CLARIFIDE: Breeding Advice

CLARIFIDE® is the veterinary genomics package that aligns genomic testing with breeding objectives and herd health goals on your farm.

The service utilises the CLARIFIDE® genomic test. CLARIFIDE® is the most commonly used genomic test in North America. This low density 19k single nucleotide polymorphism (SNP) chip is run on a hair sample. Resulting genomic predicted transmitting abilities (GPTA’s) are significantly more reliable than traditional parent average/pedigree index values.

As part of the CLARIFIDE® package a structured consultancy package is delivered alongside testing. This ensures that you maximise your return from an investment in genomics and utilise to full effect the extensive amount of data that you get back from testing.

Delivery of the CLARIFIDE® package is available from trained vets within the XL vets group. The package is available to ALL UK dairy farmers, including both clients and non-clients of an XL vets practice.

Vets from fourteen XL vets practices have already undertaken rigorous training to become certified providers. A list of trained vets/vet practices can be found on the CLARIFIDE® website. Alternatively please contact the RAFT solutions office on 01765 645893 or email clarifide@raftsolutions.co.uk

At present testing can be conducted on purebred (>87.5%) Holsteins, Jersey and Brown Swiss animals. As the UK has not yet developed a SNP-key for Jersey and Brown Swiss animals US figures are used in isolation. When UK figures become available retesting will not be necessary and UK figures for any animals already tested will be available upon request from AHDB. We hope soon to be able to offer a test for Friesian cattle.

For Holstein animals both UK (Profitable Lifetime Index – £PLI) and US (Net Merit – $NM & Total performance index – TPI) GPTA’s are returned alongside a comprehensive suite of UK/US core production, type, health and fitness traits (Jerseys and Brown Swiss – only US figures at present). Other key production indexes and parentage confirmation are included to accurately predict genetic merit. Additionally information on inbreeding, genetic recessives/conditions/characteristics and haplotypes are included. This includes ALL fertility haplotypes (Holstein 1-5, Jersey 1&2 and Brown Swiss 1&2) Holstein cholesterol deficiency (HCD), CVM and Brachyspina.

Total performance index is owned by Holstein Association US. In order to receive an official TPI for the animal it must be registered within the US herd book. We have put in place a mechanism for this to occur should you wish to receive an official GTPI. This process is subject to an additional registration fee.

NO.

Testing is available to ALL herds irrespective of milk recording status. However where available, access to milk records and subsequent PTA data (through the AHDB herd genetic report) does add value to the consultancy package.

When considering genomic test results it is important to remember that the number of SNP’s does not impact the value of the technology, increases in reliability are what impacts the value of the test result.

Imputation is used to enhance the value of low density chips. This is the process whereby available genotypes on reference animals are used to estimate high density genotypes in cattle tested with LD chips. The imputation call rate describes the percentage of SNP’s in the higher density genotype that are correctly estimated. Imputation call rates for CLARIFIDE® are over 99% accurate, amongst the highest in this field of science. The reliability of figures produced using CLARIFIDE® are as high as those received from other tests that utilise a moderate density (e.g. 50-65k) chip.

Whilst this varies slightly between animals dependant on the amount of ancestry data that is available, for most animals reliabilities for the following GPTA’s are achieved; PLI 55-60%, Milk 65-70%, Type 60-65% and Health and Fitness traits (Fertility, SCC and lifespan) 55-70%.

NO.

When they occur resamples are a frustrating feature of any genomic test. However they only occur infrequently with the CLARIFIDE® test. The resample rate between hair and ear notch sampling is thought to be very similar. The high usage of hair sampling in North America is testament to the fact that this is an incredibly quick and user friendly method of capturing a DNA sample for analysis.

Results are returned within 6-8 weeks. A set of samples submission and publication deadline dates is available upon request.

CLARIFIDE® results are presented in an easy to understand format so that the predefined action plan that you put in place with your CLARIFIDE® vet can be implemented easily. This includes both an electronic and hard copy of results. Results are also updated on the Holstein-UK website (pedigree Holstein animals only), milk records and on the AHDB herd genetic report.

Genetics is a fundamental part of herd health. As independent advisors armed with an understanding of your herd data your CLARIFIDE® vet is well placed to help set breeding objectives specific to your farm. As vets we have both a scientific understanding of genomics and the statistical nature of breeding.

Once testing is initiated your CLARIFIDE® vet is well placed to develop a ranking that is bespoke to your herd – your CLARIFIDE® vet will focus on those areas where an improvement through breeding would help to improve performance on YOUR farm.

We are very keen to work with any breeding advisors that may be involved in the breeding decisions that are made on your farm. This collaborative approach will ensure that a maximum return on your investment in genomic testing is realised.