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Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs
Author(s) -
Stratz P.,
Wimmers K.,
Meuwissen T.H.E.,
Bennewitz J.
Publication year - 2014
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12107
Subject(s) - biology , linkage disequilibrium , genome , genetics , population , haplotype , selection (genetic algorithm) , sire , genome wide association study , genetic association , evolutionary biology , gene , allele , single nucleotide polymorphism , genotype , zoology , demography , artificial intelligence , sociology , computer science
Summary The aim of this study was to study the population structure, to characterize the LD structure and to define core regions based on low recombination rates among SNP pairs in the genome of Piétrain pigs using data from the Porcine SNP 60 BeadChip. This breed is a European sire line and was strongly selected for lean meat content during the last decades. The data were used to map signatures of selection using the REHH test. In the first step, selection signatures were searched genome‐wide using only core haplotypes having a frequency above 0.25. In the second step, the results from the selection signature analysis were matched with the results from the recently conducted genome‐wide association study for economical relevant traits to investigate putative overlaps of chromosomal regions. A small subdivision of the population with regard to the geographical origin of the individuals was observed. The extent of LD was determined genome‐wide using r 2 values for SNP pairs with a distance ≤5 Mb and was on average 0.34. This comparable low r 2 value indicates a high genetic diversity in the Piétrain population. Six REHH values having a p‐value < 0.001 were genome‐wide detected. These were located on SSC 1, 2, 6 and 17. Three positional candidate genes with potential biological roles were suggested, called LOC 100626459, LOC 100626014 and MIR 1. The results imply that for genome‐wide analysis especially in this population, a higher marker density and higher sample sizes are required. For a number of nine SNP s, which were successfully annotated to core regions, the REHH test was applied. However, no selection signatures were found for those regions (p‐value < 0.1).