Industry welcomes the arrival of new SNP Chip

Friday 23 Aug 2019

The era of genomics for forestry is here! Scion and the Radiata Pine Breeding Company (RPBC) have developed the world’s first commercial SNP chip for radiata pine. SNPs (pronounced “snips”), or single-nucleotide polymorphisms, are a type of DNA marker, and SNP chips are a way to test tens of thousands of these markers across whole populations in a single experiment.

As part of their Genomic Selection programme, the RPBC has been working towards making such a tool available for the last five years. Scion began the process of uncovering SNP markers for radiata pine back in 2012, finding more than a million of them. However, there was no easy way to test them cost-effectively across the breeding programme.

Collaborating with like-minded researchers in an International Conifer SNP Consortium enabled access to cutting edge developments in genomic testing technologies at extremely competitive pricing, and the programme is now pleased to report that this goal has now been achieved.

The accuracy and affordability of this SNP chip over previously-available technologies will be a game changer for the breeding programme. In the few short months since its design, it has already been tested across more than 8,000 trees – at less than a third of the cost it took to test about 4,000 trees over the previous five years – and indications are that it is working really well. We are seeing less than 2% missing data across the ~36K SNPs that this chip can test, and accuracy is consistently higher than 99%.

Furthermore, the chip is performing equally well on a wide range of samples, from ancestral genotypes through to the very latest 2018/19 elites from New Zealand, as well as on Australian material. This tool makes pedigree confirmations achievable within months, and the implementation of genomic selection can start in 2020/21, which makes the RPBC one of the first commercial forest tree breeding programmes in the world to use genomics on an operational scale.

RPBC Chief Executive, Brent Guild, said “the programme is a credit to those individuals and organisations who had the vision to develop and support it back in 2013. We are delighted with the outcome and look forward to entering a phase of practical application for the Radiata Pine breeding programme”.

Photo: Each radiata pine SNP chip can test 36,285 SNPs across 384 samples at a time, with each of the 384 “pegs” measuring 2 mm x 2 mm.”

Source: Radiata Pine Breeding Company

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