Ideal markers for tropically adapted cattle -proof of concept: causative mutations for bull fertility

Summary

​This project was a 'proof of concept' for identifying functional mutations via a combination of genome-wide association studies (GWAS) and sequenced genomes. Targeting 69 sequenced genomes enabled exploration of genes identified via GWAS (during the Beef CRC) with greater detail, leading to the discovery of 13 putative functional mutations. These mutations are new genetic markers and 10 of them were significantly associated with scrotal circumference and percentage of normal sperm in an independent population of mixed-breed beef cattle. These associations pointed to 9 genes in the X chromosome and one key gene in chromosome 5. The key genes in X were LOC100138021, CENPI, TAF7L, NXF2, CYLC1, UXT, SPACA5, TEX11, and AR. The gene HELB, mapped to chromosome 5, was associated to scrotal circumference. We also confirmed the association between the PLAG1 gene mutation and scrotal circumference. Such validation of markers justified further exploitation of the mixed-breed population.  Subsequently, 1,012 bulls of this population were genotyped using the 74,000 SNP chip. Chip genotyping enabled new genome-wide association studies and genomic selection analyses. All genotypes were incorporated to the Beef CRC legacy database, to support continued improvement of genomic selection strategies for tropical beef cattle. In our analysis, incorporating these new 1,012 bulls in the training dataset improved the genomic selection accuracy (1 to 4% higher accuracies) for scrotal circumference measurements across populations and breeds. The inclusion of the functional mutations had a significant (P < 0.001) and positive impact in the genomic prediction models for scrotal circumference. Functional mutations are likely to have similarly significant impact in other traits and can be incorporated in genomic models once they are discovered. Further research is required to discover more functional mutations related to female reproductive traits and production traits (i.e. meat traits or adaptation traits).