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Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome
Author(s) -
Gärke C.,
Ytournel F.,
Sharifi A. R.,
Pimentel E. C. G.,
Ludwig A.,
Simianer H.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12150
Subject(s) - biology , breed , genetics , single nucleotide polymorphism , genome , snp , selection (genetic algorithm) , genomic selection , coat , genotype , gene , paleontology , artificial intelligence , computer science
Summary The Göttingen Minipig ( GMP ) developed at the University of Göttingen is a synthetic breed that is widely used in medical research and toxicology. It combines the high fertility of the Vietnamese potbellied pig, the low body weight of the Minnesota Minipig and the white coat colour of the German Landrace pig. The aim of this study was to find genomic regions that may have undergone selection since the creation of the breed in the 1960s. Therefore, the whole genome was screened for footprints of recent selection based on single nucleotide polymorphism ( SNP ) genotypes from the Illumina Porcine SNP 60 BeadChip using two methods: the extended haplotype homozygosity ( EHH ) test and the estimation of the genomic proportion of the three original breeds at each SNP using a Bayesian approach. Local deviations from the average genome‐wide breed composition were tested with a permutation‐based empirical test. Results for a comprehensive whole‐genome scan for both methods are presented. Several regions showing the highest P ‐values in the EHH test are related to breeding goals relevant in the GMP , such as growth ( SOCS 2, TXN , DDR 2 and GRB 10 genes) and white colour ( PRLR gene). Additionally, the calculated proportion of the founder breeds diverged significantly in many regions from the pedigree‐based expectations and the genome average. The results provide a genome‐wide map of selection signatures in the GMP , which leads to a better understanding of selection that took place over the last decades in GMP breed development.