Goat reproductive traits are complex quantitative traits controlled by polygenes and multipoint. To date, some high-fertility candidate genes in livestock have been unearthed and the growth differentiation factor 9 (GDF9) gene is one of them, which plays a crucial role in early folliculogenesis. According to the relevant previous studies and the National Center for Biotechnology Information Search database (NCBI), a total of 45 single nucleotide polymorphisms (SNPs) have been detected in the goat GDF9 gene, but which one or which ones have important effects on goat fecundity is still uncertain. Hence, in order to find effective molecular markers for goat genetic breeding and accelerate the goat improvement, this study summarized and classified the above 45 SNPs into four kinds, as well as compared and analyzed the same SNP effects and the different SNPs linkage effects on the reproductive traits in different goat breeds. Since there were many SNPs in the goat GDF9 gene, only 15 SNPs have been identified in more than 30 goat breeds worldwide and they showed different effects on the litter size. Therefore, this study mainly chose these 15 SNPs and discussed their relationship with goat productivity. Results showed that three non-synonymous SNPs A240V, Q320P, and V397I and three synonymous ones L61L, N121N, and L141L played a “true” role in the litter size trait in many goat breeds around the world. However, the regulatory mechanisms still need further research. These results provide an effective tool for follow-up research developing the goat molecular breeding strategies and improving the goat reproductive traits.

In the process of anterior pituitary gland development and maturation, numerous transcription factors were involved in the pituitary organogenesis. To date, the lack of knowledge on POU1F1-PROP1-PITX1-SIX3 pathway genes affecting growth traits was reported in Chinese goat breeds. The objective of this work was to identify genetic variants of the POU1F1, PROP1, PITX1 and SIX3 genes, as well as to evaluate their associations with growth traits in goats. The results showed that one novel and five reported single nucleotide polymorphisms (SNP) were confirmed in above four genes. The novel SNP (NC_019460.2:g.1100T>A) was located in intron 1 of SIX3 gene. Among these loci, DQ826397.1:g.102T>G (SNP1), DQ826397.1:g.279T>C (SNP2) and NC_019460.2:g.1100T>A (SNP6) were associated with growth traits. In details, the SNP1 locus had significant association with hucklebone width (P<0.05) and hucklebone width index (P<0.05) in the Guanzhong dairy goat. The SNP2 locus was associated with body weight (P<0.05), chest circumference (P<0.01), chest width (P<0.05), hucklebone width (P<0.05), cannon circumference (P<0.01) and trunk index (P<0.01) in the Hainan black goat. The SNP6 locus was significantly associated with hucklebone width index (P<0.05) and chest width (P<0.05) in the Guanzhong dairy goat and Hainan black goat, respectively. These findings indicated that goat POU1F1-PROP1-PITX1-SIX3 pathway genes were important genetic factors, which could affect growth traits. Three SNPs detected in this study may be useful for potential marker-assisted selection programs in goat breeding and production.