Genomic selection - genomic breeding values: What is this?
For more than a year the press reports and breeders discuss about genomic selection, typing, genomic breeding values and so on
This new method of selection and the breeding evaluation developed out of the typing are in use for Black and Red Holstein cows in Schleswig-Holstein since 2010 and already dominate our breeding programs.
The goal of animal breeding is to change the genetic disposition of the animals and improve their performance doing so. So far a selection based on phenotype (shown) performance as indicator for genetic performance disposition was used. It would be ideal if one would be able to read the performance disposition directly from the genetic information without using the indirect feature of the phenotype. The genomic breeding evaluation and selection come very close to this old dream now. Although the cattle genome is already decrypted we still know little about position and usage of genes for the larger number of the features needed for breeding. That is why the genomic breeding evaluation does not work on the basis of information to the genes but on the basis of markers. The development of this new method of genetic analysis and the adjustment of the breeding evaluation was developed with the support of the Federal Ministry for Education and Research in the funding measure FUGATO.
The German training sample is the largest and best structured training sample worldwide. The used markers are the so-called SNP (Single Nucleotide Polymorphism) marker. They only have the length of one genetic letter and each marker only has two variants in the population. Each animal has the genetic information in the form of a double set of chromosomes, one from the dam and one from the sire. This means that each marker for one animal could have three states: homozygous AA, heterozygous BB or heterozygous AB. Heterozygous AB means that the animal got different variants from sire and dam.
Many hundreds of thousands of such SNP markers of cattle are known. 54,001 of them are shared equally in the entire genome i.e. all chromosomes, can now be extracted through a relatively cheap lab method in a one step process. This process is called “typing“. The unit used in the laboratory for testing the 54,001 markers is called a chip or 54K chip to indicate the number of markers simultaneously tested.
A little of the animal’s genetic material is used for the typing. As all cells of an animal have genetic material, blood (approx. 2 ml) or semen (approx. 2 doses) can be used. You can also extract enough gene material for the typing from approx. 30 roots of hair. However, the danger of contamination of hair samples with genetic material of other animals is higher and the result could be incorrect.
The typing’s result is 54,001 times AA or BB or AB.
Because of the even distribution of many markers over the genome people believe one of the 54,001 markers lies close to each gene that influences the performance of features needed for breeding. That means that the marker will almost always be inherited together with the gene. But we dont know the gene and its usage. To find the genomic breeding value for an animal several preliminary steps have to be done.
To find out which SNPs, which markers are combined with which feature, the SNP patterns of selected animals with a known (genetic) performance tendency have to be compared. Animals with known genetic performance are daughter proven sires. Out of the comparison of SNP patterns with genetic performance of those sires will be ascertained, which SNP has how much influence on one feature, which means the genomic estimation formula is derived like this. The more proven sires are available for this formula derivation, the better one can assign the SNPs to a feature and find out the amount of influence. The proven sires that are used for this analysis are the so-called training sample. The genomic estimation formulas, derivated from the training sample, are then used to calculate genomic breeding values for all other (younger) animals that dont have their conventional breeding information yet.
The reliability of the genomic breeding values depends on the size and structure of the training sample as well as the safety of the daughter breeding values of the training sample sires. The amount of data and the safety of the conventional breeding values for all also for functional features are leading in the world. The size and structure of the German training sample becomes unique because of the exchange with three European partners from France, Scandinavia and the Netherlands. No other training sample worldwide has such a good structure, which means it represents all current Holstein genetic from Europe and Northern America.
The genomic formulas are only able to calculate the breeding values of young animals if their genetic is represented in the training sample by as many related animals (sire, sire of dam, half siblings from the side of the sire, ). That is why the training sample has to be constantly extended. The safety of genomic data only (SNP typing) based breeding values for young animals is shown in table 2 in the middle column. The safety is the realized safety, which means it has already been corrected by all recognized overestimations from all genomic test.
Out of the typing (SNP-patterns) the genomic quality is calculated for all features. For all animals with known pedigree still conventional breeding values are available. To ensure that each animal has only one breeding value with maximum information and safety we do not publish the immediate genomic breeding value but the genomically improved breeding value (gBV) as a combination of immediate genomic value and conventional breeding value.
