Genomics
Genomic evaluation is the process of estimating the genetic merit of an animal based on the animal’s DNA information. Genomic evaluation can be carried out for a number of dairy breeds including Holstein, Friesian, Guernsey, Ayrshire and Jersey.
Reference population
The first step in genomic evaluation is to build up a reference population for a breed. A reference population contains the DNA information of sires with a high reliability daughter-based proof. Any animal with a high reliability proof can be used, whether they have poor or excellent genetics. This wide spectrum of genetics allows geneticists to identify markers (SNPs) in the animal’s DNA that are related to poor or favourable traits shown in the animal’s genetic proof. These associations are then used to create a so-called ‘SNP-key’, which can then be used to evaluate young animals without daughter or production information based only on the DNA present in a tissue or hair sample.
Reliability of genomic proofs
Genomic proofs are produced by the Agricultural and Horticultural Development Board (AHDB) and are identical in layout to production and daughter-proven proofs but are flagged a green ‘G’ symbol to indicate that the proof uses DNA in addition to parent average information to estimate the animal’s genetic potential. Genomic proofs have a higher reliability than traditional proof testing pedigree indexes, as illustrated in Table 1. Genomic tested young bulls retain this gain in reliability over traditionally tested bulls, up until the second crop daughter information is available.
Table 1. Reliability of genomic and traditional testing sire genetic proofs over time
| Sire testing stage | Age of sire | Traditional | Genomic |
|---|---|---|---|
| 0 | 35% | 70% | |
| DNA analysis | 1 | 35% | 70% |
| Semen collection | 2 | 35% | 70% |
| Progeny born | 3 | 35% | 70% |
| Progeny bred | 4 | 35% | 70% |
| Progeny milking | 5 | 85% | 90% |
| Second crop daughter proof | 6 | 99% | 99% |
It is only when second crop daughter production information is available that the gap between traditionally proven sire proofs and genomic proofs is fully closed. Although genomic young bulls have a higher reliability than their traditional counterparts, caution should be taken when using them across a herd. The reliability indicates how likely the bull’s proof will change as more information contributes towards his proof. Therefore, a genomic proof with reliability of 65–70 per cent could still drop or improve when daughter information becomes available. Using a team of around five or six genomic young bulls across your herd is advised to ensure that if one bull changes significantly, his genetics will not contribute to a large proportion of your replacement heifers.
Genomic evaluation within the CAFRE dairy herd
All female Holstein cattle have been genomically tested within the CAFRE dairy herd since 2017. Replacement heifer calves are genotyped once all heifer calves have been born. The genomic data for individual replacement heifers and cows is used to decide which animals are used for breeding replacements, or if there is a surplus of heifers, which animals should be sold. In addition to the genomic data, consideration is given to timing of calving and thus breeding as a key objective is to have the replacement heifers born early in the calving season to have a uniform batch of heifer calves to rear as a batch.
Since 2019 all replacement heifers have had their recessive genes for various conditions made available as part of the genomic testing package. This enables bulls to be selected that are also not positive for that gene(s) to avoid associated problems with the progeny. The list of genetic defects for Holstein cows is available below. Any bull or cow having a defect with a C after it is a carrier and any defect with a T or F after it is free from that defect.
Inbreeding
Inbreeding is to some extent unavoidable when breeding purebred, because genetic diversity decreases. This is good if the genes have a positive impact, but bad if the reverse is true. Inbreeding is increasing in all the main dairy breeds and is increasing at an increasing rate. The relatedness of bulls is increasing as current bulls are usually the sons of the last crop of popular bulls. It might have been expected with the advent of genomics that more outcross bulls would be available, but this does not seem to be the case. A technology investigation on inbreeding depression, i.e. the negative impacts of inbreeding is available below.
Inbreeding can be managed by several means:
- Start a crossbreeding program (see below technology investigation on crossbreeding).
- Use genomics to ascertain the level of inbreeding for each animal in the herd and only breed replacements from the animals with the lowest inbreeding co-efficient
- Use an inbreeding checker such as available from AHDB to check the inbreeding co-efficient of potential progeny from the bulls selected for the current season and breed from the bull with the lowest inbreeding co-efficient.
CAFRE have started using the AHDB inbreeding checker this season and found it to be a very useful tool once the list of bulls for the season have been selected and can be obtained on time. This will enable the progeny to have a lower inbreeding co-efficient than the average of the parents or at least not increasing it above the parental average.
