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Previous studies have found that the copy number variation (CNV) and insertion/deletion (indels) located in the sorting nexin 29 <i>(SNX29</i>) 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 <i>SNX29</i> 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 <i>SNX29</i> and to explore the genetic effects of CNV and indel within <i>SNX29</i> on growth traits and gene expression in XDB goat. The <i>SNX29</i> mRNA expression profile showed that the <i>SNX29</i> was highly expressed in adipose tissues, indicating that the <i>SNX29</i> 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 <i>SNX29</i> CNV with growth traits in XDB goats showed that <i>SNX29</i> CNV was significantly correlated with chest circumference and abdominal circumference (<i>p</i> < 0.01), and the normal type of <i>SNX29</i> CNV goat individuals were more advantageous. For the mRNA expression of <i>SNX29</i> gene, individuals with <i>SNX29</i> copy number normal type had a higher trend than that of <i>SNX29</i> gene with copy number gain type in longissimus dorsi muscle (<i>p</i> = 0.07), whereas individuals with <i>SNX29</i> copy number gain type had a higher trend in abdominal adipose (<i>p</i> = 0.09). Overall, these results suggested that the <i>SNX29</i> 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.