Reproduction Traits of Tropical Composite Bulls through Genome-Wide Association

Summary

Reproductive traits are important targets for genetic improvements programs, especially in Australia's northern beef industry. Genomic selection for reproduction or other traits, based on genetic marker panels or on genome-wide predictions, is set to become a widely-adopted tool.  The accuracies for genomic selection predictions for reproductive traits, currently available in Australia, are not very high. Higher accuracies in selection predictions will be achieved by increasing the size of datasets on which to base predictions, but also by identifying the causative mutations for the traits in question. Further, when applying DNA-based selection methods, their impact on other traits needs to be assessed so that genomic selection for reproductive traits does not result in adverse effects in other production traits.   
Building on previous investments in genomic selection for reproductive traits in Tropical Composite and Brahman, astudy was undertaken to calculate SNP effects in a population of Tropical Composite bulls (n=1,019) with deep phenotypes for a range of production traits, including reproductive traits. By comparing this study with results previously obtained on linked populations of Brahman cows and bulls, and Tropical composite cows, we were able to confirm a number of genome areas that appear to be important for reproductive and endocrine traits across breeds, and in at least one case across both sexes.   For example we were able to confirm the findings from our previous study of Brahman bulls, that the X chromosome is harbouring significant associations with scrotal circumference and sperm morphology. The 25 Mb region on chromosome 14 was shown to be associated with IGF1 levels at 6 months, in agreement with our findings in Brahman cows and bulls and Tropical Composite females. 
These findings illustrate that it is possible to identify DNA-based predictions that will work across different cattle breeds. The study of Tropical Composite bulls revealed clear differences between breeds in the mapping of SNP associations. For example, the level of inhibin in pre-pubertal bulls, which in Brahman bulls has been mapped to the INHA gene on chromosome 2, appears to map to the INHBE and INHBC genes on chromosome 5 in Tropical Composites. These two examples illustrate why most DNA-based predictions have to be calibrated for each breed, to account for the differences in genomic architecture between them. 
The data generated in this study have provided the foundation for the development of more accurate DNA-based selection, and for estimating its effects in both Brahman and Tropical Composite breeds in both sexes, on a large number of important production traits.  We recommend further investment in R&D on these datasets to ensure the industry derives maximum benefit from its investment in creating them. One aspect of this R&D will be the integrative analysis of the 4 reproduction populations that have now been genotyped.  Another aspect will be detailed molecular biology investigations of genome regions targeting the discovery of causative mutations.