Runs of homozygosity patterns in beef cattle

Acta Fytotechnica et Zootechnica

View Publication Info
 
 
Field Value
 
Title Runs of homozygosity patterns in beef cattle
 
Creator Olšanská, Barbora
Lehocká, Kristína
Kasarda, Radovan
Moravčíková, Nina
 
Description Received: 2020-10-22 Accepted: 2021-02-08 Available online: 2021-02-28https://doi.org/10.15414/afz.2021.24.mi-apa.7-10The study presents an approach to detect selection signals by the scan of runs of homozygosity (ROH) in two beef cattle populationsbred Slovakia. The frequency and distribution of runs of homozygosity in the genome are affected by natural and artificial selection,recombination rate and structure of the population. After quality control, the final data set included 43,427 single nucleotidepolymorphisms with overall length 2,504 Mb. Across the genome, sixteen regions under strong selection pressure with a totallength of 73.94 Mb were identified. The functional analysis of selection signals revealed several quantitative trait loci for bodystructure, fitness and milk production. In the region with a high frequency of ROH reflecting the intense artificial selection genesrelated mainly to muscle development (MSNT, ROCK1, LAMTOR5) were observed. Besides, genes related to the control of theimmune system (PTX3, FGL2) and reproduction (ADCYAP1R1) were localized within selection signals. The results confirm theintention to improve the production and reproduction traits of Charolais and Limousine cattle according to established breedingobjectives for each breed.Keywords: beef production, genomic region, homozygosity, quantitative traits, signatures of selectionReferencesClarke, A.M. et al. (2009). Intake, live animal scores/measurements and carcass composition and value of late-maturing beefand dairy breeds. Livestock Science, 126, 57–68.Connor, E.E. et al. (2008). Effects of increased milking frequency on gene expression in the bovine mammary gland. BMCGenom, 9, 362.Ferenčakovi ć, M. et al. (2013). Estimating autozygosity from high-throughput information: effects of SNP density andgenotyping errors. Genetics Selection Evolution, 76(4), 325–329.Gaud et, P. et al. (2011). Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.Brief Bioinform., 12(5), 449–462.Chang, C.C. et al. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 25(4).Marras , G. et al. (2015). Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmedin Italy. Animal Genetics, 4,110–121.Morav číkov á, N. et al. (2018). Genomic Response to Natural Selection within Alpine Cattle Breeds. Czech J. Anim. Sci., 63(4),136–143.Purfield, D.C. et al. (2012). Runs of homozygosity and population history in cattle. BMC Genet, 13.Randhawa , I.A.S. et al. (2016). A Meta-Assembly of Selection Signatures In cattle. PLOS One, 11(4).Sifuentes, A.M. et al. (2015). Loci asociados con enfermedades genéticas y calidad de carne en bovinos Charolais mexicanos.Revista Mexicana De Ciencias Pecuarias, 6(4), 361–375.Szmato ła, T. et al. (2016). Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. LivestockScience, 188, 72–80.Szmato ła, T. et al. (2019). A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing DifferentProduction Types. Animals, 9(12).Trukhach ev, V. et al. (2015). Myostatin gene (MSTN) polymorphism with a negative effect on meat productivity in DzhalginskyMerino sheep breed. J. BioSci. Biotechnol., 4(2), 191–199.Turner, S.D. (2017). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. bioRxiv.Williams , J.L. (2015). Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNPheterozygosity. Animal Genetics, 47(1), 19–27.Wyatt , A.R. et al. (2013). Protease-activated alpha-2-macroglobulin can inhibit amyloid formation via two distinct mechanisms.FEBS Lett, 587(5), 398–403.Zavar ez, L.B. et al. (2015). Assessment of autozygosity in Nellore cows (Bos indicus) through high‐density SNP genotypes.Frontiers in Genetics, 6(5).Zhang, Y. et al. (2015). Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genomics, 16,542.
 
Publisher Acta Fytotechnica et Zootechnica
 
Contributor APVV-14-0054 and APVV-17-0060
 
Date 2021-02-26
 
Type info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion

 
Format application/pdf
 
Identifier http://www.acta.fapz.uniag.sk/journal/index.php/on_line/article/view/802
 
Source Acta Fytotechnica et Zootechnica; Vol 24 (2021): Actual Concepts in Agrobiology::Invited Editor: Ing. Jaroslav Andreji, PhD.
1336-9245
1336-9245
 
Language eng
 
Relation http://www.acta.fapz.uniag.sk/journal/index.php/on_line/article/view/802/pdf
 
Rights Copyright (c) 2021 Acta Fytotechnica et Zootechnica
 

Contact Us

The PKP Index is an initiative of the Public Knowledge Project.

For PKP Publishing Services please use the PKP|PS contact form.

For support with PKP software we encourage users to consult our wiki for documentation and search our support forums.

For any other correspondence feel free to contact us using the PKP contact form.

Find Us

Twitter

Copyright © 2015-2018 Simon Fraser University Library