Dear RosEXEC and RSCPW Steering Committee,
Below is some valuable correspondence with Luca Gianfranceschi regarding HiDRAS. I also talked on this matter with Eric van de Weg this past weekend. Although the specifics are not yet clear, Luca and colleagues are generous in considering the possibility of future US collaboration, and there is tremendous opportunity for a RosCAP to build on the experiences and outcomes of the HiDRAS project. There are many parallels with that European project and RosCAP strategies we discussed in our workshop last week. There is much we can learn from a project of similar scope and required coordination, including how to standardize phenotyping, standardize genotyping, ensure high data quality, merge datasets, keep participants well-informed, and publicize results. We also do not have to reinvent the wheel in determining the most appropriate marker types for the tasks at hand. SSRs, SNPs, AFLPs, SCARs, CAPs, (etc), and sequencing all have their place, depending on whether it’s research to identify new important genomic regions, to verify the utility of reported regions/markers in a breeder’s specific germplasm set, to perform allele mining, or to figure out the controlling gene itself, and whether it’s routine running of markers for progeny screening in a breeding program. The HiDRAS project also took great strides in implementing pedigree genotyping (which as I see it, incorporates association mapping at one extreme and single-population QTL analysis at the other extreme, but mostly operates in between for our purposes of linking germplasm and data within and between breeding programs).
HiDRAS comes to an official conclusion in September this year. The consortium will be presenting much of their findings at the Eucarpia fruit breeding meeting in Spain in mid September. I will be there, as well as many of you and others in the US Rosaceae community. With appropriate preparation, that meeting is a useful time for us to hash out collaboration details with HiDRAS members. I suspect that a RosCAP-ISAFRUIT connection (esp. for Prunus) will also be considered before and during the September meeting. I believe a RosIGI meeting is planned at the Eucarpia meeting, which could be the right setting for these discussions.
First of all my most sincere congratulations for your new job position at WSU.
I apologize for it took me so long to reply to your email.
I greatly appreciated your email inquiring about ways of collaboration. I truly believe that collaborations between the groups involved in HiDRAS and other non-European groups is to be favored and promoted. HiDRAS built a tremendous infrastructure for establishing marker trait associations , and the identified QTLs for various of the most important fruit quality traits are bringing MAB close to application. However, I also realize that in many cases additional research is required to make the results applicable in practical breeding programs. Funds being in shortage, international collaborations may be an efficient way to realize the required final steps. Indeed, the topics and the work that could be done in apple breeding and more in general in Rosaceae research are so large that there is enough room for large collaborations, avoiding work duplications
HiDRAS is a research project united by the goals that were agreed upon, almost 5 years ago. The HiDRAS consortium is in fact heterogeneous and each of its members is an independent unit that in several cases has parallel projects and interests. Consequently, decisions concerning the mode of collaborating and the data that could and should be shared has to be discussed and made by the consortium. This is especially true, as HiDRAS has been an highly integrated project in which a huge collaborative effort was put together. As you might recall, the core of the project is the phenotypic and molecular characterization of about 2000 plants that are related by their pedigree. In order to produce all the necessary data, all the groups involved in the project performed only part of the work, merging the collected data only for the final QTL analysis. Therefore there is no single partner who could consider himself as the owner of the data, nor of the results. Actually, the data produced by each unit are of little value (with some exceptions) if they are not merged in the large dataset.
To come to your question, at present it is not easy for me to propose a way of collaborating. Seeing the perspectives in collaborations to an US Rosaceae CAP-consortium, I will start the required discussions in short term, aiming to finalize the essential ones during the coming HiDRAS meeting in Zaragoza (Spain), which will take place just before the Eucarpia meeting.
In the mean time we also will proceed our efforts to disclose results by publications. As usual, it is our policy to make publicly available our outcomes, as soon they are accepted for publication. Currently, a large number of SSR markers and a dense linkage map have been published, as is a paper on the role of an ACS and ACO gene on fruit softening, as is a description of the HiDRAS Data Base AppleBreed. Additional information concerning the publications and more are available at HiDRAS website (www.hidras.unimi.it).
