New Method of Genotyping in Plant Breeding

Göttingen, 20.09.2022

MBM ScienceBridge GmbH has successfully negotiated a contract for an exclusive license between the Georg-August University of Göttingen and the Lower Saxony plant breeding company KWS SAAT SE & Co. KGaA. The licensed invention is about a new, time- and cost-saving method for genotyping in plant breeding.

Complex but economically important features such as yield or pest resistance are difficult to breed for because they are influenced by several genes simultaneously. By selecting variants based on effective genotyping, it is hoped to achieve sharper selection and higher reliability in selecting suitable crossing partners.

Currently, high-throughput genotyping is mainly performed using single nucleotide polymorphism (SNP) arrays. They are relatively easy to use and usually produce robust characterization with relatively few errors. As a result, they are commonly used for diversity analysis, genomic selection or genome-wide association studies. However, limitations of the technology include the complexity and cost of array design, their inability to type de novo polymorphisms, their lack of flexibility in the markers included, and the cost of genotyping, which increases substantially with the number of SNPs on the array. Moreover, SNPs are usually selected as array markers that are located in the conserved regions of the genome and therefor they provide little information on structural variants.

The present invention describes a new method of genotyping plants for use in plant breeding and research. It is based on sequencing partial regions of the genome (shallow depth) and filling in the missing data by imputing sequence data based on haplotype libraries. Software-assisted imputation leads to increased read coverage for the haplotype, allowing parallel genotyping of a very large number of variants for a very large number of individuals. Thus, this method outperforms array genotyping in terms of cost, simplicity, performance and accuracy. Since the cost per data point is several times lower, the method has the potential to replace array-based genotyping in the next few years and possibly become the "gold standard" in plant breeding.

The invention was made in cooperation with KWS and a patent application has been filed. Led by MBM ScienceBridge, a licensing agreement has now been concluded with KWS, granting KWS exclusive use of the method for numerous plant species in its portfolio. These include sugarbeet, corn, cereals, rapeseed, sunflowers and various vegetables. The University has exclusive exploitation rights for the animal sector and all plant species not licensed by KWS.

 

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