Table_7_Hypothalamic Transcriptome Analysis Reveals the Crucial MicroRNAs and mRNAs Affecting Litter Size in Goats.XLSX

The hypothalamus was the coordination center of the endocrine system, which played an important role in goat reproduction. However, the molecular mechanism of hypothalamus regulating litter size in goats was still poorly understood. This study aims to investigate the key functional genes associated with prolificacy by hypothalamus transcriptome analysis of goats. In this research, an integrated analysis of microRNAs (miRNAs)-mRNA was conducted using the hypothalamic tissue of Yunshang black goats in the follicular stage. A total of 72,220 transcripts were detected in RNA-seq. Besides, 1,836 differentially expressed genes (DEGs) were identified between high fecundity goats at the follicular phase (FP-HY) and low fecundity goats at the follicular phase (FP-LY). DEGs were significantly enriched in 71 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome data suggested that DEGs such as BMPR1B, FGFR1, IGF1 and CREB1 are directly or indirectly involved in many processes like hypothalamic gonadal hormone secretion. The miRNA-seq identified 1,837 miRNAs, of which 28 differentially expressed miRNAs (DEMs). These DEMs may affect the nerve cells survival of goat hypothalamic regulating the function of target genes and further affect the hormone secretion activities related to reproduction. They were enriched in prolactin signaling pathway, Jak-STAT signaling pathway and GnRH signaling pathway, as well as various metabolic pathways. Integrated analysis of DEMs and DEGs showed that 87 DEGs were potential target genes of 28 DEMs. After constructing a miRNA-mRNA pathway network, we identified several mRNA-miRNAs pairs by functional enrichment analysis, which was involved in hypothalamic nerve apoptosis. For example, NTRK3 was co-regulated by Novel-1187 and Novel-566, as well as another target PPP1R13L regulated by Novel-566. These results indicated that these key genes and miRNAs may play an important role in the development of goat hypothalamus and represent candidate targets for further research. This study provides a basis for further explanation of the basic molecular mechanism of hypothalamus, but also provides a new idea for a comprehensive understanding of prolificacy characteristics in Yunshang black goats.

下丘脑（hypothalamus）是内分泌系统的协调中枢，在山羊繁殖过程中发挥重要作用。然而，下丘脑调控山羊产羔数的分子机制仍不甚明晰。本研究旨在通过对山羊下丘脑进行转录组分析，筛选与多产性状相关的关键功能基因。本研究以卵泡期云上黑山羊的下丘脑组织为材料，开展了微小RNA（microRNAs）与mRNA的联合整合分析。RNA测序（RNA-seq）共检测到72220条转录本。此外，在卵泡期高繁殖力山羊（FP-HY）与卵泡期低繁殖力山羊（FP-LY）之间，共鉴定出1836个差异表达基因（DEGs）。差异表达基因显著富集于71个基因本体（Gene Ontology）条目以及8条京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，简称KEGG）通路。转录组数据显示，BMPR1B、FGFR1、IGF1及CREB1等差异表达基因可直接或间接参与下丘脑促性腺激素分泌等多种生理过程。微小RNA测序（miRNA-seq）共鉴定出1837个微小RNA，其中28个为差异表达微小RNA（DEMs）。这些差异表达微小RNA可通过调控靶基因的表达，影响山羊下丘脑神经细胞存活，进而参与繁殖相关的激素分泌活动。它们显著富集于催乳素信号通路、Jak-STAT信号通路、促性腺激素释放激素（GnRH）信号通路以及多种代谢通路。对差异表达微小RNA与差异表达基因的联合分析显示，87个差异表达基因是28个差异表达微小RNA的潜在靶基因。构建miRNA-mRNA通路网络后，通过功能富集分析鉴定出多个参与下丘脑神经细胞凋亡的mRNA-miRNA调控对，例如Novel-1187与Novel-566共同调控NTRK3，以及Novel-566调控另一靶基因PPP1R13L。上述结果表明，这些关键基因与微小RNA可能在山羊下丘脑发育过程中发挥重要作用，可作为后续研究的候选靶点。本研究为进一步阐明下丘脑的基础分子机制提供了理论依据，同时也为全面理解云上黑山羊的多产性状提供了新的研究思路。