What Everyone Ought to Know About Fleckvieh and Genomics

Dairy Farmers can lower costs and improve herd health with a proven sire program. Consistently applied targeted mating can improve the genetics of a given herd with highly predictable outcome.

Find out how BDC and Fleckvieh use genomic estimated breeding values to increase the accuracy of genetic evaluations to assure mating predictability and precision phenotypic expression of heritable traits, and help your Dairy Herd live a healthier, more productive life.

Facts about Fleckvieh and Genomics

Sire selection as done by Bayern Genetik in Bavaria:

Bayern Genetik purchases genomically tested breeding bulls per year at local livestock auctions or directly out of the farmers’ barns. The bulls are selected from a population of 750.000 Fleckvieh herdbook cows in Bavaria. Many of these young sires (candidates) come out of matings:  The highest priority is given to selected siredams were mated to the best Fleckvieh sires available. The other bulls come out of regular but promising matings with herdbook cows.

Bayern Genetik also purchases sires from other countries like Austria, the Czech Republic, Australia and South Africa. The focus is on production and fitness traits when buying sires. The phenotypic appearance of a sire weighs heavily in the decision making process.

Testing of the chosen candidates:

After the quarantine period is over (28 days pre-quarantine and 28 days main quarantine period) 1.200 doses of semen of each candidate are collected and used in farms that take part in milk recording. The goal is to get as much data of first lactations of daughters of a candidate as possible in order to judge his hereditary performance.

This testing period lasts for six weeks. Each bull is tested in different regions (crop farming, grassland). This guarantees that regional effects do not have a major influence on a bulls breeding value.

Waiting bulls:

After the testing period further 15,000 semen straws are collected from each sire. Afterwards the sire is kept on one of our waiting stations at Börnchen / Saxony or Anzing, till the first production data of his daughters are published. This takes about four years.

Genomically selected young bulls:

The German Animal Breeding Law now allows us to sell semen of bulls without previous progeny testing that have genomic breeding values with an accuracy of 50%. This means that semen of all bulls that finished the quarantine period can now be immediately marketed. Naturally there is a huge time saving of at least two years – since the wait for progeny results is not there.

Proven sires:

Bavarian Fleckvieh Genetics attaches great importance to the fact that the bulls still run through a field progeny testing. Especially the estimation of the type traits is subject to variations. After production results of the progeny are published and the daughters were inspected for their type traits, “the wheat is separated from the chaff” and the bulls marketed as “proven sires” are chosen.

New selection methods:

New methods of biotechnology allow us a precise testing of single traits of the hereditary performance of a sire, as for example beef quality traits or milk quality traits. Of course we take advantage of these methods and test our sires.

The History Of Genomics in Dairy Cattle

The use of genomic information in genetic evaluation has brought about revolutionary change in dairy cattle selection. Genomic evaluations increase the accuracy of genetic evaluations and have the potential to rapidly increase the rate of genetic improvement in many traits.

Their use is especially effective where there is limited information such as with females and young bulls, and with traits of lower heritability. The sequencing of the bovine genome in 2004 spurred a worldwide effort to use basic information about genetic coding to improve how the genetic values of cows and bulls are estimated. The bovine genome is made up of about 25,000-30,000 useful genes.

For genomic selection, the genome researchers look for markers or single nucleotide polymorphisms (SNPs). An SNP is a place in a chromosome where the DNA sequence can differ among individuals. SNPs are particularly useful when they occur on a gene or close to a gene that contributes to an important trait. As most traits are controlled by many genes, the process is complex, and real progress was not made until a genotyping computer chip, called the Illumina 50K test, was developed that could be used to identify over 50,000 SNPs on the genome.

Although the 50K test continues to be used for high-end breeding stock and screening young artificial insemination (AI) sire entries, a simpler, cheaper test called the 3K test, which identifies about 3,000 carefully chosen SNPs, has been developed to allow herd owners to make use of genomic testing on a wider basis. Provided that at least one parent has been tested with the 50K test, the more economical 3K test can be used with only a small loss in accuracy due to the use of a method called imputation, which uses knowledge of the parental genome in the calculations. Recently, more SNPs and improved accuracy have been added to the 3K test, now called the 6K test.

Tests Available

The initial genomic test available used the Illumina 50K chip, which evaluated about 54,000 SNPs that were of value on the bovine genome. This has become the accepted standard for genomic testing of AI sires, potential bull dams and screening of young sires. The cost of using this test has declined since it was first introduced, however, it is still very expensive for widespread use by dairy farmers. In 2010, Holstein Canada and the Semex Partners launched GenoTest, a program that makes the 3K test, and an even better one – the 6K test, available to Canadian dairy producers at a cost of $47 per animal.¹Although genomic testing can be carried out on a variety of tissue samples, the preferred samples are hair, including roots, or, in the case of young calves, a nasal swab. Test kits are available from Holstein Canada and the Semex Partners. Detailed instructions are available from the Holstein Canada website

Genetic Improvement:

The publication of the August 2009 dairy genetic evaluations marked a new era in Canada for bull “proofs,” when the majority included genomic information. With a few exceptions, all bulls available in Canada in the top 100 Lifetime Profit Index (LPI) list published by the Canadian Dairy Network now have genomic estimated breeding values (GEBVs) – breeding values in which genomic information was used.

