Genetic Variation and Haplotype Structure of CFAP299 and PRDM8 Associated with Fiber Yield and Hair Length Traits in Tianzhu White Yak

Fiber yield and hair length are important economic traits in Tianzhu White Yak. However, the genetic variants associated with fiber production performance in this breed remain insufficiently characterized. This study aimed to investigate the associations of single nucleotide polymorphisms (SNPs) in the CFAP299 and PRDM8 genes with fiber yield and hair length traits in Tianzhu White Yak and to identify potential molecular markers for marker-assisted selection. A total of 759 Tianzhu White Yaks were included in this study. Genomic DNA was extracted from blood samples, SNP detection and genotyping were performed using GATK (v. 4.2.6.1), and candidate SNPs were validated by PCR amplification and Sanger sequencing. Five SNPs in CFAP299 and three SNPs in PRDM8 were selected for analyses of genetic diversity, Hardy–Weinberg equilibrium, linkage disequilibrium, haplotype structure, and associations with phenotypic traits. All eight loci displayed three genotypes. No significant departure from Hardy–Weinberg equilibrium was detected at any locus (p > 0.05), and PIC values of 0.25–0.50 indicated moderate polymorphism. After adjustment for sex and age and FDR correction, all eight SNPs remained significantly associated with head hair length (HL) and fiber yield (FY), while several loci were also significantly associated with body-side hair length (BSL) and back hair length (BL) (q < 0.05). Individuals carrying mutant homozygous genotypes generally exhibited higher phenotypic values for the corresponding traits, whereas heterozygous genotypes generally showed intermediate values between the two homozygous genotypes. Linkage disequilibrium and haplotype analyses revealed that the eight SNPs formed three haplotype blocks. Haplotype combinations in Blocks 1 and 3 were significantly associated with variation in HL, FY, and SL, whereas no significant associations were detected for Block 2. Overall, SNPs and haplotype combinations in CFAP299 and PRDM8 were associated with variation in fiber yield and hair length traits in Tianzhu White Yak. These findings support CFAP299 and PRDM8 as candidate genes associated with fiber-related traits and provide potential molecular markers for further validation and marker-assisted selection.