Metabolomic Profiling Screening for Molecular Level Associations Related to Cashmere Quality Related Phenotypic Types in Liaoning Cashmere Goats

Background/Objectives: Distinct cashmere-related traits are observed between long cashmere short wool (LC-SW) and short cashmere long-hair (SC-LW) Liaoning cashmere goats. Yet metabolic differences associated with these phenotypes remain poorly characterised. This study explored skin metabolic divergence between two specific farm-raised maternal families that consistently exhibit LC-SW and SC-LW phenotypes, providing preliminary references for improving cashmere traits. Considering experimental limitations, phenotype is confounded by maternal family genetic background; therefore, this work does not aim to uncover universal mechanisms underlying breed-wide LC-SW/SC-LW subtypes. Methods: 120 healthy adult female Liaoning cashmere goats from two independent maternal families were used for phenotypic measurement. Among them, six animals from each family (total n = 12) were randomly selected for untargeted metabolomic analysis of skin tissue using GC-TOF-MS. Results: The two maternal families differed significantly in body weight, cashmere yield and cashmere fibre length (p < 0.05), whereas cashmere fibre diameter showed no significant difference. In total, 89 nominally associated candidate metabolites were mapped to the following KEGG pathways: amino acid biosynthesis, ABC transporters, and central carbon metabolism in cancer (KEGG database annotations for core carbon-related metabolites; no cancer-related physiology is implied). The LC-SW family showed higher relative abundances of metabolites associated with glycolysis/TCA-related metabolism, as well as multiple amino acid-related metabolites. These energy-related and keratin precursor-related metabolites exhibit higher relative abundance in the LC-SW-related maternal family. The SC-LW family exhibited reduced levels of γ-aminobutyric acid and glutamate, indicating metabolite-level differences that warrant further investigation into links with cashmere length traits. Conclusions: This study characterises skin metabolomic profiles of two phenotype-divergent maternal families. These findings offer preliminary data for cashmere trait research, but cannot be generalised to all LC-SW and SC-LW goats. Further validation using materials from multiple unrelated families is required.