Linkage disequilibrium, haplotype blocks and historical effective population size in Arabian horses and selected Polish native horse breeds

Igor Jasielczuk , Artur Gurgul , Tomasz Szmatoła , E. Semik-Gurgul , Klaudia Pawlina-Tyszko , Monika Stefaniuk-Szmukier , G. Polak , Iwona Tomczyk-Wrona , Monika Bugno-Poniewierska

Abstract

This study was conducted to investigate linkage disequilibrium (LD), historical effective population size (Ne) and haplotype block structures in genomes of highly selected Polish Arabian (AR; n=124) horses and conserved horse breeds derived from Polish native breeds, in particular, Malopolski (MLP; n=56), Sokolski (SOK; n=107), Sztumski (SZTUM; n=69), Hucul (HC; n=116) and Polish Konik (KN; n=99) horses, based on single nucleotide polymorphisms (SNPs) from the Neogen Equine Community BeadChip assay (Illumina, San Diego, CA). LD analysis was performed based on the pairwise r2 statistic of SNPs at a distance up to 5Mb. At a short distance, up to 100kb, the lower average r2 was observed in SOK (0.09) and SZTUM (0.10) breeds, representing draft horse type, and the highest average r2 was observed in AR (0.19) and MLP (0.17) breeds, representing light horse type. At a distance of 4-5Mb, the average values of r2 were 0.03 for HC and KN, 0.02 for AR and MLP and 0.01 for SOK and SZTUM. About 100 generations ago, effective population size (Ne) ranged from 518 (SOK) to 310 (AR) and five generations ago from 85 (SOK) to 40 (HC). A total of 6,162 (AR), 5,792 (MLP), 5,744 (HC), 5,429 (KN), 5,542 (SOK) and 4,848 (SZTUM) haplotype block structures, spanning 656.2Mb (AR), 439.4Mb (MLP), 381.2Mb (HC), 344.3 (KN), 206.7 (SOK) and 171.0Mb (SZTUM) of the genome were detected. Mean block lengths were estimated as 106.5±138kb, 75.9±120kb, 66.4±109kb, 63.4±109kb, 37.3±80kb and 35.3±81kb for AR, MLP, HC, KN, SOK and SZTUM, respectively. A visible similarity in the decay of LD across the genome, as well as in trends of historical Ne, were found for breeds representing the same horse type. Differences in the span of haplotype block structures were found between AR and Polish native horse breeds, which may reflect different demographic population histories and differences in intensity of selection.
Author Igor Jasielczuk (VET / CfEaIM) - The National Research Institute of Animal Production
Igor Jasielczuk ,,
- Center for Experimental and Innovative Medicine
, Artur Gurgul (VET / CfEaIM) - The National Research Institute of Animal Production
Artur Gurgul,,
- Center for Experimental and Innovative Medicine
, Tomasz Szmatoła (VET / CfEaIM) - The National Research Institute of Animal Production
Tomasz Szmatoła,,
- Center for Experimental and Innovative Medicine
, 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,,
-
, Monika Stefaniuk-Szmukier (FoAS / Department of Animal Reproduction, Anatomy and Genomics)
Monika Stefaniuk-Szmukier,,
- Department of Animal Reproduction, Anatomy and Genomics
, G. Polak - The National Research Institute of Animal Production
G. Polak,,
-
, Iwona Tomczyk-Wrona - The National Research Institute of Animal Production
Iwona Tomczyk-Wrona,,
-
, Monika Bugno-Poniewierska (FoAS / Department of Animal Reproduction, Anatomy and Genomics)
Monika Bugno-Poniewierska,,
- Department of Animal Reproduction, Anatomy and Genomics
Journal seriesLivestock Science, ISSN 1871-1413, e-ISSN 1878-0490, (N/A 140 pkt)
Issue year2020
Vol239
Pages1-8
Publication size in sheets0.5
Article number104095
Keywords in EnglishArabian horse, Hucul, Inbreeding, Malopolski horse, Polish Konik, Sokolski horse, Sztumski horse
ASJC Classification3400 General Veterinary; 1103 Animal Science and Zoology
DOIDOI:10.1016/j.livsci.2020.104095
URL https://www.sciencedirect.com/science/article/pii/S1871141320300433/pdfft?md5=f03cd91dc12b330f8bd63af7351fd6eb&pid=1-s2.0-S1871141320300433-main.pdf
Languageen angielski
LicenseJournal (articles only); author's original; Uznanie Autorstwa - Użycie Niekomercyjne - Bez utworów zależnych (CC-BY-NC-ND); after publication
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Linkage disequilibrium, haplotype blocks and historical effective population size in Arabian horses and selected Polish native horse breeds of 01-06-2020
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Score (nominal)140
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Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2017 = 1.036; WoS Impact Factor: 2018 = 1.376 (2) - 2018=1.747 (5)
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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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