Table_2_Goat SNX29: mRNA expression, InDel and CNV detection, and their associations with litter size.docx

The sorting nexin 29 (SNX29) gene, a member of the SNX family, is associated with material transport and lipid metabolism. Previous studies have shown that lipid metabolism affects reproductive function in animals. Thus, we hypothesized there is a correlation between the SNX29 gene and reproductive trait. To date, studies on the relationship between the SNX29 gene and reproductive traits are limited. Therefore, the purpose of this study was to examine the polymorphism in the SNX29 gene and its correlation with litter size. Herein, the mRNA expression levels of SNX29 were assayed in various goat tissue. Surprisingly, we found that SNX29 was highly expressed in the corpus luteum, large and small follicles. This result led us to suggest that the SNX29 gene has a critical role in reproduction. We further detected potential polymorphisms in Shaanbei white cashmere (SBWC) goats, including insertion/deletion (InDel, n = 2,057) and copy number variation (CNV, n = 1,402), which were related to fertility. The 17 bp deletion (n = 1004) and the 20 bp deletion (n = 1,053) within the SNX29 gene were discovered to be significantly associated with litter size (P < 0.05), and individuals the ID genotype of P1-Del-17 bp and the DD genotype of P2-Del-20bp had larger litter size. Additionally, the four CNV loci had significant correlations with litter size (P < 0.01) in our detected population. In CNV5, individuals with the median genotype were superior compared to those with loss or gain genotype in term of litter size, and in other three CNVs showed better reproductive trait in the gain genotype. Briefly, these findings suggest that SNX29 could be used as a candidate gene for litter size in goat breeding through marker-assisted selection (MAS).

分拣蛋白29 (sorting nexin 29, SNX29) 基因属于SNX家族成员，与物质转运及脂质代谢密切相关。既往研究表明，脂质代谢可影响动物的生殖功能。据此，本研究推测SNX29基因与繁殖性状存在关联。截至目前，有关SNX29基因与繁殖性状之间关联的研究仍较为有限。因此，本研究旨在探究SNX29基因的多态性及其与山羊产羔数的相关性。
本研究首先检测了SNX29基因在山羊各组织中的mRNA表达水平，意外发现SNX29在黄体、大卵泡及小卵泡中均呈高表达，由此提示SNX29基因在生殖过程中发挥关键作用。
本研究进一步在陕白绒山羊 (Shaanbei white cashmere, SBWC) 群体中检测了与繁殖性能相关的两类潜在多态性位点：插入/缺失 (insertion/deletion, InDel，样本量n=2057) 与拷贝数变异 (copy number variation, CNV，样本量n=1402)。
研究发现，SNX29基因内的17 bp缺失（样本量n=1004）与20 bp缺失（样本量n=1053）位点均与产羔数显著相关（P < 0.05）；其中携带P1-Del-17 bp位点ID基因型及P2-Del-20 bp位点DD基因型的个体产羔数更高。
此外，本研究检测的4个CNV位点均与山羊产羔数呈极显著相关（P < 0.01）：在CNV5位点中，携带中等拷贝基因型的个体产羔数显著优于缺失型及扩增型个体；而其余3个CNV位点中，扩增型个体的繁殖性状表现更优。
综上，本研究结果表明，SNX29可作为山羊标记辅助选择 (marker-assisted selection, MAS) 育种中产羔数性状的候选基因。