How to use genomic indices

This week sees the release of the first UK genomic bull proofs, but what does it mean and how should farmers use them? Aly Balsom speaks to DairyCo’s Marco Winters to find out

What is genomics?

Genomics enables an animal’s genetic potential to be predicted from a young age by comparing its DNA with a “SNP key” which is produced using a bank of genetic information representative of the national population. This allows younger bulls to be used quicker, rather than waiting for progeny testing.

How does it affect me?

From now on the DairyCo bull proofs will include genomic Predicted Transmitting Abilities (PTAs) for Holstein bulls. Two-thirds of Holstein bulls on the active list will have genomic PTAs.

Why are we using genomics?

  • Genomic indices allow farmers to have more confidence in using younger sires
  • With the new technology, a bull’s performance can be predicted from birth by taking a DNA sample from hair or a nasal swab. So rather than waiting for milking daughters and a progeny test proof – which usually takes five years from birth – they can get an indication of performance early on
  • By using a bull early, generation interval is reduced, potentially increasing genetic gain
  • Mr Winters says it is important for the industry to use new technologies as a modest 15% improvement in genetic gain could be worth about £20m over 10 years.

What do the new proofs look like?

From now on, the dairy bull proof run will include two lists:

  1. A daughter proven list, with the “G” tag for bulls with genomic data
  2. A young bulls list which will include bulls with just genomic data – this is the main point of difference

The genomic PTAs will look exactly the same as traditional PTAs, but will be accompanied by the “G” flag.

Key to table:

  • G = Genomic
  • P = Protein
  • L = Lifespan
  • F = Fertility
  • M = Mammary
 Example genomic young bull list      
  G Rel. Milk Fat P Fat % P % SCC L F M L&F TM £PI
A G 68 649 27.8 24.3 0.03 0.04 -1.8 0.5 6.4 0.93 1.52 1.28 253
 E G 69 856 21.4 19.6 -0.14 -0.09 1 0.1 -6.2 0.89 1.91 1.41 96
 Example proven bull list      
 Bull G Rel. Milk Fat P Fat % P % SCC L F M L&F TM £PI
V   73 717 24.7 22.4 -0.04 -0.01 -10 0.6 5.4 0.50 0.44 0.71 219
W G 82 796 25.0 24.6 -0.07 -0.01 -26 0.3 3.2 0.64 0.89 0.84 205
A: “G” indicates that genomic component is included in the index. This bull has a very good balanced proof; transmitting well in all main traits, which is reflected in a very high PLI of 253. Bull A can therefore be considered for limited use on farm (up to maximum of 13% of the herd)
 E Poor daughter fertility index alongside slightly positive (ie bad) SCC, gives low PLI. So even though this is a young bull with a genomic evaluation, it’s a mediocre bull that is best avoided.
 V Top daughter proven bull. No “G” component, which is why the reliability is lower at 73%. However, the PLI is good and therefore is worth using on farm. But beware of the lower reliability.
 W “G” component, alongside daughter information increases reliability. This bull has a solid proof and over 200 PLI

How should I use the new proofs?

The new proofs should be interpreted in the same way as the traditional proofs – bulls should be selected on PLI and lifespan. See our how to guide for using breeding indices at

How reliable are genomic indexes?

The key consideration with genomically tested young bulls is reliability, explains Mr Winters.

“Reliability of these tested young bulls is a lot lower than progeny tested bulls, so there is a risk/reward balance to be assessed.”

However, although the risks of using second crop, high reliability bulls is lower, farmers could be missing out on the potential genetic gains that could come from a younger generation.

  • Young bulls that only have parent average information and no genomic information generally only have a low reliability index of 30-40%
  • A bull with a genetic index based on performance of thousands of daughters (“second crop indexes”) could have a reliability of 99%
  • Genomic indices have reliabilities in between the two at about 55-65%

Genomic valuations

How could genomic indices be used on farm?

Generally, Mr Winters said a good rule of thumb was:

  • No more than 7% of a herd should be bred to a young sire with no genomic information
  • Up to 12.5% of a herd could be served to genomically evaluated young bulls
  • A first crop daughter proven bull could be used on 25% of the herd
  • A highly reliable, second crop index bull could be used on 50% of the herd
  • If a farmer is comfortable using low reliability bulls, a mix of 55-65% of the herd bred to proven bulls and 25% to genomic young bulls is a good suggestion

Genomically testing females

Genomic testing also has a role to play in establishing the genetic merit of females.

Later this year it will be possible to fully genomically test females against a UK base, through a service offered by the milk recording companies and Holstein UK. This will enable the generation of cow specific PTAs via DairyCo.

At the moment, it is possible to genomically test cows, but there is currently only a USA base to compare with. This tool is currently being used by pedigree producers to screen top end females in order to sell bulls or embryos.

As soon as the cost of screening comes down, it may be more cost effective for commercial producers to screen their youngstock to select out poorer animals and serve the best to sexed semen, for example.

Costs may vary, but will be roughly about £40-100 depending on size of the “SNP key” used.

Genomics: What’s been happening in the UK?

  • Over the past year, industry members have been working together to collate genetic information to produce a genotypic bank
  • The bank now includes 16,000 genotypes from USA, Canada, Italy and UK – this information is used to produce a “SNP key”(DNA base) to which individual UK animals can be compared and their performance predicted
  • Within the UK, genotypes have been supplied through direct partnership with Cogent and Genus
  • Indirect partners include WWS, Semex, Dairy Daughters, Alta Genetics and which will have provided genomic information through the USA and Canada data
  • Phenotypic information (the way a gene is expressed) such as yields, fertility, longevity, calving ease and SCC have been provided by NMR, CIS, UDF and Holstein UK. This information is crucial to enable a correlation to be found between specific genes and specific traits
  • The existing bull PTAs are now being linked to this new genetic information

Do’s and don’ts of genomic indexes:


  • Carefully study the bull’s index, just as though he were a conventionally-tested sire
  • Remember that the lower the reliability of the index, the greater the chance the index will change
  • Ask your AI company to show you how many daughters the bull has and in how may herds
  • Use a mix of daughter-proven and young genomically evaluated bulls to obtain a balance between risk and reward


  • Over-estimate the reliability of genomic indexes which will be lower than those of most progeny tested bulls
  • Over-use any young, low reliability bull with or without a genomic index


  • There’s nothing mystical about genomic evaluations in themselves. A young bull marketed as a “genomic young sire” may be no better or worse than any other bull.