The emphasis is calculated on the basis of the safety of both values, that means for young animals with conventional pedigree breeding value the immediate genomic value counts and the insecure pedigree value can only improve the genomically improved BV (gBV) by 3-5% (as shown in the right column of the table). As soon as the conventional breeding value is more secure through daughter information than the immediate genomic value that value counts more in the combined gBV. That is why the combined gBV does not differ much from the conventional breeding value for daughter proven sires.
The realized safety of the genomically improved breeding values of young sires is with 75% for dairy characters and 50% for daughter fertility higher than the safety of the pedigree breeding value of test bulls. That means that young bulls now qualify as sires with their official gBV and test bulls as you have known them before no longer exist. The comparison with the safety of daughter proven sires shows that the highly important features such as performance, exterior and udder health have even better breeding value safeties for bulls with test daughters in their first lactation.
Although the German genomic breeding values are the safest in the international comparison, due to the bigger training sample with more than 30,000 bulls, the genomic breeding values are less secure than the breeding values of daughter proven sires. With a higher emphasis on functional features the importance of sires with thousands of daughters from the reuse has increased because they also offer high security for features such as usage life and daughter fertility. The realized safeties of the genomic breeding values for these functional features are still quite limited with only 50%. For people who dislike the securities of the first published daughter breeding values of new sires will not find a new alternative in genomically tested sires. On the other hand the young generation of genomically tested sires opens new breeding possibilities. With the usage of the young gBV-sires one should always pay attention to the limited safety. The safety calculations and the data for genomic breeding values are not yet internationally standardized. The data for the German genomic breeding values are realistic.
To get a correct estimation the German breeding values will still have the data of the daughters with performance information next to the safety in percent. So everybody is able to choose the matching sire from the young, only genomically testes sire, via the current proven sire with test usage daughters up to the proven sire out of the reuse.
On the base of the genomic breeding values all young bulls of the RSH eG and co-operations are selected within the NOG. This means that we have high-valued information for each feature about the genetic tendency of the young bull and that we wont take bull calves that are under the average in some features, into stud. The selection level increases a lot but the quality of bulls will be higher and also the breeding progress.
To find the right bulls many calves have to be typed and genomic breeding values have to be calculated to select the calves for the studs. This means higher costs. On the other hand the number of new bulls in the stud will be reduced because bulls with bad performance disposition dont come into usage.
In the future the RSH will only take 30 Black Holstein and 20 Red Holstein young bulls with gBV into stud to find an optimal offer with their NOG partners.
Requirements for optimal genomic breeding values are reliable performance tests. Only then it is possible to get reliable breeding values of young gBV sires out of the offspring test, which again is the base for the derivation of genomic breeding values. Without reliable performance test there will be no reliable genomic breeding values. The classical test use that we had so far, does no longer exist because bulls with a gBV are handled as sires and will get reliable offspring breeding values because of the wide spread acquisition of own performances. This also means that the contracted testing farms are no longer needed.
A short-term notice of the members about the latest gBV young sires is necessary. You can find this information on the internet sire database with the latest gBV sires under the label RSHgenomic as well as on leaflets that show the latest sires according to the product lines. There will be a bull chart once in a while in the leaflets that also give the needed price information. As a highlight the NOG partners will exchange their top young sires with genomic breeding values and outline the 10 best sires.
At the moment conventional daughter proven sires with a large number of daughters have the highest safety and reliability in all breeding features. This will also be valid for the future. The offspring proven sire will still be our premium product with the smallest amount of variation. You will not get the highest breeding progress but the highest amount of safety.
The gBV sires belong to every advanced farm because they offer highest breeding progress and latest genetic. The average use of genomic young sires in companys of Schleswig-Holstein will be around 50 %. From todays point of view we can only give you the advice to use a wide variety of young sires and not only one selected sire.
It is not easy for farmers to select the right sires for their herd because of the variety of sires. The RSH with their breeding technicians is trying to provide an optimal selection of genomic young sires. This is logistically THE challenge in the genomic age.
The genomic selection is the breeding instrument of the future and will continually be improved and developed. This development every dairy farmer should use to realize his individual breeding goal. A new era started for the Black and Red Holstein breed with the genomic selection.
There are no genomic breeding values available for Red Holstein double usageat the moment because the population is much smaller. This means that nothing will change in the current breeding programs.
The breed of German Red Anglers tackled al lot in the last years with the genomic selection and became established in January of 2016.