Identifying Causal Mutations Associated With Bull and Cow Fertility and How They Link to Feed Efficiency

Background

Current cattle genotyping panels only include genetic markers identified in non-coding regions which are assumed to affect gene regulation of traits. However, recent studies revealed that functional/causal genetic markers may explain a large proportion of the heritability of complex traits. The discovery of genetic and functional regions in the cattle genome is critical for understanding and enhancing complex traits like feed efficiency and fertility, where selecting for one negatively impacts the other, in the Canadian beef cattle herd.

Cattle have two copies of each gene, with one coming from each parent. In theory, each parent is equally likely to pass either one of its copies to each one of its offspring however, genes can be expressed in a variety of forms, and sometimes one form of the gene is more likely to show up in the offspring compared to another form. This phenomenon is called transmission ratio distortion (TRD) and occurs frequently. Despite this, some gene forms can lead to significant consequences like embryonic death. This project searched for regions of the genome that are affected by TRD, identified single nucleotide polymorphisms (SNPs) in those regions, and examined whether these SNPs are functionally associated with fertility and feed efficiency traits in beef cattle.

Objectives

• Develop new methodology and software to identify TRD regions and validate the results across 9 beef breeds.
• Identify causal genetic mutations associated with fertility and feed efficiency in the most promising genes found from commercial herds.
• Understand the genetic relationship between fertility and feed efficiency traits in young bulls.

What They Did

This project developed two computer-software that can identify genomic regions exhibiting TRD (TRDscan v1.0) and determine biological information about genomic markers and regions (GALLO). These resources can be used by researchers to continue searching for TRD regions and haplotypes related to important cattle traits, as well as validate it with biological information.

Using the computer software and methodology developed from this project, the researchers were able to discover 19 haplotypes, which are groups of genes inherited together from one parent, that could be linked to lethality in the offspring, if the animal inherits identical gene forms from both parents. They also discovered 52 genomic regions with patterns that suggested the absence of lethal gene forms. The discovered regions were further studied for biological information, and it was found that these genomic regions overlap with previously discovered regions known to affect production (i.e. gestation length, calving ease, conception rate etc.) and reproduction traits (i.e. mature body weight, methane production, body weight gain etc.).

What It Means

These newly discovered genomic regions in cattle can help us identify and sort out animals that carry the lethal gene forms. Therefore, producers and genetics companies can use this information to select for animals with a reduced rate of embryonic losses or calf death. This will lead to improved breeding strategies to reduce the negatively affects when selecting for fertility and feed efficiency traits in beef cattle. This includes the ability to actively avoid selection for lethal regions allowing producers to avoid at-risk mating that could compromise reproductive success in their herds, as well as the ability to breed elite breeding animals by genetics companies without this region.