Application of sequence-based multi-allelic markers in genetics and breeding of polyploids
Highly diverse and polyploid breeding populations may contain multiple alleles at any trait locus of interest, each of which may have various positive, neutral or negative effects on a trait. Multi-allelic markers (i.e. haplotypes) are needed to analyze and catalogue the effects of different alleles in trait loci that are important for breeding. We will develop methods for haplotyping in breeding populations from low depth sequence data, catalog haplotypes and use these for genetic prediction.
The project contributes to Missions A and B (Circular and Climate-neutral Agriculture and Food production) as it aims to develop key technologies for breeding polyploid crops (MMIP ST2 Biotechnology and Breeding 44 & 45). Important polyploid crops can be found within the ornamental, fruits, vegetable and arable sectors (including biobased and protein crops). The project has a crop and sector-transcending character: methods and tools will be generic and can be used for breeding in any of those polyploid (and diploid) crops and sectors.
By supporting breeding companies with methods and tools to select for difficult traits, varieties can be developed that are more resistant to pathogens (lower losses in the chain) but also that have other important characteristics (e.g. resilience for abiotic stresses, production and quality traits). Improvement of these traits in varieties will contribute to either one or both Missions. Many of the traits that society demands for improving sustainability of production or that are needed for mitigating global warming, are physiologically complex and polygenic, and multiple alleles may be present within individuals and in breeding pools. To enable breeding companies to efficiently breed for such traits, the proposed methods and tools need to be developed and demonstrated.
The project is a genetics project, that aims to develop and validate tools (methods and software) for haplotyping large numbers of plants in especially polyploid breeding material, multi-parental populations and association panels, and for detection and selection purposes. These tools will be tailored to be useful in practical breeding programs, for which mostly low depth sequencing data will be produced, for cost reasons. With a focus on local haplotyping at gene level. Next to that the project aims to explore genetic prediction in polyploids and the use of haplotypes therein for several traits of interest depending of the genetic architecture of a trait. To assist a breeder in making rational choices in the breeding program, data visualization is a powerful tool. In close collaboration with our industrial partners, we will develop a novel visualization tool that can help a breeder make selections in a specific set of germplasm in a running breeding program based on haplotypes and estimated effects of haplotypes on traits.
The aim is to have a first version software for haplotyping and a simulation pipeline to generate data for genomic prediction at the end of year 1.
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