The Ovigen multi-breed sheep genetic and genomic evaluation project is entering into its third year. The project spans across the six main performance-recording Irish sheep breeds – Belclare, Beltex, Charollais, Suffolk, Texel and Vendeen.

Delivering an update of progress to date, Teagasc geneticist Noirin McHugh reported that over 10,000 genotypes were collected from participating flocks in 2015 and 2016, with the number of samples collected detailed by breed in Table 1.

Genotyping carried out in the first two years of the four-year project was a mixture of 50k and 15k single-nucleotide polymorphism (SNP) chips, which Noirin explains in its easiest terms is essentially using SNPs as a signpost to find specific genes.

Its potential is huge, ranging from using genomic evaluations to increase accuracy levels of predicted performance to monitoring major and lethal genes, along with identifying parentage, inbreeding and scrapie profiling.

There was a 4% failure rate in all samples taken. The contributors were a mixture of sampling errors leading to insufficient tissue collected in the sample, some of which was caused by the initial tags used not containing sufficient desiccant to preserve the tissue sample, to handling errors and inappropriate storage, while there were minimal errors at lab level. Noirin outlined that animals that had a failed genotype can now be re-genotyped free of charge through Sheep Ireland.

In total, there were 12,733 animals genotyped. Of these, 5,008 animals had a parent (sire or dam) genotyped, with 1,602 having both the sire and dam genotyped.

An error in the sire recorded was recorded in 271 or 10% of all sires recorded, while there was an incorrect dam recorded in 7.6% of dams. These incorrect errors are likely to stem from a mixture of sampling errors, mismatched lambs at birth and a difference in parents recorded in flock books and the Sheep Ireland database.

There was also an error in the SNP chip developed for identifying scrapie and work is under way to develop a new SNP chip for genotyping in 2017, which will also hopefully include the potential to determine scrapie profiling.

Noirin concluded that significant progress has been made to date, but to really get a positive outcome, genotyping must continue.

New genotyping option

Cost is a major barrier in genotyping, with the 50k SNP chip used to identify DNA markers costing €104 in 2015 and €61 in 2016. The lower cost in 2016 stemmed from higher volumes being ordered.

Teagasc geneticist Donagh Berry has been working on developing a new SNP chip (11k) for genotyping that will lower the cost of genotyping. Donagh has developed an SNP chip that identifies 10,000 important DNA markers that can then be used to predict the full 50,000 DNA marker set with 98% accuracy.

The new SNP chip is attracting demand from collaborators in other countries, which is bringing about another increase in the number of SNP chips ordered, while also opening tenders up to more than one company.

This has the potential to greatly reduce costs, with the new Irish custom platform reducing the cost of an 11K SNP chip by €10 to €16.61 excluding the price of the tag. It is hoped that this new platform will also be able to identify the scrapie profile, but Donagh says further validation is needed on this.

2017 target

Sheep Ireland’s Eamon Wall said that the aim in 2017 is to continue with genotyping, with 2015- and 2016-born females and stock rams and AI sires the priority to genotype.

Ram lambs born in 2017 are less critical, he says, as information cannot be guaranteed to be returned for 2017 premier sales. Where breeds wish to aim for having 2017 data available, samples must be returned by 11 May.

While the lower cost of genotyping is €16.61, Eamon says there are still some funds left in the Ovigen project to heavily subsidise genotyping costs in 2017. Female genotyping will cost €3 plus €2 where a tag is required to collect the sample, while male genotyping will cost €6 and, again, €2 extra if a tag is required.

Sheep Ireland will be writing to pedigree breeders in the coming week with information of animals in the flock that are yet to be genotyped. A new web screen will be available in the coming days where flock owners can select and order the animals they wish to genotype.

Meanwhile, Thierry Pabiou of ICBF/Sheep Ireland reported the inclusion of a new health index in €uro-Star evaluations, which will be covered in more detail soon. The benefit of all these measures for commercial farmers is verified parentage and increased accuracy of through genomic evaluations.