Analysis of the Association of Two SNPs in the Promoter Regions of the PPP2R5C and SLC39A5 Genes with Litter Size in Yunshang Black Goats

SIMPLE SUMMARY: The protein phosphatase 2 regulatory subunit B’gamma (PPP2R5C) and solute carrier family 39 member 5 (SLC39A5) genes are essential in mammalian growth and development. Here, KASP genotyping was used to analyze the association between polymorphisms of PPP2R5C and SLC39A5 and litter size in Yunshang black goats, a cultivated goat breed with high prolificacy in China. The results show that PPP2R5C g.65977743C>T and SLC39A5 g.50676693T>C were significantly associated with litter size of the third parity in Yunshang black goats. Luciferase assays and RT-qPCR showed that individuals with the CC genotype of PPP2R5C and TT genotype of SLC39A5 showed higher expression of these genes in goat ovarian tissues than those with other genotypes. Transcription factor predictions showed that SOX18, ZNF418, and ZNF667 and NKX2-4 and TBX6 bind to the polymorphisms of two respective genes. These two polymorphisms provide new insights into the study of fertility in goats. ABSTRACT: Screening for candidate genes and genetic variants associated with litter size is important for goat breeding. The aim of this study was to analyze the relationship between single nucleotide polymorphisms (SNPs) in PPP2R5C and SLC39A5 and litter size in Yunshang black goats. KASP genotyping was used to detect the SNP genetic markers in the PPP2R5C and SLC39A5 in a population of 569 Yunshang black goats. The results show that there were two SNPs in the PPP2R5C and SLC39A5 promoter regions. Association analysis revealed that the polymorphisms PPP2R5C g.65977743C>T and SLC39A5 g.50676693T>C were significantly associated with the litter size of the third parity of Yunshang black goats (p < 0.05). To further explore the regulatory mechanism of the two genes, the expression of different genotypes of PPP2R5C and SLC39A5 was validated by RT-qPCR and Western blotting. The expression of PPP2R5C was significantly higher in individuals with the TT genotype than in those with the TC and CC genotypes (p < 0.05). The expression of SLC39A5 was also significantly higher in individuals with the TT genotype than in TC and CC genotypes (p < 0.05). Dual luciferase reporter analysis showed that the luciferase activity of PPP2R5C-C variant was significantly higher than that of PPP2R5C-T variant (p < 0.05). The luciferase activity of SLC39A5-T variant was significantly higher than that of SLC39A5-C variant (p < 0.05). Software was used to predict the binding of transcription factors to the polymorphic sites, and the results show that SOX18, ZNF418, and ZNF667 and NKX2-4 and TBX6 might bind to PPP2R5C g.65977743C>T and SLC39A5 g.50676693T>C, respectively. These results provide new insights into the identification of candidate genes for marker-assisted selection (MAS) in goats.