Sorry if you've received this more than once. I sent it yesterday and it seems to have bounced.
Bryon
Begin forwarded message:
> From: Bryon Sosinski <bryon_sosinski(a)ncsu.edu>
> Date: March 7, 2011 4:49:37 PM EST
> To: Jay Norelli <Jay.Norelli(a)ARS.USDA.GOV>, rosexec-list(a)bioinfo.wsu.edu
> Subject: Re: Bryon's Executive Summary Assignments
>
> All,
>
> In addition to the comments that others have made, and to reinforce them in some cases, here's what I am thinking for this section of the Executive Summary:
>
> - In the context of having three rosaceous genomes, it is critical to perform detailed comparative studies (both micro and macro synteny) to evaluate gene copy number, presence or absence of pathways and their genes. This would provide a needed stepping stone for functional genomics. This would also ameliorate the need to deeply sequence another genome (e.g. rose or raspberry) in order to capture the genes, and provide the context for genome structure.
>
> - Continue to develop at least one species' genome as a "reference genome" for the family (obviously I would propose peach due to the existing high level coverage and alignment). A reference genome is a key component for the above mentioned analyses, and is also important for the pursuit of "gene and regulatory element discovery, transcriptome analysis, and characterization of epigenetic influences" This is particularly true to do thorough epigenetics.
>
> - The portion that deals with "High-density genotyping..." should be rewritten to discuss RosBREED (and the EU counterpart) in the development of markers, and the coordination of those projects that will presumably mean less redundancy etc.
>
> So I think what I just proposed is striking the 2nd and 3rd sentences, writing something dealing with a reference genome(s), and to promote comparative studies for the 2nd sentence. This would allow "cheap" sequencing for upcoming genomes. Discussing RosBREED et al. and coordination of those projects would be a substitute for the 3rd sentence. The final 2 sentences would remain largely unchanged.
>
> Also, I did another quick skim of the entire document, and found little on standardized phenotyping. Therefore, I would argue that putting a line in here stating, "The availability and reliability of affordable high throughput phenotyping, is a critical consideration for conducting detailed functional genomics."
>
> Bryon
>
>
>
>
>
> On Feb 24, 2011, at 6:21 PM, Norelli, Jay wrote:
>
>> Byron,
>>
>> Please develop bulleted revision suggestions for “Define and exploit the Rosaceae genome” section of the Executive Summary.
>>
>> Current text:
>> Define and exploit the Rosaceae genome<image001.gif>
>>
>> Comprehensive analyses of Rosaceae genomes combined with comparative and functional genomics will provide the basis for understanding the complex biological processes underlying the array of diverse and unique traits seen in this family. This initiative will maximize knowledge transferability among the breadth of rosaceous crops, while concurrently developing key crop-specific resources. Sequencing peach (Prunus) as a ’reference’ species while concurrently obtaining skim sequence of strawberry (Fragaria) and apple (Malus) are high priorities. Sequencing will be followed by the development of resources and tools optimized for gene and regulatory element discovery, transcriptome analysis, and characterization of epigenetic influences. High-density genotyping and polymorphism discovery will accelerate forward genetic approaches and provide insight into genome evolution. Functional genomic approaches will exploit tractable systems and target physiological and developmental pathways contributing to key crop attributes. Collectively this approach will streamline discovery of beneficial genes, leading to sustained improvements in fruit quality and plant productivity throughout the range of rosaceous crops.
>>
>> · develop bullet points for suggested change/revision/addition/deletion for your assigned section
>> · Proposed additions should be balanced with proposed deletions
>> · DEADLINE for distribution to RosEXEC is Monday, March 7, 2011
>> · You will distribute your suggestions directly to RosEXEC via email as soon as you have it available. Email should include 1) current text, 2) bulleted suggestions and 3) request for feedback via email before March 16 .
>> · Responses received should be forwarded to other members of revision committee.
>>
>> Thanks,
>> Jay
>>
>> John (Jay) Norelli
>> Research Plant Pathologist
>> USDA-ARS, Appalachian Fruit Research Station
>>
>> telephone: (304) 725-3451 x264
>> email: jay.norelli(a)ars.usda.gov
>> fax: (304) 728-2340
>> address: 2217 Wiltshire Road
>> Kearneysville, WV 25430
>>
>
Hi Folks,
To post to the rosexec list, you must use the email that you registered with or provide any alternative email address you use. I can then add them to the list and then you can post from those addresses as well. If you post from a non member email address it will bounce.
Cheers
Dorrie
Dorrie Main, PhD
Associate Professor of Bioinformatics
Dept of Horticulture and Landscape Architecture
Washington State University
45 Johnson Hall, Pullman, WA 99164-6414
Email: dorrie(a)wsu.edu
Tel: (509) 335 2774
Fax: (509) 335 8690
URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>
Dear RosEXEC,
If you need a refresher of the White Paper:
* Scope of White Paper is limited to Genomics, Genetics and
Breeding of Rosaceae Crops (will remain the same).
* Current White Paper is divided into 3 main sections: Executive
Summary, Strategic Planning Document and Appendix (will remain the
same).
* The Executive Summary and Strategic Planning Document are
basically a short (summary) and long versions of same material (will
remain the same).
