Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle

Abstract

Fertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.

Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle

“…The sperm flagellar 2 ( SPEF2 ) gene is a well-known gene in cattle because of its association with important traits, such as adaptation to heat stress [ 71 ], fertility [ 72 ], and milk production and composition [ 60 ]; however, no reports related to behavioral traits for this gene were found. The SPEF2 gene was found for all scenarios investigated, and beyond the GO_BP related to immune system and fertility, the embryonic neurocranium, brain morphogenesis, and respiratory system development GO_BP were also functionally annotated.…”

Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

“…The BPs and metabolic pathways significantly associated with the gene lists were determined based on their FDR (Ashburner et al, 2000). Functional evidence of the relationship between the significant GO terms (FDR = 0.05) and the DEGs was identified (Sweett et al, 2020). The FDR thresholds of 0.05 for genes involved in the BPs or metabolic pathways were applied to filter significant candidate genes by function, pathway, and network effects (Cardoso et al, 2017).…”

Uncovering the architecture of selection in two Bos taurus cattle breeds

“…We contrasted it with signatures identified in the full dataset, where introgression from other breeds is also responsible for changing allele frequencies. In the full dataset, the most significant COJO SNP ( 9:85445646:T:C, COJO p = 2.51 10 -276 ) is located immediately upstream of SASH1, a gene implicated in various fertility phenotypes in beef cattle (Fortes et al 2010;Xiang et al 2017;Sweett et al 2020). We also identified strong selection on variants (4:94308044:A:G, COJO p = 2.17 x 10 -170 ) in the imprinted gene COPG2 (Khatib et al 2007).…”