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.
Cameron
From: Luca Gianfranceschi [mailto:luca.gianfranceschi@unimi.it]
Sent: Tuesday, June 26, 2007 10:43 AM
To: Peace, Cameron
Subject: Re: Extension of HiDRAS outcomes to the US?
Dear Cameron,
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 <http://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.
Sincerely,
Luca G.
At 20.17 30/05/2007, you wrote:
Dear Luca,
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
<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.
Cameron
***************************************************************
Cameron Peace
Assistant Professor/Scientist
Tree Fruit Molecular Genetics
Department of Horticulture and Landscape Architecture
Washington State University
39 Johnson Hall
PO Box 646414
Pullman, WA 99164-6414
USA
Email: cpeace(a)wsu.edu
Tel: +1 509-335-6899 (office)
+1 509-432-4280 (mobile)
+1 509-335-6586 (lab)
Fax: +1 509-335-8690
***************************************************************
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Luca Gianfranceschi
Dept. of Biomolecular Sciences & Biotechnology
University of Milano
via Celoria 26 - 20133 Milano
Phone (+39) 02503.15013 - Fax (+39) 02503.15044
E-mail: luca.gianfranceschi(a)unimi.it
Web site: http://users.unimi.it/camelot
HiDRAS website: http://www.hidras.unimi.it/
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