College of Animal Science and Technology, China Agricultural University, Beijing, China.
Animal Husbandry and Veterinary Station of the 8th Division, Shihezi City, Xinjiang Production and Construction Corps, Shihezi, China.
Anim Biotechnol. 2024 Nov;35(1):2404042. doi: 10.1080/10495398.2024.2404042. Epub 2024 Sep 20.
Weaning weight is a key indicator of the early growth performance of cattle. An understanding of the genetic mechanisms underlying weaning weight will help increase the accuracy of selection of breeding animals. In order to identify candidate genes associated with weaning weight in Simmental-Holstein crossbred cattle, this study generated RNA-Sequencing (RNA-seq) data from 86 crossbred calves (37 males and 49 famales) and measured their weaning weight and body size traits (wither height, body length, chest girth, rump width, and rump length). Differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) were performed. A total of 498 differentially expressed genes (DEGs) were identified between the low weaning weight (LWW) group and the high weaning weight (HWW) group. Weaning weight was transcriptionally correlated (FDR < 0.05) with four of the eleven co-expression gene modules. By intersecting DEGs and hub genes of the four modules, we identified a final set of 37 candidate genes enriched in growth, development, or immune-related processes. In addition, one co-expression module was significantly correlated with all the five body size traits (P < 0.05), from which was identified as a key candidate gene through protein-protein interaction (PPI) analysis of hub genes. Further evidence from cattle transcriptome-wide association study analysis (TWAS) and human phenome-wide association study (PheWAS) validated significant associations of , , , , , and with growth and development traits (P < 0.05). Notably, and were also associated with typical immune traits such as B cell proliferation, differentiation, and activation. In conclusion, this study reveals new candidate genes significantly associated with weaning weight in Simmental-Holstein crossbred cattle, providing a basis for further exploration of the genetic mechanisms behind growth traits of cattle.
断奶体重是牛早期生长性能的关键指标。了解断奶体重的遗传机制将有助于提高选育动物的准确性。为了鉴定西门塔尔-荷斯坦杂交牛中与断奶体重相关的候选基因，本研究对 86 头杂交牛（37 头公牛和 49 头母牛）进行了 RNA 测序（RNA-seq）数据生成，并测量了它们的断奶体重和体尺性状（肩高、体长、胸围、臀宽和臀长）。进行了差异基因表达分析和加权基因共表达网络分析（WGCNA）。在低断奶体重（LWW）组和高断奶体重（HWW）组之间共鉴定到 498 个差异表达基因（DEGs）。断奶体重与 11 个共表达基因模块中的四个模块的转录相关（FDR<0.05）。通过将 DEGs 和四个模块的枢纽基因进行交集，我们鉴定出一组最终的 37 个候选基因，这些基因富集在生长、发育或免疫相关过程中。此外，一个共表达模块与所有五个体尺性状显著相关（P<0.05），通过枢纽基因的蛋白质-蛋白质相互作用（PPI）分析，从该模块中鉴定出一个关键候选基因。牛全转录组关联研究分析（TWAS）和人类表型全关联研究（PheWAS）的进一步证据验证了、、、、和与生长和发育性状显著相关（P<0.05）。值得注意的是，和还与典型的免疫特征如 B 细胞增殖、分化和激活相关。总之，本研究揭示了西门塔尔-荷斯坦杂交牛中与断奶体重显著相关的新候选基因，为进一步探索牛生长性状的遗传机制提供了基础。
