The agouti gene encodes the agouti signaling protein (ASIP) which regulates pheomelanin and eumelanin synthesis in mammals. To investigate the role of agouti in coat color variation of alpaca, we characterized the agouti gene and identified three mutations potentially involved with the determinism of eumelanic and pheomelanic phenotypes. The exon-4 hosts the mutations g.3836C>T, g.3896G>A and g.3866_3923del57. Further analysis of these mutations revealed two genotypes for black animals. The reverse transcription analysis of mRNA purified from skin biopsies of alpaca revealed the presence of three transcripts with different 5' untranslated regions (UTRs) and color specific expression. The white specific transcript, possibly originating from a duplication event (intra-chromosomal recombination) of the agouti gene is characterise by a 5'UTR containing 142bp of the NCOA6 gene sequence. Furthermore, the relative level expression analysis of mRNA demonstrates that the agouti gene has up-regulated expression in white skin, suggesting a pleiotropic effect of agouti in the white phenotype. Our findings refine the structure of the agouti locus and transcripts and provide additional information in order to understand the role of agouti in the pigmentation of alpaca.

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