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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.

SUBMITTER: Schachler K

PROVIDER: S-EPMC7747725 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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

Schachler Kathrin K Distl Ottmar O Metzger Julia J

Scientific reports 20201217 1

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 ...[more]

PMID: 33335158

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Project description:Abstract The detection of selection signatures can help to understand the mechanisms of artificial selection. The purpose of this work is to determine the selection signatures in Civil pig relatively Large White breed. The research was carried out on Large White of three breeding centers (LW_1_New=16, LW_2_New=12, LW_3_New=15) and Civilskay, bred in Russia on the basis of local pigs and Large White boars, (Civil=17). GeneSeek GGP Porcine HD BeadChip (San Diego, USA) was used. A heatmap plot of genomic relationship matrix (GRM) was used to evaluate genetic variability between populations. The signals of diversifying selection were detected using Fst and Smoothing Fst (R package Lokern). QTLs and genes were identified and annotated in the Ensembl genome browser (Sscrofa 11.1) (https://www.ensembl.org/index.html), Panther 15.0 (http://www.pantherdb.org/) and QTLdb (https://www.animalgenome.org/cgi-bin/QTLdb/index).Data visualization from heatmapplot (Fig.) showed that all individuals are grouped in relation to their groups. However, the groups LW_1_New, LW_3_New and CIVIL were separated from LW_2_New. We have selected LW_1_New, LW_3_New and CIVIL to identify the selection signatures. After smoothing of the data by moving average, top 0.1% of the observations were considered as pinpointing CIVIL-specific selection signals. As a result, genome regions with strong selection signals on SSC1:214634036-217738857, SSSC2:137533941-138048506, SSC4:24655041-30832595, SSC7:27386432-28655399 and SSC8:55806826-56299366 were found. In these areas, 535 QTLs have been identified, including 347 QTLs for Meat and Carcass Traits (the majority related to Backfat), 67 QTLs Production (Average daily gain or Body weight), 62 QTLs Health (Mean corpuscular volume, Actinobacillus pleuropneumoniae susceptibility et al.), 32 QTLs Reproduction (Teat number) and 27 QTLs Exterior (Leg conformation). In general, 32 genes are defined in these regions (SSC1-11; SSC2-5; SSC4-10; SSC7-3; SSC8-3) (Table). They are mainly involved in the following biological processes: metabolic (GO:0008152), cellular (GO:0009987) and biological regulation (GO:0065007). This research was supported by the Russian Scientific Foundation (RSF) within Project No. 19-16-00109.

Dataset Information

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

Publications

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

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