TrackGene: video-tracking insect resistance genes in field and greenhouse crop populations

There is a rapidly increasing demand for robust crops with resistance to pests. On the one hand there is a direct economic benefit for the farmer if he can spend less on inputs to control pests, and on the other hand society, motivated by environmental and health concerns, imposes more and more limits on the use of pesticides such as neonicotinoids. Insect resistance is usually polygenic and can be introduced from wild germplasm if plant breeders have access to the best tools to phenotype plant populations in conjunction with powerful genetics tools like genomic prediction.

Conventional assays are less effective because they mostly score population size only, take 2-3 weeks to complete, are difficult to implement with quarantine organisms and only generate single data points per plant. Recently, video tracking (EntoLab) was introduced by WPR and Noldus IT as a promising alternative or complement which requires only a few hours of recording of multi-arena assay plates with insects placed on a leaf fragment taken from a plant/genotype in its regular field growth condition.

The aim of this project is to make the video tracking method of identifying resistance directly useable in plant breeding by direct association of the video tracking data to the genetic variation of the tested plant populations through development of TrackGene, a package that performs statistical genetic association analysis and optimizes settings by machine learning with graphic output to quickly assess results. The functionality will be tested by a unique international consortium of 3 plant breeders of horticultural and field crops, each contributing their own genotyped populations. The broad variety of crops including sweet pepper, maize and rice and the broad variety of pests (thrips, fall army worm, plant hoppers, etc) guarantees major impact on industry when the project is successful both in terms of genomic prediction models for resistance in the various crops and in terms of QTL detection technology. The project has a strong dissemination component. All companies will be trained in use of the software on their own populations and may purchase the platforms for own use. The user company from India will be trained to apply the video tracking technique on site in India and share experiences and data with the development team in Wageningen. WPR will take up further development of the EntoLab assay platform with dedicated assay plates for the different pest insects and technical optimizations.