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

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.

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat

“…Among these, the IFT88 and CHRM2 genes are regarded as candidate genes for mohair fineness in Tibetan cashmere goats ( Bai et al, 2022 ), while the SDC1 gene is associated with coarse and fine skin tissues of Liaoning cashmere goats ( Nazari-Ghadikolaei et al, 2018 ). Similarly, the ITCH gene plays a potential role in regulating mohair and coat color traits in the Iranian Markhoz goat ( Wang et al, 2021 ), whereas the FGF12 gene is involved in the production of fleece in Inner Mongolia Cashmere goats ( Chen Y et al, 2022 ).…”

“…The literature on complete genomic architecture, including population structure, genome diversity and evolutionary selective sweeps, in relation to this important genetic resource is scant. Earlier, studies relied on mapping of the mitochondrial genome ( Mao-Liang et al, 2016 ) and elucidating single-gene associations with growth traits ( Chen Y et al, 2022 ).…”

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats

“…Subsequently, six primer pairs were designed for amplification using the Primer-BLAST tool (https://www.ncbi.nlm.nih.gov/tools/primer-blast/; accessed on 1 August 2023). MC1R and GAPDH were used as reference genes [31]. The relevant primers are listed in Table S1.…”

“…The total qPCR reaction system consisted of 10 µL, comprising 5 µL of 2 × SYBR Premix Ex Taq (Takara, Japan), 0.5 µL of DNA, 0.5 µL of each primer, and 3.5 µL of ddH 2 O. The reaction conditions and thermal profiles were as previously described by Chen et al [31]. Relative copy number (RCN) was calculated from the ∆∆Cq value using the following formula [32]:…”

Detection distribution of CNVs of SNX29 in three goat breeds and their associations with growth traits

“…A circRNA of the SNX29 gene regulated the proliferation and differentiation of muscle cells ( 9 ). Studies have shown that the SNX29 gene plays a key role in subcutaneous fat deposition in Xiangdong black (XDB) goats, and the SNX29 CNV is significantly associated with the chest and abdominal girth of XDB goats ( P < 0.01) ( 10 ). Based on the above, the SNX29 gene was selected to be studied in this study.…”