Comparison of linkage disequilibrium, effective population size and haplotype blocks in Polish Landrace and Polish native pig populations
Igor Jasielczuk , Artur Gurgul , Tomasz Szmatoła , E. Semik-Gurgul , Klaudia Pawlina-Tyszko , Magdalena Szyndler-Nędza , Tadeusz Blicharski , Karolina Szulc , Ewa Skrzypczak , Monika Bugno-Poniewierska
AbstractThe aim of this study was to characterize in detail linkage disequilibrium (LD), effective population size (Ne) and haplotype blocks at the genome level using single nucleotide polymorphism (SNP) information in Polish Landrace (PL; n = 135) and compared these data with information obtained for conserved pig breeds derived from Polish native Puławska (PUL; n = 155), Złotnicka White (ZW; n = 141) and Złotnicka Spotted (ZS; n = 99) pigs based on single nucleotide polymorphism markers from Illumina PorcineSNP60 v2 BeadChip. LD analysis was performed based on the pairwise r2 statistic of SNPs at a distance up to 5 Mb. At a short distance up to 100 kb the lower average r2 were observed in PL (0.33) and PUL (0.34) breeds compared to ZW (0.39) and ZS (0.45) breeds. At a distances of 4–5 Mb - the average values of r2 were 0.05, 0.07, 0.11 and 0.15 for PL, PUL, ZW and ZS, respectively. Ne ranged from 147 (ZS) to 263 (PL) 100 generations ago and from 23 (ZS) to 91 (PL) five generations ago. A total of 2,318 (PL), 2,593 (PUL), 2,705 (ZW) and 2,361 (ZS) haplotype blocks spanning 695.5 Mb (PL), 831.3 Mb (PUL), 1104.2 Mb (ZW) and 1290.7 Mb (ZS) of the genome were detected. Mean block lengths were estimated as 299.2 ± 448 kb, 320.6 ± 446 kb, 408.2 ± 614 kb and 546.7 ± 1034 kb for PL, PUL, ZW and ZS, respectively. It may be assumed that the observed differences in the decay of LD across genome, as well as in Ne and haplotype blocks characteristics are a results of different demographic population histories and differences in intensity of selection in highly productive PL and unselected native pig breeds.
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