Genetic and genomic tools for polyploids are lagging behind diploid crops, because of their genetic complexity. This project aims to provide such tools, building on up-to-date tools for mapping and QTL analysis in tetraploids as developed in our earlier successful TKI-U project 263, to now include higher ploidy levels and additional types of inheritance, introduce haplotype-based approaches and the use of pedigree information, and the development of advanced QTL mapping software to deal with genetically complex traits.
a) In time SNP genotyping will be replaced/supplemented by haplotype genotyping
Current tools are restricted to analyses of single SNPs, whereas haplotype based approaches are more powerful because multiple alleles can be distinguished resulting in higher specificity. This is of particular importance for polyploids because of the higher number of homologous chromosomes that need to be distinguished. Haplotypes can be inferred from multiple independently scored SNPs, but also from sequence reads, resulting in multi-SNP, multi-allelic sequence markers. Our mapping and analysis tools will be designed to take advantage of haplotype information from both types of data and thereby provide higher power to genetic analyses such as mapping studies, genome-wide association studies and pedigree-based QTL analyses. The active use of pedigree information to derive and validate haplotypes will further strengthen the accuracy.
b) The tools to use haplotypes in mapping and QTL analysis for polyploids will be developed here
We will extend the QTL analysis methodology and software tools developed in TKI project 263 to deal with haplotype data, both for allopolyploid and autopolyploid crops, to be able to include pedigree information in inference of haplotypes, and to be able to consider mixtures of disomic and polysomic inheritance (such as we have encountered in at least two polyploid crops). As for QTL mapping, multi-allelic QTL analysis will be made possible and extended to higher ploidy levels, and will include testing for multiple QTLs simultaneously and the possibility of dominance of QTLs and QTL dosage effects.
c) Validation will be done using simulations and in crop-specific parts of the project
The methods and tools developed will be validated using datasets generated for various polyploid crops, produced in crop-oriented parts of this project, including field crops, fruits and ornamentals, in which the partners have an interest. Some pilot datasets for this validation are currently being developed in TKI 263 or by private partners (e.g. potato, leek, strawberry). Where necessary, simulation studies will be used for validation as well.
d) The tools will improve breeding of polyploid crops across widely different sectors
These tools improve possibilities for genetic and genomic analysis in polyploid crops and help accelerate breeding of these crops by enabling the effective use of next-generation molecular markers. Faster breeding will contribute to improving yield, product quality and sustainability of production of field crops, fruits, vegetables and ornamentals.