Neogen Support Creation of Charollais Genomic Archive

Data from the past may hold the key to the future - Article from the Charollais 2021 Yearbook

The Charollais breed was one of the first in the UK to establish a Sire Reference Scheme (SRS) in 1990. The SRS supported the progeny testing of young rams and created the genetic linkage between flocks on which modern evaluations have been founded. It also brought breeders together and greatly helped in establishing the foundation from which the breed’s success has grown.

It was an exciting time for the breed, as we learnt about the genetic merit of different breeding lines and some real stars were discovered that went on to change the breed. In no breed, did the creation of a Sire Reference Scheme have such a lasting impact.

The rams from which semen was taken and stored were some of the best known, measured and evaluated Charollais sheep in the country, so when the opportunity recently arose to genotype these animals from semen held by Charollais Sires, I wanted to grab the opportunity to create a permanent legacy to capture and record the genetic architecture of the breed’s founders.

Support from Neogen for the Charollais Genomic Archive

In collaboration with Charollais Sires, AHDB approached Neogen for assistance – as Neogen have been providing RamCompare with a range of genotyping services over the last four years.

For two decades, Neogen’s DNA tests have enhanced livestock selection, breeding and marketing decisions. Today, Neogen is a world leader in genomic solutions and services, with six laboratories located around the world, including one in Ayr, Scotland. Their international footprint gives them a massive capacity for DNA testing, ensuring rapid and consistent turnaround times in processing and reporting.

Neogen customers can choose solutions from an extensive testing portfolio to make profitable choices about their animals. Using their world class laboratory, Neogen offer a range of different testing options for sheep, which include.

• DNA screening for parentage
• Genotyping to determine genetic merit & genomic breeding values
• Commercial traits, genetic recessives and causative mutations – such as Myostatin, Scrapie, Fertility and Micropthalmia markers.

 

What have we sampled in this project?

Charollais Sires made semen available from 79 Charollais rams that have been used within the former Sire Reference Scheme. These rams have produced over 13,700 Signet recorded progeny, showing the massive impact they have had on the breed – not to mention the generations of lambs that followed them.   

Rams included in this new genomic hall of fame include those with lots of progeny (progeny number in brackets), such as Crogham Centurion (1056), Rutland Ensign (653), Inglis Lloyd (577), Arjane Master Mac (573), Crogham Commissioner (532) and Logie Durno Earl of Dunbar (462) and some of the older rams that are found in many a back pedigree; including Netherallan Majestic King, Scratchmere Benneton and Haultwick Harrier.

A significant investment was required to genotype these animals. To get the project started, AHDB provided the initial funding and an extremely generous offer of support and in-kind sponsorship from Neogen enabled us to finish the job. By the close of 2021, we will have genotyped 30 rams on the leading 600K high density genotype and completed a 50K genotype on the remaining 49.

 

Why did we want to do this?

Rams come and go, but DNA lives forever. We can’t predict the future – but in a genomic age when DNA is giving up many of its secrets it is imperative that we hold a permanent genetic record for these animals.

In the short term, we can use the data to:

• Check parentage (and perhaps grand-parentage)
• Identify major genes that existed amongst founder animals – either beneficial or perhaps deleterious, though I am pleased to say few deleterious ones have arisen over the years.
• Assess genetic diversity amongst founder animals

Longer term this information is vital for a time when the Charollais breed moves to genomic breeding values or for that matter genomic inbreeding values.

Seeing the genetic foundation from which the breed has arisen is an important step in understanding where to go next and enabling us to do so more quickly than ever before.

 

What next?

AHDB is constantly thinking about where genomic information will take us next. At the moment that activity is mostly focused on preserving a genomic record from which other studies can build; in RamCompare for example, all Charollais rams have been genotyped and the data saved. While, we don’t have the funds to do it at the moment – it is logical that in the future we save tissue from lambs of known genetic merit, like those being CT scanned for example.

As breeders, if you have important sires in your semen flask I would strongly suggest that one or two semen straws are retained for future genotyping. If you have living rams, you may also consider collecting tissue samples using some of the modern tissue sampling kits that are available and storing samples behind your frozen peas at home. The cost of tissue sampling and storage is low relative to the value of the information it may hold.

For those interested in genotyping their rams, regardless of your gene test provider, consider whether the money you are investing in one or two individual gene tests could be used to get the same information as part of a low density, 50K genotype – and get another 49,998 bits of information at the same time.

 

Summary

AHDB is delighted to have had this opportunity to build a genomic archive for these important sires. We greatly appreciate the support of Carroll Barber and Charollais Sires in facilitating this work and of course Neogen for their extremely generous sponsorship in setting the genomic future of the breed on a firm foundation.

Article by Samuel Boon, Signet Manager and AHDB Breeding Specialist