Identification of six genomic regions associated with pigment intensity in alpacas

Abstract

Context Currently, there is a growing consumer demand for more ecologically sustainable practices in the textile industry. Fabric dyeing is highly pollutive, and one way to avoid dyeing is to use naturally coloured fibres. Alpacas exhibit a wide range of fleece colours, thereby making them a good source of fibre for sustainable textile production. Our understanding of the colour genetics of alpacas is improving, but there is still no explanation for all the variation seen in alpaca coat colours. Aims To identify a region or regions in the alpaca genome that contribute to differences in pigment intensity. Methods Colorimetric analysis using L*a*b* colourspace of fibre from white and black alpacas, that had been genotyped using the Neogen Australasia alpaca coat colour test, was used to classify the samples into intense and dilute groups for each colour. Illumina short-read genotyping by sequencing of the DNA from these alpacas was used to identify single nucleotide polymorphisms that were subsequently used in a case–control genome-wide association study (GWAS) comparing the extreme dilute and intensely pigmented animals. Key results Intense eumelanic fibre is darker (P = 0.0003), less red (P = 0.004), and more blue (P = 0.001) than is dilute eumelanic fibre. Intense pheomelanic fibre is darker (P = 1 × 10−7), more red (P = 3 × 10−20), and more yellow (P = 2 × 10−6) than is dilute pheomelanic fibre. The GWAS showed six regions of genome-wide significance. After manual inspection of these six regions, the best candidate region was upstream of KITLG, a gene previously associated with pigment intensity in dogs. Conclusions In combination with ASIP genotype, a regulatory mutation in a region upstream of KITLG in alpacas potentially has a major effect on pigment intensity in the species. Implications Successful identification of a marker for pigment intensity will allow breeders to select more precisely for breeding and production animals that will assist them in supplying the desired fibre colours to the textile industry.