With proven sires, which have many daughters and a reliability over 90%, the estimated breeding value (EBV) is already a pretty accurate measure of the genetic value that a bull passes on to his offspring. For these sires, the addition of genomic information improves this accuracy only a small amount for most traits. However, the improvement can be substantial for traits with low heritability, which are difficult to evaluate accurately through traditional methods. With genomic testing, it is now possible to screen thousands of candidate young sires for AI selection and select the best possible candidates to enter the progeny testing program. This increases the selection intensity and also reduces the costs of maintaining large numbers of young sires awaiting proofs. A definite advantage using this technology becomes evident here.

Dairy producers can now use young sires that have genetic information (genomic parent averages or GPAs), as well as proven sires. These bulls’ GEBVs are equivalent to the addition of 9-20 daughters for production and type traits in a traditional proof. They are not as accurate as a progeny proof, and breeders should use them in groups rather than trying to select one or two top bulls to use extensively. Research has shown that, in most situations, a group of five genotyped young sires has an average reliability nearly as good as that of proven bulls. A group of 10 such sires has the same average reliability as proven bulls. These young bulls, on average, can impart superior genetics as long as one does not concentrate on one particular bull, given their lower reliability.

Strategies and potential advantages of genomics:

#1. A strategy could be to use top, highly proven sires on 50% of the herd and a group of young sires on the remaining 50% of the herd. Set a limit on the number of breedings to any one sire and then replace it with a new top bull. Review the list of sires at every genetic evaluation and add and delete individuals as better bulls come along.

#2. An added advantage to GPAs is the availability of accurate information on individual traits. The breeder can take advantage of top young bulls that meet criteria such as calving traits and fertility, for use on heifers in the breeding program. This is an opportunity to bring the best available young genetics into the herd as quickly as possible.

Female Selection
#3. Test cows and replacement heifers that are candidates for bull mothers, embryo transfer and/or export of genetic material with the 50K test or at least with the cheaper 6K test. The ease of use and availability as well as low cost of the 6K test makes genomic selection within herd a real possibility. Genomics are the most useful for heifers, which can be tested shortly after birth, allowing selection decisions and planning well in advance of their potential entry into the milking herd.  Genomics provides the opportunity to make meaningful in-herd selection decisions.

 Genomics in Herd Management:

The availability of genotype parent averages, or GPAs, for replacement heifers provides new tools by which the owner may make management and breeding decisions. GPAs are calculated for all traits allowing the owner to select sires to use on heifers using complete production, type, health and fitness trait information. Genomic information may alter management of some heifers. Replacements that have an exceptionally high GPA for production may be managed differently prior to calving and in the milking herd. Heifers with a high genetic value for somatic cell score – meaning they may be prone to mastitis but are otherwise good quality heifers – might be managed differently to reduce exposure to mastitis infection. If an owner uses sexed semen on a selective basis, the high-GPA heifers could be chosen for sexed semen to ensure they have female offspring. Genotyping is a very new scientific development, and its uses and applications are developing very quickly. Dairy producers will quickly adapt to the many ways this technology can be used to better manage and improve their herds.


The availability of genomic testing for dairy selection purposes has improved selection for AI sires and females within herd. For sires, genomic testing has improved accuracy such that young sires may be screened prior to entering a bull stud. With GEBVs, the accuracy of genetic evaluations is improved for young sires as well as for traits with lower heritabilities such as health and fertility across all sires. As the dairy industry takes advantage of genomic testing, the rate of genetic progress could be improved by as much as 60%. This could be accomplished as AI studs take advantage of more efficient bull proving, producers make better use of younger sires and use more accurate genetic evaluation of cows and heifers to select the best animals within their herds. GEBVs, however, do not take away the need for participation in progeny-proving programs and keeping records of production, calving and other traits. These data are required to update the reference values on which the effects of the various SNPs are estimated.

BDC Interpretation of Fleckvieh Genomics:

The information provided above gives a general oversight but warns of the fact, that there is a huge value in traditional progeny testing in a proven sire program. Mating predictability and precision phenotypic expression of heritable traits can not be surpassed with this method in the author`s opinion. Consistency of applied targeted mating with highly predictable outcome improves genetics in a given herd. The AI stud takes on the challenge and investment in developing and making available the best semen. The farmer ends up with the best calves. Semen pricing? Well again – the progeny tested Fleckvieh Genomics provides the best investment and this is because there are less mishaps with the the newborn animal. Industry reports from farms and veterinarians have reinforced this in discussions with the author.

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