Genome-wide association study using haplotype alleles for the evaluation of reproductive traits in Nelore cattle

André Vieira do Nascimento; Ândrea Renata da Silva Romero; Yuri Tani Utsunomiya; Adam Taiti Harth Utsunomiya; Diercles Francisco Cardoso; Haroldo Henrique Rezende Neves; Roberto Carvalheiro; José Fernando Garcia; Alexeia Barufatti Grisolia

doi:10.1371/journal.pone.0201876

Genome-wide association study using haplotype alleles for the evaluation of reproductive traits in Nelore cattle

PLoS One. 2018 Aug 8;13(8):e0201876. doi: 10.1371/journal.pone.0201876. eCollection 2018.

Affiliations

¹ Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, UFGD, Dourados, Mato Grosso do Sul, Brazil.
² Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, São Paulo, Brazil.
³ Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, São Paulo, Brazil.
⁴ Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP, Araçatuba, São Paulo, Brazil.
⁵ GenSys Consultores Associados S/S Ltda, Porto Alegre, Brazil.
⁶ International Atomic Energy Agency (IAEA), Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil.

Abstract

Zebu cattle (Bos taurus indicus) are highly adapted to tropical regions. However, females reach puberty after taurine heifers, which affects the economic efficiency of beef cattle breeding in the tropical regions. The aims of this study were to establish associations between the haplotype alleles of the bovine genome and age at first calving (AFC) in the Nelore cattle, and to identify the genes and quantitative trait loci (QTL) related to this phenotype. A total of 2,273 Nelore cattle (995 males and 1,278 females) genotyped using the Illumina BovineHD BeadChip were used in the current study. The association analysis included females with valid first calving records as well as open heifers. Linkage disequilibrium (LD) analysis among the markers was performed using blocks of 5, 10, and 15 markers, which were determined by sliding windows shifting one marker at a time. Then, the haplotype block size to be used in the association study was chosen based on the highest r2 average among the SNPs in the block. The five HapAlleles most strongly associated with the trait (top five) were considered as significant associations. The results of the analysis revealed four genomic regions related to AFC, which overlapped with 20 QTL of the reproductive traits reported previously. Furthermore, there were 19 genes related to reproduction in those regions. In conclusion, the use of haplotypes allowed the detection of chromosomal regions associated with AFC in Nelore cattle, and provided the basis for elucidating the mechanisms underlying this trait.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles*
Animal Husbandry
Animals
Breeding*
Cattle / genetics*
Female
Genome-Wide Association Study
Haplotypes*
Linkage Disequilibrium
Male
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Reproduction / genetics*

Grants and funding

This research was supported by: Foundation Support to Development of Education, Science and Technology of the State of Mato Grosso do Sul (FUNDECT) and Coordination for the Improvement of Higher Education Personnel (CAPES). The funder (GenSys Consultores Associados S/S Ltda) provided support in the form of salaries for authors HHRN, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.