Genomic scan of selective sweeps in an alpaca population subjected to directional selection for fibre quality traits

Abstract

Improving fibre quality traits is a key objective in alpaca breeding programmes. A total of 630 alpaca individuals managed at the Pacomarca experimental farm located in Puno, Perú, and subjected to selection for fibre quality traits were genotyped using the Affymetrix Custom Alpaca genotyping array (76 508 SNPs). Two tests, the integrative Haplotype Score (iHS) and the number of segregating Sites by Length (nSL), aimed at identifying incomplete sweeps, were applied on all sample genotypes to identify selective candidate genomic regions spanning genes putatively involved in fibre production. The Cross-Population Extended Haplotype Homozygosity (XP-EHH) statistic was applied to two divergent subpopulations included in the total genotyped population: one less selected (reference; 49 individuals) and one highly selected (target; 127 individuals) to assess if some of the selective sweeps identified with both iHS and nSL were fixed in the target subpopulation. A total of 544 single-nucleotide polymorphisms (SNPs) were identified as candidate selective signals using both the iHS and nSL tests. Furthermore, 27 SNPs were identified as surrounding selective signals and further considered as candidate selective signals as well. A total of 509 candidate selective genomic regions covering 14.6 Mb of the alpaca genome were constructed. Gene-annotation enrichment analyses enabled to identify 293 candidate genes in these selective candidate genomic regions. Up to 11 candidate genes (e.g. PTPRN, FRK, PTPN23, and PTPRT) were associated with Gene Ontology (GO) terms related to phosphorylation and dephosphorylation and 28 candidate genes (e.g. FOXP1, MITF, RNF10, and ZNF664) with GO terms related to RNA polymerase activity. These genes have been reported to play a crucial role in the development of animal hair follicles, as well as in regulating hair growth and quality across different livestock species. Functional annotation conducted allowed to identify four significantly enriched functional term clusters including a total of 32 candidate genes. These functional clusters may be involved in the modulation of fibre growth and quality as well as skin and hair follicle development. Moreover, enrichment analyses within candidate selective genomic regions identified with XP-EHH allowed to identify 54 candidate genes, 10 of which were also identified using both the iHS and nSL tests. However, no functional clusters were identified. The results presented suggest that the genomes analysed were shaped by directional selection for fibre quality traits, involving multiple chromosomal areas of the alpaca genome. This fits well with traits expected to be mainly controlled by genes of additive effect