Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome.

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 SNP60 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 (SOCS2, TXN, DDR2 and GRB10 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.

Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations.

Many studies in human genetics compare informativeness of single-nucleotide polymorphisms (SNPs) and microsatellites (single sequence repeats; SSR) in genome scans, but it is difficult to transfer the results directly to livestock because of different population structures. The aim of this study was to determine the number of SNPs needed to obtain the same differentiation power as with a given standard set of microsatellites. Eight chicken breeds were genotyped for 29 SSRs and 9216 SNPs. After filtering, only 2931 SNPs remained. The differentiation power was evaluated using two methods: partitioning of the Euclidean distance matrix based on a principal component analysis (PCA) and a Bayesian model-based clustering approach. Generally, with PCA-based partitioning, 70 SNPs provide a comparable resolution to 29 SSRs. In model-based clustering, the similarity coefficient showed significantly higher values between repeated runs for SNPs compared to SSRs. For the membership coefficients, reflecting the proportion to which a fraction segment of the genome belongs to the ith cluster, the highest values were obtained for 29 SSRs and 100 SNPs respectively. With a low number of loci (29 SSRs or ≤100 SNPs), neither marker types could detect the admixture in the Gödöllö Nhx population. Using more than 250 SNPs allowed a more detailed insight into the genetic architecture. Thus, the admixed population could be detected. It is concluded that breed differentiation studies will substantially gain power even with moderate numbers of SNPs.