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.
Highlights
Fertility is a complex trait and, it is regulated in part by genetics
This is evident from genome wide association studies (GWAS) in which genetic variation in a trait is partitioned into associations with individual single nucleotide polymorphism (SNP)
A population of 550 Holstein bulls with divergent genetic merit for daughter pregnancy rate (DPR), where bulls of low DPR were those with a Predicted transmitting ability (PTA) of -2 or lower, and bulls of high DPR had a PTA of +1.7 or higher was used to test association of SNP with fertility traits (DPR, conception rate (CCR), and heifer conception rate (HCR))
Summary
Fertility is a complex trait and, it is regulated in part by genetics. In the dairy cow, genetic merit for fertility and production are negatively correlated ranging from 0.35 - 0.60 (Boichard and Manfredi, 1994; VanRaden et al, 2004; Pritchard et al, 2013) and the intense selection for milk production during the last five decades has been one of the causes of a decrease in the genetic merit for fertility in dairy breeds (Butler, 2003). Mean that reproductive traits are not under genetic control, many specific genes have been identified that contain mutations that are associated with reproductive function. Cole et al (2011) used a population of 1654 animals to identify 1586 SNP distributed in 486 genes that were associated with 31 production, reproduction, health and body conformation traits in Holstein cows.
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