Table 1_The expression of genes in different sites of gut tract regulates the meat quality of semitendinosus muscle in sheep and goats.xlsx

IntroductionFor small ruminants, meat quality—an economically significant characteristic—results from the combined effects of genetic, dietary, and physiological elements. However, the contribution of gastrointestinal (GI) tract gene expression to meat quality remains unclear.
MethodsHere, we performed bulk RNA-seq on 130 samples from Liangshan Black Sheep and Meigu Black Goats, including 10 GI tract segments and semitendinosus muscle, integrating these data with measurements of amino acid composition, fatty acid profiles, and volatile flavor compounds.
Results and discussionWe found distinct, segment-specific transcriptional programs across the GI tract, with major functional shifts at the rumen–reticulum, omasum–abomasum, and abomasum–duodenum transitions. In the ileum and jejunum, genes involved in lipid metabolism showed links to fatty acid profiles, whereas genes governing amino acid metabolism in the small intestine were connected to the amino acid composition of muscle. Cecum- and colon-enriched genes were linked to flavor precursor biosynthesis. Species-specific differences revealed that sheep muscle contained higher levels of key amino acids (Asp, Glu, Hyp, Cys, Tyr), whereas goats showed higher α-linolenic acid and other polyunsaturated fatty acids. This work establishes a gut–muscle transcriptomic axis in small ruminants, identifying candidate genes (e.g., GKN2, APOC3, AQP5) and pathways that may be involved in regulating amino acid, fatty acid, and flavor traits of meat quality.

引言：对于小型反刍动物而言，肉质是一项具有重要经济价值的性状，其形成受到遗传、日粮及生理因素的共同作用。然而，胃肠道（gastrointestinal, GI）基因表达对肉质的调控贡献仍未明确。
方法：本研究对凉山黑羊与美姑黑山羊的130份样本开展批量RNA测序（bulk RNA-seq），样本涵盖10个胃肠道节段与半腱肌；同时将测序数据与氨基酸组成、脂肪酸谱及挥发性风味物质的检测结果进行整合分析。
结果与讨论：本研究发现胃肠道内存在显著的节段特异性转录程序，在瘤胃-网胃、瓣胃-皱胃以及皱胃-十二指肠的交界区域发生了主要的功能重塑。在回肠与空肠中，参与脂质代谢的基因与脂肪酸谱呈现显著关联；而小肠内调控氨基酸代谢的基因则与肌肉的氨基酸组成存在相关性。富集于盲肠与结肠的基因与风味前体物质的生物合成密切相关。物种特异性差异分析显示，绵羊肌肉中关键氨基酸（天冬氨酸Asp、谷氨酸Glu、羟脯氨酸Hyp、半胱氨酸Cys、酪氨酸Tyr）含量更高，而山羊的α-亚麻酸及其他多不饱和脂肪酸水平更优。本研究构建了小型反刍动物的肠道-肌肉转录调控轴，鉴定出可能参与调控肉质氨基酸、脂肪酸及风味性状的候选基因（如GKN2、APOC3、AQP5）与相关通路。