KeyGene: New selection technology broadens possibilities in plant and animal breeding

Date:11-01-2018

Scientists of the Netherlands-based breeding research company KeyGene have recently published in the scientific journal PLoS ONE, detailing a flexible and scalable technology named SNPSelect for faster and more effective plant & animal breeding. The technology is based on SNPs (Single Nucleotide Polymorphisms), genetic variants in which the DNA differs in only one nucleotide at a given location. The total combination of these genetic variants, also called the genotype, is unique for each individual.

Important differences between plants or animals of one and the same species can be caused by very small differences in DNA. The distinction between red or white flowers can be caused by a mutation in one single base pair, the building blocks of DNA, where the total DNA of that plant may be well over 1,000,000,000 base pairs. Such a small difference in DNA is called a SNP.

The SNPSelect technology can help plant and animal breeders across the world to work faster and more effectively. For example, it can aid in developing more sustainable, higher yielding and/or higher quality plant varieties and selecting better farm animals.

SNPs can be very helpful for breeders of plants and farm animals as small differences in DNA can cause crucial improvements in important traits. Where other technologies often allow for only one, or a small/fixed number of SNPs per analysis, KeyGene’s new technology called KeyGene® SNPSelect can detect and follow thousands of SNPs in a single assay.

Breeders want to be able to select plants or animals with the best combination of SNPs that are involved in as many crucial traits as possible. Think of resistances against pest or diseases, improved yield or better food quality. Once they have identified the useful SNPs, breeders want to use these small DNA differences to optimise their breeding program.

The newly scientifically published SNPSelect technology expands the breeders’ toolbox:

• the technology is scalable: it allows for the screening from just a few to up to thousands of SNPs in only one DNA-analysis. In their scientific paper, KeyGene scientists show that the technique can be used for the analysis of 1,000 SNPs at the same time. In further research, the scientists were able to screen for up to 10,000 SNPs in one single DNA-analysis.
• the technology is very flexible: it allows breeders to easily change the set of SNPs they work with from year to year, and even from experiment to experiment.

How it works

In SNPSelect, three small DNA fragments, so-called probes, are designed and synthesised for every SNP the breeder wants to select. If we are working with 1,000 SNPs, 3,000 different probes, each having a unique DNA-identification part, are mixed and added to DNA-samples of the plants or animals the breeder wants to have genotyped.

Subsequently using the probes and plant DNA in a treatment that includes a so called polymerase chain reaction (PCR), DNA-molecules are being produced that represent the variants of all SNPs of interest present in every plant or animal. These DNA molecules are then identified using a next generation DNA sequencer. Specifically designed software translates the sequencing results into actual genotypes. With the SNPSelect technology, all SNPs of plants or animals of interest are thus simultaneously analysed in just one experiment.

Using these genotyping data the breeder can select the best plants or animals for his breeding program.

The SNPSelect technology can be used by DNA service providers, breeding companies and academic groups through licensing.

Link to the paper in PLoS ONE: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205577