Whole genome sequencing analysis of alpaca suggests TRPV3 as a candidate gene for the suri phenotype

• Published in: BMC genomics Vol. 25; no. 1; p. 185
• Main Authors: Pallotti, Stefano, Picciolini, Matteo, Deiana, Giovanni, Pediconi, Dario, Antonini, Marco, Napolioni, Valerio, Renieri, Carlo
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 16.02.2024; BioMed Central; BMC
• Subjects: Alpaca; Alpacas; Amino acids; Animals; Camelidae; Camelids; Camelids, New World - genetics; Chromosomes; Codon; Codon, Nonsense; Cold tolerance; DNA sequencing; Domestication; Fibers; Folding; Follicles; Gene sequencing; Genes; Genetic aspects; Genetic crosses; Genetic research; Genomes; Genomics; Genotype & phenotype; Guanaco; Hair; Huacaya; Humans; Ion channels; Methods; Mice; Mutation; Nonsense mutation; Nucleotide sequencing; Offspring; Phenotype; Phenotypes; Physiological aspects; Proteins; Sensation; Suri; T cell receptors; Transient receptor potential proteins; TRPV Cation Channels - genetics; TRPV3; Vicugna; Whole Genome Sequencing; Zoological research; Italy; South American camelids; Huacaya; Guanaco; TRPV3; Alpaca; Vicugna; Fibre production; Suri
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10086-8

Alpaca is a domestic South American camelid probably arising from the domestication of two wild camelids, the vicugna and the guanaco. Two phenotypes are described for alpaca, known as huacaya and suri. Huacaya fleece is characterized by compact, soft, and highly crimped fibers, while suri fleece is longer, straight, less crimped, and lustrous. The gene variants determining these phenotypes are still unknown, although previous studies suggested a dominant inheritance of the suri. Based on that, the aim of this study was the identification of the gene variants determining alpaca coat phenotypes through whole genome sequencing (WGS) analysis. The sample used includes two test-cross alpaca families, suri × huacaya, which produced two offspring, one with the suri phenotype and one with the huacaya phenotype. The analyzed sample was expanded through the addition of WGS data from six vicugnas and six guanacos; this because we assumed the absence of the gene variants linked to the suri phenotype in these wild species. The analysis of gene variant segregation with the suri phenotype, coupled with the filtering of gene variants present in the wild species, disclosed the presence in all the suri samples of a premature termination codon (PTC) in TRPV3 (transient receptor potential cation channel subfamily V member 3), a gene known to be involved in hair growth and cycling, thermal sensation, cold tolerance and adaptation in several species. Mutations in TRPV3 were previously associated with the alteration of hair structure leading to an impaired formation of the hair canal and the hair shaft in mouse. This PTC in TRPV3, due to a G > T substitution (p.Glu475*), results in a loss of 290 amino acids from the canonical translated protein, plausibly leading to a physiological dysfunction. The present results suggest that the suri phenotype may arise from a TRPV3 gene variant which may explain some of the suri features such as its longer hair fibre with lower number of cuticular scales compared to huacaya.