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

Abstract

The 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.
Author Igor Jasielczuk (VET)
Igor Jasielczuk ,,
- University Centre for Veterinary Medicine UJ-UR
, Artur Gurgul (VET / CfEaIM)
Artur Gurgul,,
- Center for Experimental and Innovative Medicine
, Tomasz Szmatoła (VET) - The National Research Institute of Animal Production
Tomasz Szmatoła,,
- University Centre for Veterinary Medicine UJ-UR
, E. Semik-Gurgul - The National Research Institute of Animal Production
E. Semik-Gurgul,,
-
, Klaudia Pawlina-Tyszko - The National Research Institute of Animal Production
Klaudia Pawlina-Tyszko,,
-
, Magdalena Szyndler-Nędza - The National Research Institute of Animal Production
Magdalena Szyndler-Nędza,,
-
, Tadeusz Blicharski - Institute of Genetics and Animal Breeding
Tadeusz Blicharski,,
-
, Karolina Szulc - Poznań University of Life Sciences
Karolina Szulc,,
-
, Ewa Skrzypczak - Poznań University of Life Sciences
Ewa Skrzypczak,,
-
, Monika Bugno-Poniewierska (FoAS / IoVS)
Monika Bugno-Poniewierska,,
- Institute of Veterinary Sciences
Journal seriesLivestock Science, ISSN 1871-1413, e-ISSN 1878-0490, (N/A 140 pkt)
Issue year2020
Vol231
Pages1-8
Publication size in sheets0.5
Article number103887
Keywords in EnglishHaplotype block; Linkage disequilibrium; Effective population size; Pig; Polish native breed; Polish Landrace
ASJC Classification3400 General Veterinary; 1103 Animal Science and Zoology
DOIDOI:10.1016/j.livsci.2019.103887
URL https://www.sciencedirect.com/science/article/pii/S1871141319311485/pdfft?md5=411b077e8fc60b6537384ddb5347d72b&pid=1-s2.0-S1871141319311485-main.pdf
Languageen angielski
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Comparison of linkage disequilibrium, effective population size and haplotype blocks in Polish Landrace and Polish native pig populations of 29-01-2020
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Score (nominal)140
Score sourcejournalList
Publication indicators WoS Citations = 1; Scopus SNIP (Source Normalised Impact per Paper): 2017 = 1.036; WoS Impact Factor: 2018 = 1.376 (2) - 2018=1.747 (5)
Citation count*
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FinansowanieThe study was financed from funds of the project: “Directions for use and conservation of livestock genetic resources in sustainable development” co-financed by the National Research and Development Center (Poland)under the Strategic Research and Development Program: “Environment, Agriculture and Forestry”–BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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