Effects of Genetic Variation of the Sorting Nexin 29 (SNX29) Gene on Growth Traits of Xiangdong Black Goat

SIMPLE SUMMARY: With the development of goat industry, the improvement of goat production performance has become the primary task of goat industry. Studies have shown that SNX29, known for binding to microtubule motor protein activity and phosphatidylinositol, could be a candidate gene for carcass and dorsal fat traits. Many studies have been provided that CNV and indel can affect their phenotypic traits in livestock. However, there are no reports on investigating SNX29 genetic variation in Hunan local goats. In this study, two indels (17 bp-indel and 21 bp-indel) and CNV of SNX29 were identified in 516 individual Xiangdong black goats (a representative Chinese native goat breed in Hunan), while SNX29 CNV was significantly associated with chest circumference and abdominal circumference (p < 0.01). These findings suggested that the SNX29 gene could be used for marker-assisted selection in meat goats. For the first time, this report reveals a novel application prospect for the SNX29 CNV to improve the Chinese local goats. ABSTRACT: Previous studies have found that the copy number variation (CNV) and insertion/deletion (indels) located in the sorting nexin 29 (SNX29) gene, which is an important candidate gene related to meat production and quality, are associated with growth traits of African goats and Shaanbei white cashmere goats. However, the genetic effects of SNX29 genetic variation on growth traits of Xiangdong black (XDB) goat (a representative meat goat breed in China) are still unclear. The purpose of this study was to detect the mRNA expression level of SNX29 and to explore the genetic effects of CNV and indel within SNX29 on growth traits and gene expression in XDB goat. The SNX29 mRNA expression profile showed that the SNX29 was highly expressed in adipose tissues, indicating that the SNX29 gene could play a key role in subcutaneous adipose deposition of XDB goat. 17 bp indel (g.10559298-10559314), 21 bp indel (g.10918982-10919002) and CNV were detected in 516 individuals of XDB goat by PCR or qPCR. The association analysis of SNX29 CNV with growth traits in XDB goats showed that SNX29 CNV was significantly correlated with chest circumference and abdominal circumference (p < 0.01), and the normal type of SNX29 CNV goat individuals were more advantageous. For the mRNA expression of SNX29 gene, individuals with SNX29 copy number normal type had a higher trend than that of SNX29 gene with copy number gain type in longissimus dorsi muscle (p = 0.07), whereas individuals with SNX29 copy number gain type had a higher trend in abdominal adipose (p = 0.09). Overall, these results suggested that the SNX29 gene could play an important role in growth and development of XDB goats and could be used for marker-assisted selection (MAS) in XDB goats.