Signatures of selection in Charolais beef cattle identified by genome‐wide analysis

Autor:	Francisco Joel Jahuey-Martínez, Ana María Sifuentes-Rincón, Víctor Ricardo Moreno-Medina, Gaspar Manuel Parra-Bracamonte
Rok vydání:	2019
Předmět:	0301 basic medicine Linkage disequilibrium Meat Genotype Quantitative Trait Loci biology.animal_breed Population Single-nucleotide polymorphism Quantitative trait locus Polymorphism Single Nucleotide 03 medical and health sciences Food Animals Animals education Selection (genetic algorithm) Genetic association Genetics education.field_of_study biology Haplotype 0402 animal and dairy science 04 agricultural and veterinary sciences General Medicine Chromosomes Mammalian 040201 dairy & animal science 030104 developmental biology Cattle Animal Science and Zoology Charolais cattle Genome-Wide Association Study
Zdroj:	Journal of Animal Breeding and Genetics. 136:378-389
ISSN:	1439-0388 0931-2668
DOI:	10.1111/jbg.12399
Popis:	Charolais cattle are one of the most important breeds for meat production worldwide; in Mexico, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8-59.3 Mb on BTA 4; 67.5-69.3 on BTA 5; 39.5-41.0 Mb on BTA 6; and 26.4-29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits.
Databáze:	OpenAIRE
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