Abstract:
BACKGROUND : Reproduction is a key feature of the sustainability of a species and thus represents an important
component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain
a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted
for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African
Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were
available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed
models.
RESULTS : Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic
heritability’s of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51
suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs
were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes
were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL
containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass,
fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate
catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian
follicle development and the regulation of DNA transcription and RNA translation.
CONCLUSIONS : This was the first attempt to study the underlying polymorphisms associated with reproduction in
South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were
detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may
have been associated due to the unique genetic composite background of the SA Bonsmara breed.
