A Genome-wide association study of fertility and maternal traits in South African Bonsmara cattle

Abstract

Reproductive wastage is of major economic importance and limits overall herd efficiency. Fertility traits are lowly heritable but are an essential component in selection programs for the genetic improvement of all livestock species. In order to gain a better understanding of the underlying genetic basis of these traits a GWAS was conducted to investigate fertility and maternal traits within the SA Bonsmara breed. Traits of interest were age at first calving (AFC), inter-calving period (ICP), scrotal circumference (SC) and weaning weight maternal (WWMAT). Estimated breeding values, pedigrees and genotypes for 3 291 SA Bonsmara animals were available for the study. Three different commercial arrays underwent quality control (QC), principal component analysis (PCA), with the amalgamation of the three arrays via imputation to a density of 128 793 SNPs and finally an association analysis by single SNP regression. Gene annotation was done for significant SNPs (≤1x10-8), with four associated with ICP (BTA 4, BTA11, BTA17, BTA19), twenty with AFC (BTA1, BTA2, BTA4, BTA5, BTA7, BTA8, BTA9, BTA11, BTA12, BTA16, BTA20, BTA24, BTA27, BTA28, BTA29), twenty-two with SC (BTA1, BTA2, BTA3, BTA4, BTA5, BTA6, BTA8, BTA10, BTA11, BTA15, BTA16, BTA20, BTA22, BTA24, BTA26, BTA28) and forty-four with WWMAT on all chromosomes except BTA10, BTA13, BTA16, BTA17, BTA23, BTA24, BTA25 and BTA26. The three SNPs significantly associated with AFC on BTA3 were all in gene regions. Of the six SNPs associated with WWMAT on BTA15, five were identified in four genes, with two SNPs annotating to the same gene (LRRC4C). Three genes for SC, eight genes for AFC and nineteen genes for WWMAT were identified. Genes associated with SC (PPP3CA), AFC (AKT3, GRM8, KIF1B, OVOS2) and WWMAT (BMP1, LRRC4C, MACROD1, RBM47, THSD7B) were reported for cattle in other studies. Genes associated with AFC (AKT3; BTA16) and SC (PPP3CA, TRPM6; BTA6, BTA8) where shown to share serine/threonine biological pathway processes. Chromosomes and SNPs that yielded novel associations with previously uncharacterised genes and previously not reported in literature may possibly be unique to the SA Bonsmara beef breed and will require further investigation.