Integrative Analysis of the Metabolome and Transcriptome Reveals the Mechanism Underlying Differences in Skin Development Between the New Zealand Rabbit and the Rex Rabbit

Abstract

Rex rabbit fur is a high-value material in the textile industry; however, the integrated metabolomic and transcriptomic mechanisms underlying differences in fur traits between fur-type Rex rabbits and meat-type New Zealand White rabbits remain incompletely understood. In this study, 40 rabbits (20 per group) raised under identical feeding conditions were used to evaluate fur quality traits. Dorsal skin samples were collected for metabolomic and transcriptomic analyses. The results showed that Rex rabbits had significantly lower fibre length and fur thickness than New Zealand White rabbits (p < 0.01). Metabolomic analysis identified 267 DMs, mainly comprising lipids and organic acids. These metabolites were enriched in butanoate metabolism, steroid hormone biosynthesis, cysteine and methionine metabolism, and the citrate cycle. Key metabolites included histamine, L-arginine, creatine, and indoxyl. Transcriptomic analysis identified 895 DEGs, enriched in MAPK, cAMP, and HIF-1 signaling pathways, including keratin family genes (KRT34, KRT84, KRT82), FGFR4, EGF, BMP5, and DKK2. Integrated analysis identified 211 DEGs and 97 DMs co-enriched in 103 pathways, including HIF-1, cAMP, and AMPK signaling pathways. These findings reveal a gene–metabolite regulatory network involved in skin and hair follicle development, provide molecular markers for improving rabbit fur quality, and enhance understanding of the genetic and metabolic basis of mammalian hair follicle development.