Multi-breed genomic predictions and functional variants for fertility of tropical bulls

Abstract

Worldwide, most beef breeding herds are naturally mated. As such, the ability to identify and select fertile bulls is critically important for both productivity and genetic improvement. Here, we collected ten fertility-related phenotypes for 6,063 bulls from six tropically adapted breeds. Phenotypes were comprised of four bull conformation traits and six traits directly related to the quality of the bull's semen. We also generated high-density DNA genotypes for all the animals. In total, 680,758 single nucleotide polymorphism (SNP) genotypes were analyzed. The genomic correlation of the same trait observed in different breeds was positive for scrotal circumference and sheath score on most breed comparisons, but close to zero for the percentage of normal sperm, suggesting a divergent genetic background for this trait. We confirmed the importance of a breed being present in the reference population to the generation of accurate genomic estimated breeding values (GEBV) in an across-breed validation scenario. Average GEBV accuracies varied from 0.19 to 0.44 when the breed was not included in the reference population. The range improved to 0.28 to 0.59 when the breed was in the reference population. Variants associated with the gene HDAC4, six genes from the spermatogenesis-associated (SPATA) family of proteins, and 29 transcription factors were identified as candidate genes. Collectively these results enable very early in-life selection for bull fertility traits, supporting genetic improvement strategies currently taking place within tropical beef production systems. This study also improves our understanding of the molecular basis of male fertility in mammals.

Fig 1. Overview of the analysis.

The assembled multi-breed reference population (A) comprised 6,063 bulls from six tropically adapted breeds (BRM = Brahman; TRC = Tropical Composite; SGT = Santa Gertrudis; DMT = Droughtmaster; UBK = Ultra Black; and BTC = Belmont Tropical Composite) with measures on 10 fertility-related quantitative phenotypes including four measured on the bull’s body (WT = body weight; COND = condition score; SC = scrotal circumference; and SHEATH = sheath score) and six measured on the bull’s semen (DENS = density; MASS = mass; MOT = motility; PNS = percent normal sperm; PD = proximal droplets; and MD = midpiece deformities). Together with the high-density SNP genotypes, the inference step (B) used multi-variate and multi-breed GREML analytical models which can be split into two categories: Full-Data Models with all phenotypic records and used to generate GEBV_Whole genomic predictions, and Cross-Validation Models where phenotypes from individuals in the validation group were set as missing values and used to generate GEBV_Partial genomic predictions. For the validation step (C), GEBV_Whole and GEBV_Partial were combined using Method LR approaches to compute accuracy, bias, and dispersion, while GEBV_Partial and the adjusted phenotypes were combined to compute correlation-based accuracy. Measures of accuracy, bias and dispersion were subjected to an ANOVA model that contained the effects of heritability (h²), breed and phenotype. The final step (D) aimed at identifying functional variants. SNP effects were estimated and, when anchored to individual genes, subjected to the Association Weight Matrix to infer a network that exploited the triple concept of degree connectivity, pleiotropy, and sperm expression to identify key transcription factors harbouring causal mutations.

Fig 2. Population structure according to the first two principal components (PC) based on genotypic information of 6,063 bulls.

Colors correspond to the six breeds: BTC = Belmont Tropical Composite; BRM = Brahman; DMT = Droughtmaster; SGT = Santa Gertrudis; TRC = Tropical Composite; and UBK = Ultra Black.

Fig 3. Genes highlighted through functionality analysis.

(A) Network containing the 29 genes selected as top10 in either connectivity, pleiotropy and/or sperm expression, extracted from a bigger network containing their directly correlated genes (S2 Fig in S1 File)–continuous and dashed edges correspond to positive and negative correlations, respectively; and colors correspond to the most associated trait (SC = scrotal circumference; MOT = motility; MD = midpiece abnormalities; PD = proximal cytoplasmic droplets; PNS = percent normal sperm; MASS = mass; DENS = density; SHEATH = sheath score; COND = condition score; and WT = body weight). (B) Co-association scores (AWM output) of the 29 genes. (C) Number of transcription factors (TF) selected for being above average according to connectivity, pleiotropy, and sperm expression–the 29 top10 TF for the three selection criteria are represented in parenthesis–Refer to S3 Fig in S1 File, for the complete list of genes.