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.

Figure 1

ROH analysis in Mangalitza pigs. Size in kilobasepairs (kb) of consensus ROHR specific for Mangalitza per chromosome (displayed in bars) and their chromosomal coverage in percent (%) (displayed as curve) inferred from WGS data (a) and SNP chip genotyping data (b).

Figure 2

Phenotype in a resource family generated for detailed investigation of curly hair inheritance in Mangalitza. (a) Pedigree of resource family: black circle = female, curly-haired; black square = male, curly-haired; white circle = female, straight-haired; white square = male, straight-haired (b) Detailed presentation of hair types in curly and straight-haired parenteral generation: the hair in Mangalitza is constituted of curly bristles and of tightly curly wool hair (triangle), whereas in straight-haired breeds bristles are straight (star) (c) Development of curly hair in a mating between a Mangalitza boar and an Angeln Saddleback sow at the age of 4 months (left) and 16 months (right) recorded in March. The figure displays one black male (above) and one belted female (below) individual of the litter. At the age of 4 months, the degree of curliness was variable within the litter, but at the age of 16 months, curly coat was completely expressed in all individuals of the litter. (d) Development of curly hair in crossbreeds from mating a Mangalitza sow and a miniature pig boar. The figure presents one male (above) and one female (below) individual of the litter. With 5.5 months (September—left) no curly hair was observed within the litter, but at the age of 11 months (March—right), curly coat was expressed all individuals.