96-genotype set
Our mission is to inspire the potato value chain worldwide by delivering innovative products and services, which includes R&D on our favorite crop. Royal HZPC Group values the research community and aims to promote and facilitate research on the potato, the world's third-largest food crop, in the broadest sense. For this purpose, we have set up a program that will stimulate many researchers to start exploring this complex, polyploid crop, as easy as if they are working on the model species Arabidopsis.
Collaboration
For many years, we have been working on harnessing the genetics of potato. We do this through advanced clonal tetraploid breeding, as well as through diploid hybrid breeding. Over the last decade, we have built up many resources to help us in deciphering the polyploid (and often polygenic) traits that are found in this crop. As potato is genetically also one of the most diverse crops on the planet, there are very many traits hidden in the cultivated germplasm. We feel it is time to start exploring this crops’ germplasm to the fullest, and we cannot do this alone: We would love to collaborate with you!
A set of 96 genotypes
We have selected 96 genotypes that together represent the vast majority of the genetics found in cultivated potato. The genotype set will be provided as in-vitro plantlets, which allows you to maintain the collection over a long period, and will enable the user to start experiments at any given time. Also, we will yearly provide field-grown tubers of the same genotype set, but this is of course subjected to seasonality.
Royal HZPC Group has a high density genetic map of this genotype set, allowing traits to be mapped with high accuracy and speed. For several of the selected genotypes, public reference sequences are available, allowing for rapid interpretation of identified QTLs. As the number of genotypes is limited, capturing complex traits involving many loci will likely not be a feasible option, but many (relatively) simple traits remain to be identified. Also, we estimate that accurate phenotyping of 96 genotypes will by itself probably be challenging enough to realize.
The second option is reverse genetics: upon request, we can share read mapping data (BAM-files) of your gene(s) of interest of all 96 genotypes, allowing you to explore the complete allelic diversity in cultivated potato. This may allow you to assist in the design of specific experiments, or perform targeted bioinformatic analyses.
Additional support
Next to in-vitro plants and field-grown tubers, we have made segregating seed populations for each of the 96 genotypes, which are ready for use. Such populations can be used to quickly confirm a candidate QTL as identified in the 96 set. And, we will help you by developing and running haplotype-specific markers in the shared segregating populations. Also, we will supply assistance in correlating phenotypes with the genotypes. Our polyploid GWAS pipeline is perfectly attuned to this job, and will most certainly show if genetics are involved in variation of the trait you have identified.
Next to WGS data, we have RNAseq data available for most of the haplotypes that were found in the 96 genotypes, allowing for estimation of basic expression levels, alternative splicing, etc.
Limitations of use
For this genotype set to be broadly adopted by the research community, we strive to keep the barriers as low as possible. The proposed approach does however give great advantage in studying any trait of interest.
To safeguard that sharing this tool with the world does not explicitly harm our own interests, there will be a few limitations to its use:
- This genotype set will only be shared with parties that do not have a commercial interest in potato breeding. Sharing of the provided plant material with 3rd parties is not allowed.
- The topics to be studied will be discussed with HZPC before starting. Obvious, direct breeding traits may be excluded from our assistance, to prevent oversharing with our competitors in the market.
- To keep at least a small head-start in the findings, most of the genotype names will be anonymous, and will be referred to as HZPC96XX, going from 01 to 96. Publication or sharing the identities of the provided genotypes will not be allowed without explicit permission from HZPC. The identities of twelve genotypes are revealed, including the ones for which public reference sequences are published and freely available.
- The set includes genotypes that are registered cultivars, and are thereby protected by law against multiplication for commercial purposes. So use them for research only!
- Our minimum standard IP request is royalty free Freedom To Operate (FTO). Discoveries made with our help should not be able to get in the way of HZPC breeding efforts.
- European Union only.
Publication
As we are aware that publication is an important part of academic science, we strive to fully cooperate wherever possible. Our selection is done at the start of a project: is this a topic that we feel as being non- or pre-competetive? If so, we will support publication of the all necessary details. These requirement can be modified in a case-by-case manner. The raw genomic dataset (including full sequences of all 96 genotypes) will however NOT become publicly available.
