# The expression of genes in different sites of gut tract regulates the meat quality of semitendinosus muscle in sheep and goats

## TL;DR

This study explores how gene expression in the gut of sheep and goats influences meat quality traits like amino acids, fatty acids, and flavor.

## Contribution

The study identifies a gut–muscle transcriptomic axis and candidate genes regulating meat quality in small ruminants.

## Key findings

- Segment-specific transcriptional programs in the GI tract show functional shifts at key anatomical transitions.
- Genes in the ileum and jejunum are linked to fatty acid profiles, while small intestine genes influence muscle amino acid composition.
- Cecum and colon genes are associated with flavor precursor biosynthesis, and species-specific differences in meat composition are observed.

## Abstract

For 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.

Here, 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.

We 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.