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

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science

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

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.
Competing Interests: Haroldo H. R. Neves is an employee of GenSys Consultores Associados S/S Ltda. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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Date Created: 20180809 Date Completed: 20190131 Latest Revision: 20190131

20221213

PMC6082543

10.1371/journal.pone.0201876

30089161