At present, a publication is in preparation on 80 markers from expressed genes, which we hope to have it published before the end of 2007. In addition, various presentations on QTL mapping are in preparation for the coming Eucarpia meeting.
I will keep you updated about any decision we can come up with, concerning possible collaborations and that could be a support to your iCAP-proposal. I appreciated your email informing me about the intention of presenting this proposal and I would appreciate if you could keep my name in the mailing list to be updated about the evolving situation.
At 20.17 30/05/2007, you wrote:
I am writing to determine the degree to which the outcomes of the HiDRAS project may be taken up and further refined by US groups. As I understand from recent discussions with Eric, the results of pedigree genotyping analysis within the HiDRAS project are turning out quite well, and there will likely be many interesting loci with closely linked markers for perhaps direct use in breeding, as well as useful QTL regions with more distantly-linked markers that will require further development. I have recently become involved in apple molecular genetics (adding to my previous experience and continuing work in Prunus) after settling into a permanent position at Washington State University six months ago. In this position, I am working closely with the Washington apple breeding program run by Bruce Barritt. In getting familiar with Bruce’s program, I have also come to better understand the needs and capabilities of other apple breeding programs in the US. My overall plan is to enable marker-assisted breeding for tree fruit and better exploitation of wider germplasm, and I’m seeking to overcome the major barriers that remain – lack of markers (for use in breeding and germplasm screening), lack of comprehensive phenotyping (to find new markers), and lack of access to high-throughput genotyping for breeding programs.
Next month, the US Rosaceae genomics, genetics, and breeding community, including industry stakeholders, educators, and extension agents, are holding a meeting where we will discuss the barriers to practical application of genomics to industry needs (primarily through breeding), how to overcome those barriers, and devising an implementation plan to revitalize US Rosaceae breeding programs ( http://www.bioinfo.wsu.edu/gdr/community/conferences/CAP08/index.shtml ). We will also put together a plan and writing team for a CAP (Coordinated Agricultural Project) USDA-NRI proposal. CAPs are awarded just one per year – of course we hope it is to Rosaceae in 2008 – to achieve this very thing (practical application of genomics). Such projects are for up to US$5 million over 4 years – therefore equivalent in scope to HiDRAS. There are numerous possibilities for such a proposal, but from the success of HiDRAS, a group of us are planning a proposal where the use of pedigree genotyping across Rosaceae breeding programs forms the core. Experiences of pedigree genotyping and large scale genotyping and phenotyping from HiDRAS will be valuable to such a proposal. Specifically for apple (and other crops for which we can establish synteny), further investigation of markers and promising genomic regions from HiDRAS would also be of tremendous value.
Whether or not the US Rosaceae community ultimately chooses this idea for our CAP proposal in early 2008, or whether a Rosaceae CAP is eventually funded, there are still opportunities in apple for US groups coordinating with EU partners in the post-HiDRAS era to make use of HiDRAS outcomes – in smaller trait-specific and germplasm-specific studies.
So my overall question to you is, is it possible, and how do you think it can be done, for US researchers – whether specific groups working with apple or in a general sense as for a CAP approach – to get access to the outcomes from HiDRAS? Suggestions are for specific QTL regions to be further refined by US researchers to obtain closely-linked markers for use in breeding, or for promising loci to be verified in US germplasm and under US growing conditions. In either case, there should be close partnership with EU groups so that any new information gained here would be open to HiDRAS participants. I hope that this also fulfills a need within HiDRAS for the application of outcomes following the project.
I look forward to hearing from you.
Tree Fruit Molecular Genetics
Department of Horticulture and Landscape Architecture
Washington State University
39 Johnson Hall
PO Box 646414
Pullman, WA 99164-6414
Tel: +1 509-335-6899 (office)
+1 509-432-4280 (mobile)
+1 509-335-6586 (lab)
Fax: +1 509-335-8690
Dept. of Biomolecular Sciences & Biotechnology
University of Milano
via Celoria 26 - 20133 Milano
Phone (+39) 02503.15013 - Fax (+39) 02503.15044
Web site: http://users.unimi.it/camelot
HiDRAS website: http://www.hidras.unimi.it/