct sequencing in this study. The purpose of this study was to uncover the effects of CEBPA gene and Six1 gene on the carcass traits and body size traits of Wuliang Mountain black-bone chicken (Gallus gallus). The results showed that three SNPs (i.e. 74 C＞G, 552 G＞A and 936 C＞T) were found in CEBPA gene, and two SNPs (i.e. 375 G＞A and 564 G＞A) were found in Six1 gene. All SNPs except two SNPs (i.e. 936 C＞T of CEBPA gene and 375 G＞A of Six1 gene) exhibited three genotypes, and the predominant alleles were non-mutation allele. The chi-square test showed that allelic frequency and genotype frequency of two SNPs (i.e. 552 G＞A of CEBPA gene and 564 G＞A of Six1 gene) didn't agree with the Hardy-Weinberg equilibrium (P＞0.05), while others did. As for polymorphic information content, all SNPs were in a low polymorphism. The mutation (C→G) of 74 bp in CEBPA gene caused the change of amino acids (i.e. Threonine → Serine), while others didn't. Moreover, there was no strong linkage disequilibrium(LD) among each gene's respective SNPs. In the group of Wuliang Mountain black-bone chicken, 5 haplotypes and 7 diplotypes were formed on CEBPA gene, and 4 haplotypes and 5 diplotypes were formed on Six1 gene. Association studies of genotypes of SNPs and diplotypes with carcass traits and body size traits were performed by using the GLM. The results showed that four SNPs (i.e. 74 C＞G and 936 C＞T of CEBPA gene, 375 G＞A and 564 G＞A of Six1 gene) were significantly or highly correlated with carcass traits and body size traits (P＜0.05 or P＜0.01). 74 C＞G of CEBPA gene was significantly correlated with the percentage of half-eviscerated yield, the percentage of eviscerated yield, body slope length, breast width, breast depth and fossil bone length (P＜0.05). 936 C＞T of CEBPA gene was significantly correlated with live weight, dressed weight, half-eviscerated weight, eviscerated weight, breast muscle weight, body slope length, pelvis width and shank length (P＜0.05 or P＜0.01). The percentage of half-eviscerated yield and eviscerated yield of diplotype H1H1 and H4H4, breast muscle weight, pelvis width and shank length of diplotype H1H2, body slope length of diplotype H1H4 and H4H4, breast width, breast depth and fossil bone length of diplotype H4H4 were significantly higher than other partial diplotypes, respectively (P＜0.05 or P＜0.01). 375 G＞A of Six1 gene was significantly correlated with breast depth and pelvis width (P＜0.05 or P＜0.01), while it was not significantly associated with carcass traits. 564 G＞A of Six1 gene was significantly correlated with breast muscle weight, the percentage of breast muscle, breast angel, shank length and shank circumference (P＜0.05 or P＜0.01). The breast muscle weight and the percentage of breast muscle of H6H6, H6H7 and H6H8 diplotypes, dressed percentage of H6H7 diplotype, eviscerated weight, breast depth and pelvis of H6H8 diplotype, breast angel, shank length and shank circumference of H7H7 diplotype were significantly higher than other partial diplotypes, respectively (P＜0.05 or P＜0.01). The present research suggested that CEBPA gene and Six1 gene had significant genotype effects on the carcass traits and body size traits of Wuliang Mountain black-bone chicken and could be potential candidate genes for molecular marker-aid selection in Wuliang Mountain black-bone chicken and other chicken breeds.
