Abstract
The use of genomics has improved response to selection for functional traits with low heritability such as fertility traits. Much of the work on fertility traits has been performed through use of genome-wide association studies (GWAS) to identify genetic loci associated with reproductive traits. Under a GWAS approach, the assumption is that the markers on the panel are in linkage disequilibrium with causative mutations. In many cases, identification of the causative mutation is difficult because an associated genetic marker can be in intergenic regions and can be in linkage disequilibrium with variants in several nearby genes. Another approach is to identify candidate genes using knowledge of the biological pathways controlling a trait to search for single nucleotide polymorphism (SNP) in genes in those pathways. This should reveal putative causative markers responsible for genetic variation in biological function, and it is expected that the marker will be more strongly associated with a trait than one in linkage disequilibrium. An example of how a series of candidate gene studies demonstrate that identification of markers in genes involved in reproductive processes can lead to discovery of additional markers associated with genetic variation in reproductive traits is presented. In addition, the inclusion of candidate markers for fertility can improve reliability of genetic estimates for fertility traits, and the repeatability of the effects across a separate population of animals gives confidence that association elucidated by this set of markers is likely to be real. More importantly, the use of candidate genes can provide insights into the biology underpinning genetic variation in fertility, and that this understanding can lead to physiological interventions to improve reproductive function.