Association of ASIP and MC1R genotypes with the quantitative color variation in Huacaya alpaca

Pinares R.; Daverio M.S.; Cruz A.; Gutiérrez-Reynoso G.A.; Munyard K.A. · Small Ruminant Research (2026) · DOI: 10.1016/j.smallrumres.2026.107704

Resumen

The aim of this study was to identify the variants, genotypes, and haplotypes for the ASIP and MC1R genes in vicuñas and Huacaya alpacas, and to assess the association of these variants with fiber lightness and chromaticity values. The lightness and chromaticity values of the fiber for black/brown-black, dark brown/light brown, and white Huacaya alpacas, and vicuña were measured and grouped using the CIE L*a*b system. Genomic DNA was isolated from 89 alpacas and 9 vicuñas. Exons 2 and 4 of the ASIP gene and the coding sequence of MC1R were amplified and sequenced. Two non-synonymous variants (c.292 C>T and c.353 G>A) and a 57 bp in-frame deletion (c.325_381del) were identified in exon 4 of ASIP, and c.82 A>G, c.259 A>G, c.376 A>G, c.587 T > C, and c.901 C>T single nucleotide variants (SNV) plus a frameshift 4 bp deletion were identified in MC1R. Association analysis was carried out to relate the color phenotypes with variants and haplotypes, and genotypes of both genes. Loss-of-function recessive alleles (a1, a2, and a3) of ASIP gene were more frequently associated with black/brown-black fibers. All black/brown-black alpacas have at least one E allele of MC1R gene. Thus, an interaction between the recessive ASIP alleles with the dominant alleles of MC1R defines the black/brown-black alpaca color. In conclusion, alpaca fibers with the lowest lightness and lowest chromaticity tend to exhibit black/brown-black and dark brown phenotypes, although it was not possible to identify a clear cut-off between these groups. The a1a1/E-, a1a2/E-, a3a3/E-, and a1a3/E- genotypes and variants should be used as a selection marker for black/brown-black alpacas.

Instituciones: Universidad Nacional Agraria La Molina; Universidad Nacional de San Antonio Abad del Cusco