Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA.
Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234, s/n, Fazenda Canchim, São Carlos 13560-970, SP, Brazil.
Biomolecules. 2024 Jan 26;14(2):150. doi: 10.3390/biom14020150.
Despite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factors governing fertility. Herein, we identified regulatory variants from RNA-Seq data associated with gene expression regulation in the uterine luminal epithelial cells of beef cows. We identified 4676 cis and 7682 trans eQTLs (expression quantitative trait loci) affecting the expression of 1120 and 2503 genes, respectively (FDR < 0.05). These variants affected the expression of transcription factor coding genes (71 cis and 193 trans eQTLs) and genes previously reported as differentially expressed between pregnant and nonpregnant cows. Functional over-representation analysis highlighted pathways related to metabolism, immune response, and hormone signaling (estrogen and GnRH) affected by eQTL-regulated genes (-value ≤ 0.01). Furthermore, eQTLs were enriched in QTL regions for 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05). Our study provides novel insights into the genetic basis of reproductive processes in cattle. The underlying causal mechanisms modulating the expression of uterine genes warrant further investigation.
尽管人们已经做出了共同的努力来了解生殖特征的复杂调控机制，但目前还没有报道任何因果基因和/或突变。通过整合基因组学和转录组学数据，可能会揭示潜在的调控机制，为剖析控制生育力的遗传因素提供机会。在此，我们从牛子宫腔上皮细胞的 RNA-Seq 数据中鉴定出了与基因表达调控相关的调控变体。我们鉴定出了 4676 个 cis 和 7682 个 trans eQTLs（表达数量性状基因座），分别影响 1120 个和 2503 个基因的表达（FDR < 0.05）。这些变体影响了转录因子编码基因（71 个 cis 和 193 个 trans eQTLs）和先前报道的在怀孕和未怀孕牛之间差异表达的基因的表达。功能过表达分析突出了与代谢、免疫反应和激素信号（雌激素和 GnRH）相关的途径，这些途径受 eQTL 调控基因的影响（-值 ≤ 0.01）。此外，eQTLs 在牛 QTLdb 中 13 个与生殖相关的性状的 QTL 区域中富集（FDR ≤ 0.05）。我们的研究为牛的生殖过程的遗传基础提供了新的见解。调节子宫基因表达的潜在因果机制值得进一步研究。
