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

Simple Summary The Rex rabbit is a representative fur-type breed, yet the molecular mechanisms underlying its distinct fur characteristics relative to meat-type rabbit breeds remain incompletely understood. In this study, fur quality traits were evaluated in Rex and New Zealand White rabbits, followed by integrated metabolomic and transcriptomic profiling of dorsal skin tissues. Rex rabbits showed significantly shorter fibre length and reduced fur thickness compared with New Zealand White rabbits. A total of 267 differential metabolites and 895 differentially expressed genes were identified, with joint enrichment in pathways associated with hair follicle development, including HIF-1, cAMP, and AMPK signaling. Histamine, L-arginine, keratin family genes, BMP5, and DKK2 were identified as key molecular components associated with fur development. These results provide insights into the coordinated gene–metabolite regulatory mechanisms underlying rabbit skin and hair follicle development and identify potential molecular markers for improving fur quality through selective breeding.