Genomics in Shorthorns
Genomics in Shorthorns
Genomic prediction has been recognised by the Shorthorn Beef board as a key development for genetic evaluation in the Shorthorn breed.
What is Genomics?
Genomics refers to the Genome of cattle and more specifically the DNA of the animal.
Genomic selection uses DNA markers (SNP’s) to predict phenotypes (performance) of an animal. SNP stands for Single Nucleotide Polymorphisms or the markers for gene locations within the DNA. Genomic selection uses the presence of various DNA markers (SNP’s) recorded in a SNP chip panel, which allows us to genotype an animal for thousands of markers within the whole genome.
Each panel has a predetermined number (density) of SNP’s ie; 20K (20,000 markers) or 50K (50,000 markers). The markers recorded in the SNP panel represent a cross section of the animals whole genome.
How do markers predict phenotypes?
Like any genetic evaluation, genomics requires a reference population to allow the evaluation to train the chip. Animals within the reference population must have both genotypes (SNP Panel) and phenotypes recorded. Over time, the relationship between the presence of certain markers and certain phenotypes allows genetic evaluation systems to predict phenotypes based on the presence (or absence) of those markers.
Therefore, increasing the size of the reference population is critical to developing increasing accuracy of genomic prediction.
Genomics also requires pedigree linkages across the whole breed to be able to accurately describe expected performance in all young animals within the breed. Therefore, it is critical to ensure that within the reference population, the reference animals represent the widest cross section of the breed possible.
How does genomics assist genetic evaluation?
It is important to understand that genomics will only assist in increasing the accuracy of the current genetic evaluation system, not replace it. Genetic evaluation currently requires the 3 “P”’s to build accuracy; Pedigree, (Individual) Performance and Progeny (Performance), all 3 of which are used to develop prediction of performance. Genomics will add a further element to the genetic evaluation system and further assist in developing the accuracy of the system, however, will not replace the other 3 components.
How does genomics assist breeders?
The key area where genomics will assist breeders is that it allows for young animals to be tested prior to them being old enough to collect their own phenotypes. It will also assist with traits that are hard to measure such as carcass traits, or traits that are only collected in one sex and not the other, such as scrotal size or mature cow weight.
This will assist breeders to make more accurate decisions about potentially elite animals within their herd at an earlier age and provide breeders with the opportunity to further accelerate genetic gain within their herds.
The Importance of correct Pedigree information to genomics.
Breedplan are currently moving towards a “single step” method for incorporation of genomic predictions into EBV’s. One of the key benefits of single step is that genomic predictions will not only improve the accuracy of EBV’s for the individual animal but will also flow through the animals pedigree to increase accuracy on closely related animals as well. Obviously, this means that for genomics to have full impact within the population, it is critical that the pedigree for the animal is correct. As such, whilst the Shorthorn breed builds a reference population for genomics for the future, animals will also require a paternal parent verification where possible.
Taking the first step for Shorthorns.
Creating a large reference population is the critical first step for any breed. For Shorthorns, this requires the breed to begin to add to the current genotypes recorded. As it is important that the reference population also has pedigree linkages to the rest of the Shorthorn population, the Shorthorn Beef board has moved to change the regulations regarding DNA testing for all new sires and donor dams, therefore ensuring that the necessary pedigree linkages are created.
New sires and donor dams will still require a DNA sample to be submitted to Shorthorn Beef prior to the registration of progeny as per the current regulations.
The main difference will be that the DNA samples will now have a genomics SNP panel run as the breed starts to build the necessary reference population. As a result, the new cost of the DNA testing will be $110 per new sire or donor dam (inc. GST), however this test will also include a Parent Verification to the sire and a Poll Test for each animal, to provide as much value as possible for members.