Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza

Abstract

Selection for desirable traits and breed-specific phenotypes has left distinctive footprints in the genome of pigs. As representative of a breed with strong selective traces aiming for robustness, health and performance, the Mangalitza pig, a native curly-haired pig breed from Hungary, was investigated in this study. Whole genome sequencing and SNP chip genotyping was performed to detect runs of homozygosity (ROH) in Mangalitza and Mangalitza-crossbreeds. We identified breed specific ROH regions harboring genes associated with the development of the curly hair type and further characteristics of this breed. Further analysis of two matings of Mangalitza with straight-coated pig breeds confirmed an autosomal dominant inheritance of curly hair. Subsequent scanning of the genome for variant effects on this trait revealed two variants potentially affecting hair follicle development and differentiation. Validation in a large sample set as well as in imputed SNP data confirmed these variants to be Mangalitza-specific. Herein, we demonstrated how strong artificial selection has shaped the genome in Mangalitza pigs and left traces in the form of selection signatures. This knowledge on genomic variation promoting unique phenotypes like curly hair provides an important resource for futures studies unraveling genetic effects for special characteristics in livestock.

Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

“…For example, minDP 2 resulted 32,933,744 SNPs, whereas minDP 16 provided 6,020,022 SNPs (Additional file 1: Table S1). Accordingly, we observed the highest number of SNPs (33,184,918) when minDP 2 and maxDP 95 were applied. Upscaling minDP up to 6 only slightly decreased the number of SNPs and resulted in the same size range as minDP 2.…”

“…Recent studies in pigs identified selection signatures and candidate genes related to economically important traits such as growth, reproduction, and meat quality [14,[28][29][30][31] or adaptability, disease resistance and immunity [14,29,30] in Chinese and Western breeds. ROHRs have been used to analyse selection signatures and genes linked to the phenotypic characteristics of Diannan small-ear pigs [32], Laiwu pigs [17], Mangalitza pigs [33], micro pigs [34], Piétrain pigs [35], Sicilian pigs [36], Xidu black pig [37] and different European autochthonous and commercial pigs [8,9,34,35,[38][39][40]. Previous studies in pigs were focussed mainly on longer ROHs and optimized the ROH calling parameters accordingly.…”

Atlas of Prenatal Hair Follicle Morphogenesis Using the Pig as a Model System

“…However, types III-VIII of human scalp hair were not detected in our study mainly because only Yorkshire pig was used. Other pig breeds with curly/wool hair such as the Mangalica pig (Schachler et al, 2020), Turopolje pig ( Čandek-PotokarRosa and Nieto, 2019), Canastrao pig (Rhoad, 1934), or Cuino pig (Lemus-Flores et al, 2005) could be used to identify more hair types. Thus, considering the similarity of the pig hair types to human scalp hair, pig proves to be an ideal model for human HF research.…”

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

“…Although ROHs are known to arise from several genetic factors, including genetic drift and population bottlenecks, it has been used as an indicator of selection signatures throughout the genome. In fact, ROHs have been widely used to quantify autozygosity in pigs (Schachler et al, 2020;Wu et al, 2020); because ROH are widely but not randomly distributed across the genome, some ROH overlap with genomic regions associated with economically important traits in pigs. Furthermore, ROH can be used to distinguish between recent and ancient inbreeding (Keller et al, 2011).…”