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. 2023 Jun 29;24(1):365.
doi: 10.1186/s12864-023-09475-2.

Sequence level genome-wide associations for bull production and fertility traits in tropically adapted bulls

Wei Liang Andre Tan  1 , Laercio Ribeiro Porto Neto  2 , Antonio Reverter  2 , Michael McGowan  3 , Marina Rufino Salinas Fortes  4
Affiliations

Sequence level genome-wide associations for bull production and fertility traits in tropically adapted bulls

Wei Liang Andre Tan et al. BMC Genomics. .

Abstract

Background: The genetics of male fertility is complex and not fully understood. Male subfertility can adversely affect the economics of livestock production. For example, inadvertently mating bulls with poor fertility can result in reduced annual liveweight production and suboptimal husbandry management. Fertility traits, such as scrotal circumference and semen quality are commonly used to select bulls before mating and can be targeted in genomic studies. In this study, we conducted genome-wide association analyses using sequence-level data targeting seven bull production and fertility traits measured in a multi-breed population of 6,422 tropically adapted bulls. The beef bull production and fertility traits included body weight (Weight), body condition score (CS), scrotal circumference (SC), sheath score (Sheath), percentage of normal spermatozoa (PNS), percentage of spermatozoa with mid-piece abnormalities (MP) and percentage of spermatozoa with proximal droplets (PD).

Results: After quality control, 13,398,171 polymorphisms were tested for their associations with each trait in a mixed-model approach, fitting a multi-breed genomic relationship matrix. A Bonferroni genome-wide significance threshold of 5 × 10- 8 was imposed. This effort led to identifying genetic variants and candidate genes underpinning bull fertility and production traits. Genetic variants in Bos taurus autosome (BTA) 5 were associated with SC, Sheath, PNS, PD and MP. Whereas chromosome X was significant for SC, PNS, and PD. The traits we studied are highly polygenic and had significant results across the genome (BTA 1, 2, 4, 6, 7, 8, 11, 12, 14, 16, 18, 19, 23, 28, and 29). We also highlighted potential high-impact variants and candidate genes associated with Scrotal Circumference (SC) and Sheath Score (Sheath), which warrants further investigation in future studies.

Conclusion: The work presented here is a step closer to identifying molecular mechanisms that underpin bull fertility and production. Our work also emphasises the importance of including the X chromosome in genomic analyses. Future research aims to investigate potential causative variants and genes in downstream analyses.

Keywords: Bull fertility; Genome-wide Association study; Quantitative trait loci; Sequence-level.

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Conflict of interest statement

The authors declare that they have no competing interest.

Figures

Fig. 1
Fig. 1
The Manhattan plot in A shows associations for SC in GWAS LOCO, whereas the Manhattan plot in B shows associations for SC after fitting the most significant SNP in each chromosome as a fixed effect. The inverse log p – values for each SNP are plotted along the y-axis for each chromosome on the x-axis. The dotted line represents the genome-wide significance threshold of 5 × 10− 8
Fig. 2
Fig. 2
The Manhattan plot in A shows associations for Sheath in GWAS LOCO, whereas the Manhattan plot in B shows associations for Sheath after fitting the most significant SNP in each chromosome as fixed effects. The inverse log p – values for each SNP are plotted along the y-axis for each chromosome on the x-axis. The dotted line represents the genome-wide significance threshold of 5 × 10− 8
Fig. 3
Fig. 3
Stacked bar plots showing published QTL and their associated traits that overlapped with QTL reported in this study for body conformation traits
Fig. 4
Fig. 4
Stacked bar plots showing published QTL and their associated traits that overlapped with QTL reported in this study for semen traits
Fig. 5
Fig. 5
Bar plot showing the distribution of predicted impact for each gene
See this image and copyright information in PMC

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