College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China.
Genes (Basel). 2023 Sep 27;14(10):1881. doi: 10.3390/genes14101881.
The heritability of litter size in sheep is low and controlled by multiple genes, but the research on its related genes is not sufficient. Here, to explore the expression pattern of multi-tissue genes in Chinese native sheep, we selected 10 tissues of the three adult ewes with the highest estimated breeding value in the early study of the prolific Xinggao sheep population. The global gene expression analysis showed that the ovary, uterus, and hypothalamus expressed the most genes. Using the Uniform Manifold Approximation and Projection (UMAP) cluster analysis, these samples were clustered into eight clusters. The functional enrichment analysis showed that the genes expressed in the spleen, uterus, and ovary were significantly enriched in the Ataxia Telangiectasia Mutated Protein (ATM) signaling pathway, and most genes in the liver, spleen, and ovary were enriched in the immune response pathway. Moreover, we focus on the expression genes of the hypothalamic-pituitary-ovarian axis (HPO) and found that 11,016 genes were co-expressed in the three tissues, and different tissues have different functions, but the oxytocin signaling pathway was widely enriched. To further explore the differences in the expression genes (DEGs) of HPO in different sheep breeds, we downloaded the transcriptome data in the public data, and the analysis of DEGs (Xinggao sheep vs. Sunite sheep in Hypothalamus, Xinggao sheep vs. Sunite sheep in Pituitary, and Xinggao sheep vs. Suffolk sheep in Ovary) revealed the neuroactive ligand-receptor interactions. In addition, the gene subsets of the transcription factors (TFs) of DEGs were identified. The results suggest that 51 TF genes and the homeobox TF may play an important role in transcriptional variation across the HPO. Altogether, our study provided the first fundamental resource to investigate the physiological functions and regulation mechanisms in sheep. This important data contributes to improving our understanding of the reproductive biology of sheep and isolating effecting molecular markers that can be used for genetic selection in sheep.
绵羊产仔数的遗传力较低，受多个基因控制，但对其相关基因的研究还不够充分。在这里，为了探索中国本土绵羊多组织基因的表达模式，我们选择了早期高产型兴羔羊群体研究中繁殖价值最高的三只成年母羊的 10 种组织。全基因表达分析表明，卵巢、子宫和下丘脑表达的基因最多。使用 Uniform Manifold Approximation and Projection (UMAP) 聚类分析，将这些样本聚类为 8 个簇。功能富集分析表明，脾脏、子宫和卵巢中表达的基因在共济失调毛细血管扩张突变蛋白 (ATM) 信号通路中显著富集，肝脏、脾脏和卵巢中的大多数基因在免疫反应通路中富集。此外，我们还重点研究了下丘脑-垂体-卵巢轴 (HPO) 的表达基因，发现这三个组织中有 11016 个基因共表达，不同组织具有不同的功能，但催产素信号通路广泛富集。为了进一步探讨不同绵羊品种 HPO 表达基因 (DEGs) 的差异，我们下载了公共数据中的转录组数据，对 DEGs 的分析（兴羔羊与下丘脑的苏尼特羊、兴羔羊与垂体的苏尼特羊、兴羔羊与卵巢的萨福克羊）揭示了神经活性配体-受体相互作用。此外，还确定了 DEGs 转录因子 (TF) 的基因子集。结果表明，51 个 TF 基因和同源盒 TF 可能在 HPO 中的转录变异中发挥重要作用。总的来说，我们的研究提供了第一个基本资源来研究绵羊的生理功能和调节机制。这些重要的数据有助于提高我们对绵羊生殖生物学的理解，并分离出可用于绵羊遗传选择的影响分子标记。
