Abstract: 【Objective】The Wnt signaling pathway plays an important role in the development of animal skin feather follicles. The results of previous studies indicated that the Wnt3a may be an important candidate gene that had effects on the chicken feather follicle density. In order to further verify the role of Wnt3a in the growth and development of skin feather follicle density, Wnt3a SNPs were screened and their association with feather follicle density will be analyzed in Jinling Hua chicken. It will provide a reference for“breeding by molecular writing” of slaughter-type broilers with beautiful carcasses.【Method】The SNPs of Wnt3a gene were screened by PCR amplification and direct sequencing, and the correlation between a single SNP marker and skin feather follicle density traits was analyzed. Haploview software was used to analyze the degree of linkage disequilibrium (LD) of these SNP loci, and the correlation between different haplotype combinations and feather follicle density traits was also analyzed. 【Results】A total of 14 SNP sites were found, and one SNP site (SNP1) was found in the second exon, which was a synonymous mutation. Four mutation sites (SNP2-SNP5) were found in the second intron, and 9 SNP sites (SNP6-SNP14) were found in the third intron. The chi-square test showed that one mutation site (SNP1) in the second exon and three mutation sites (SNP3-SNP5) in the second intron were all in the Hardy-Weinberg equilibrium (P >0.05), the 9 mutation sites (SNP6-SNP14) of the third intron deviated from Hardy-Weinberg equilibrium (P<0.05). The expected heterozygosity (He) of SNP1-SNP5 is less than 0.50, and the polymorphic information content (PIC) is less than 0.25. The genetic polymorphisms of these 5 SNP loci are low. The third intron had 9 mutation sites, PIC of SNP6, SNP7, SNP9 sites was less than 0.25, and the other 6 mutation sites 0.25<PIC<0.5, which were moderately polymorphic. Single-marker association analysis showed that the number of skin feather follicle with SNP2 locus of AG genotype in males and females was significantly higher than that of GG genotype (P＜0.05). The number of skin feather follicles with SNP8 locus of AA and GG genotypes in females was significantly higher than that of the AG genotype (P<0.05). The skin feather follicles density in the three genotypes in males was not significantly different. The linkage disequilibrium analysis of 14 SNPs showed that SNP6-SNP13 and SNP3-SNP5 had a strong linkage disequilibrium, respectively. SNP3, SNP4, and SNP5 produced three haplotype combinations after the combination of the two haplotypes linked by SNP3- SNP5. Association analysis found that the skin feather follicle density of the three haplotype combinations in males and females were not significantly different. After the combination of 5 main haplotypes at SNP6-SNP13 locus, males had 7 haplotype combinations, and the skin feather follicles density was not significant. Females had 8 haplotype combinations, of which H1H1 (AACCAATTTTAATTCC) had the highest skin feather follicles density. SNP2 and SNP8 are significantly correlated with skin feather follicle density, and the haplotype combination H1H1（AGAA） and H1H2 （AGAG）are the dominant haplotypes in hens.【Conclusion】Fourteen SNPs of Wnt3a were screened. Among them, individuals with different genotypes at rs2587721 G > A (SNP2) and rs2555967G>A (SNP8) locus have significant differences in feather follicle density. Eight SNPs (SNP6-SNP13) loci are in strong linkage disequilibrium, and the combination of H1H1 had the highest feather follicles density in females. The haplotype combination of SNP2 and SNP8 of Wnt3a H1H (AGAA), H1H2 (AGAG) and SNP6-SNP13 linked to produce the H1H1 （AACCAATTTTAATTCC）haplotype combination are significantly correlated with feather follicle density in females, which can provide important genetic information for“breeding by molecular writing”on chicken skin feather follicle density. 

Key words: chicken,  , Wnt3a,  , skin feather follicle,  , SNP sites,  , linkage disequilibrium