Genome-Wide Detection of Selection Signatures for Pelt Quality Traits and Coat Color Using Whole-Genome Sequencing Data in American Mink

Abstract

Domestication and selection are the major driving forces responsible for creating genetic variability in farmed species. American mink has been under selection for more than 100 years for improved body size and pelt quality. This study aimed to identify the genomic regions subjected to selection for pelt quality traits, and coat color using the whole genome sequences of 100 mink raised in the Canadian Centre for Fur Animal Research (CCFAR) at Dalhousie Agriculture Campus (Truro, NS, Canada), and Millbank fur farm (Rockwood, ON, Canada). Measurements of three dried pelt characteristics (including pelt size (n = 35), overall quality of fur (n = 27), and nap size (n = 29)), and three coat color of Black, Stardust, and Pastel (Stardust_ Black (n = 38), and Pastel_Black (n = 41)) were used to assign animals to pairwise groups. Signatures of selection were detected using integrated measurement of fixation index (Fst), extended haplotype homozygosity (XP-EHH), and nucleotide diversity (θπ) tests. In total, overlapping top 1% of Fst and XP-EHH harbored 376 genes for pelt quality traits (110 for nap size, 163 for overall quality of fur, and 98 pelt size), and 194 genes for coat color (123 for Pastel_Black and 71 for Stardust_Black) were detected in different groups. Integrating results of Fst, and XP-EHH with the θπ test supported 19 strongly selected regions on chromosomes 3, 4, 5, 6, 7, 8, 9, and 10 that contained 33 candidate genes related to fur quality, hair follicle function, and pelt size traits. Gene ontology revealed numerous genes related to the hair cycle process and molting cycle process, epidermis development, Wnt signaling pathway and muscle development. This study provided the first map of putative selection signals related to pelt quality and coat color in American mink, which could be used as a reference for future studies attempting to identify genes associated with economically important traits in mink.