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.
Highlights
Indicine cattle (Bos taurus indicus) are well-adapted to tropical environments, because of attributes like heat tolerance and partial tick resistance
Genome-wide information could be used in association studies (GWAS) to identify candidate regions associated with at first calving (AFC), and improve our understanding of the genetic basis of sexual precocity in indicine cattle
The distribution of the number of haplotype blocks per chromosome is shown in S1 Fig
Summary
Indicine cattle (Bos taurus indicus) are well-adapted to tropical environments, because of attributes like heat tolerance and partial tick resistance. As a general rule, indicine heifers present inferior reproductive performances, regarding the onset of puberty, in comparison with taurine cattle (Bos taurus taurus) [1]. Such late onset of puberty negatively affects the economic efficiency of beef cattle breeding and restricts the genetic improvement of cattle [2], and is, becoming a key concern in the tropical countries. Genome-wide information could be used in association studies (GWAS) to identify candidate regions associated with AFC, and improve our understanding of the genetic basis of sexual precocity in indicine cattle This knowledge could be used to improve the accuracy of genomic predictions by using more informative markers and discarding those that generate noise during the predictions
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