Comparative Transcriptomic Analysis of Alpaca (Vicugna pacos) Skin Identifies Candidate Genes and Biological Processes Associated with Fiber Color

The transcriptomic basis of natural fiber-color diversity in alpacas remains incompletely understood. We analyzed skin biopsies from 65 Huacaya alpacas by RNA sequencing (RNA-seq) and integrated phenotypic color categories with instrumental Commission Internationale de l′Éclairage L*a*b* CIELAB measurements, a standardized color space system used to objectively measure and quantify color. Differential expression was assessed using DESeq2 differential-expression analysis package with adjustment for collection batch, sex, and fiber-color category, while L* (lightness), a* (green–red axis), and b* (blue–yellow axis) were examined in separate continuous models. The categorical analysis included 64 samples and 25,405 genes. We identified 4968, 3993, 1469, and 7607 differentially expressed genes in light brown (LB), dark brown (DB), light fawn intensity Y (LFY), and light fawn intensity Z (LFZ), respectively, relative to white (W), with higher expression predominating in pigmented categories. Global transcriptomic structure and gene-level expression patterns were associated with CIELAB parameters, supporting the use of these measurements as complementary quantitative descriptors of fiber color. However, these associations should be interpreted cautiously because of the imbalance between collection batches and the heterogeneous cellular composition of the skin biopsies. Integration of categorical, continuous, and functional evidence prioritized TYR (tyrosinase), TYRP1 (tyrosinase-related protein 1), MITF (melanocyte-inducing transcription factor), EDNRB (endothelin receptor type B), MFSD12 (major facilitator superfamily domain containing 12), and GPR143 (G protein-coupled receptor 143), among other genes. Two regions with unassigned locus (LOC) identifiers in VicPac4 showed evidence consistent with premelanosome protein (PMEL), and a third with OCA2 melanosomal transmembrane protein (OCA2/P), although these identities remained interpretive proposal. Genes with higher expression in pigmented categories were overrepresented in pigmentation and melanosome processes, whereas genes with lower expression were associated with epidermal and keratin-related processes. These findings identify transcriptomic changes associated with natural fiber-color variation and candidates for functional validation.