The Expression Level of the Alpaca Agouti Gene has a Marked Impact on Fibre Colour Intensity

Most of the research into the molecular aspects of alpaca colour genetics has focussed on the interactions between the melanocortin-1 receptor and its ligand agouti. This information has improved our understanding of how the switch between eumelanin and pheomelanin production is controlled in alpacas. However it does not explain all of the many of different colours observed in the species, nor is there an understanding of what controls intensity of colour.

We used RNAseq to determine the expression levels of genes expressed in the skin of white, light-skinned fawn, dark-skinned fawn, light bay, bay and black alpacas in order to identify genes that may be important in controlling fibre colour intensity in the species.  These data show that agouti may play a role in controlling pigment intensity, as well as its role in pigment switching.  Agouti is most highly expressed in white alpacas (RPKM=120), is moderately expressed in fawn and bay phenotypes (RPKM=44-69), and has low expression in the black phenotype (RPKM=4). Six different alternate non-coding exon 1 agouti sequences were identified. None of the alternate agouti non-coding exon 1 sequences are restricted to any particular colour or group of colours. Interestingly, the two most common exon 1 isoforms map to the genome approximately 400Kb upstream of the agouti gene, in the incorrect orientation for a long distance alternate splicing event. Expression of tyrp1, a key gene in the production of eumelanin, is negatively correlated with agouti expression.