A copy number variant near KITLG is associated with the roan pattern in alpacas

Abstract

Context The alpaca roan pattern is characterised by white and coloured fibre interspersed together, with a distinctive lighter body and darker extremities, and commonly is believed to be inherited in an autosomal dominant manner. It is of interest to the alpaca fibre industry as it causes ‘contamination’ of coloured fibre with white fibres, but cannot be detected in white or light fawn animals. Other livestock species, such as horses, cattle, goats, and pigs, exhibit comparable phenotypes, which are associated with candidate variant(s) in either KIT or KITLG. Aims To identify a region or regions of the genome that is/are causative of the roan pattern in alpacas. Methods We conducted a genome-wide association study (GWAS) by using 13 roan and 14 non-roan alpacas sampled from the USA, Australia, and New Zealand. Regions of genome-wide significance were examined for variants that correlated with the roan phenotype. Key results A novel candidate single-nucleotype polymorphism (SNP; Super-Scaffold_15:39 742 851T > A), located 272 kb upstream of KITLG, was identified in 1 of 12 regions with genome-wide significant association (P ≤ 5 × 10−8). We identified the candidate SNP-containing region (Super-Scaffold_15:39 742 096–39 887 419) to be a 145 kb copy number variant (CNV) that is likely to be a tandem duplication. All 13 roan alpacas had one or two copies of the roan-associated T allele and all except three non-roans had zero copies. Furthermore, we determined the Mendelian inheritance of copy number haplotypes and their allelic composition in a roan and a non-roan family. Conclusions Our data support the hypothesised autosomal incomplete dominant mode of inheritance of the roan pattern in alpacas and suggests that the effect of the T allele CNV version is likely to be suppressed when in cis with the A allele CNV version. However, additional verification is required to validate the finding and determine the functional effect. Implications Identification of the cause, or a marker for roan pattern will allow alpaca breeders to select for or against the roan pattern, even when the phenotype is hidden, and therefore increase production output and profitability.