* Current Key Issues for the U.S. Rosaceae Industry:
1. Improve fresh and processed fruit quality, shelf life, and
safety
2. Reduce chemical pesticide use
3. Decrease labor and energy costs of crop production
4. Develop stress tolerant plants
* Current Priorities for Addressing Key Issues:
1. Define and exploit the Rosaceae genome
2. Enhance Rosaceae genomics database resources
3. Revitalize U.S. Rosaceae breeding programs
* The Appendix includes:
1. Evolutionary relationships within the Rosaceae
2. Rosaceae germplasm in the U.S. National Plant Germplasm System
3. Crop reports for Apple, Pear, Peach and Nectarine, Apricot,
Cherry, Plum, Almond, Strawberry, Raspberry and Blackberry, and Rose
I propose revision of Key Issue #4:
Current TEXT: Develop stress tolerant plants
Rosaceous crops require resources (e.g. water, fertile land, freeze-free
planting sites) that are becoming increasingly scarce or unavailable
because of urban sprawl and environmental regulations. With the
exception of some berries, fruit crop agriculture typically requires
long-term investments in durable infrastructure such as orchards and
irrigation systems. Similarly, the ornamental industry is heavily
reliant on expensive greenhouse-based propagation systems. For the
industry to improve its profitability, it must reduce losses due to
environmental stresses on current sites and utilize marginal resources
more efficiently. Improving plant cold and heat tolerance, salt
tolerance, and water- and nutrient-efficiencies are critical to a
profitable and sustainable future for the U.S. Rosaceae industries.
My ideas
* Refocus issue by moving emphasis toward sustainability and
response to global climate change
* Change title from "Develop stress tolerant plants" to "Ensure
sustainability and adaptive agro-ecosystems in response to climate
change"
* Maintain most of the scientific content on abiotic stress,
de-emphasize or eliminate "nutrient-efficiencies"
* Maintain text on infrastructure investment but reduce its
emphasis
* Add text on increasing need for abiotic stress tolerance due
to predicted climate change
Entire document is available at:
http://rosaceaewhitepaper.wikia.com/wiki/US_Rosaceae_Whitepaper
Thanks for your input,
Jay
John (Jay) Norelli
Research Plant Pathologist
USDA-ARS, Appalachian Fruit Research Station
telephone: (304) 725-3451 x264
email: jay.norelli(a)ars.usda.gov <mailto:jay.norelli@ars.usda.gov>
fax: (304) 728-2340
address: 2217 Wiltshire Road
Kearneysville, WV 25430
Dear RosEXEC members,
My assignment as part of the White Paper revision group is to suggest
possible alternative priorities for addressing the key issues of the US
Rosaceae industry. I have made bulleted suggestions following the KEY
issue below, and I would greatly appreciate your input about what I have
suggested. Please send your feedback via email before March 16.
The current Priorities for addressing KEY issues, that need updating,
are
1. Define and exploit the Rosaceae genome
2. Enhance Rosaceae genomics database resources
3. Revitalize U.S. Rosaceae breeding programs
* Current KEY Issues for the U.S. Rosaceae Industry:
1. Improve fresh and processed fruit quality, shelf life, and
safety
2. Reduce chemical pesticide use
3. Decrease labor and energy costs of crop production
4. Develop stress tolerant plants
Note that Jay has suggested revisions to this Key issue in an earlier
email including changing the title to read "Ensure sustainability and
adaptive agro-ecosystems in response to climate change.
Some suggestions I have for priorities for Rosaceae Genomics addressing
the KEY issues are:
* Facilitate exploitation of existing Rosaceae genomes by
a. Developing collaborative, cooperative research teams across
genera, which will enable more rapid recognition of genes important for
each of the key issues that might then be exploited by other members of
the Rosaceae.
b. Cultivating and nourishing collaborations with laboratories
already exploring related genes in highly developed model systems. This
could include something like workshops or presentations on the "wonders
of working with Rosaceae" that would be presented at all major meetings.
c. Developing and standardizing a set of plant reference systems
for testing gene function. This could actually include the use of
Arabidopsis or tobacco as well as members of the Rosaceae, but we need
to have some standards. The product of this priority might be an
Rosaceae instruction manual of sorts.
d. Continuing to support the development of databases and tools at
the GDR to allow for easy comparative genomics, and easy access to the
tremendous amount of transcriptomic data that is anticipated in the near
future.
* Improve cross-training and communication among Rosaceae
researchers working in various aspects of the industry.
I'm thinking here that growers, packers, marketers, agronomists,
engineers, geneticists, breeders, and basic researchers would benefit by
understanding what it is that each other is capable of, is needing,
and/or is dreaming about having.
This evolved somewhat from a recent visit to a packing house, and the
desire by growers at a recent meeting to know what this genomics thing
is going to do, or can do, for them.
* Explore the available gene diversity in collections and wild
populations for disease, pest, and abiotic stress resistance.
* Initiate coordinated explorations of the proteomes of organs
and tissues that contribute to growth and health of the plants/trees
I hope this email stimulates thought and discussion.
Janet
Janet Slovin, Ph.D.
Genetic Improvement of Fruit and Vegetables Laboratory USDA/ARS
10300 Baltimore Ave
Beltsville, MD 20705-2350
Tel: 301-504-5629
FAX: 301-504-5653
janet.slovin(a)ars.usda.gov
P Please consider the environment before printing this e-mail
Dear RosEXEC member,
The White Paper Revision Committee has met and begun work revising the
White Paper. Initially, we will not be soliciting input from the entire
Rosaceae Community, but will solicit input from you, the RosEXEC, as
representatives of the community.
Over the next few days you will be receiving emails from committee
members regarding portions of the White Paper being considered for
revision. These emails will contain the current Executive Summary text
and bulleted points suggesting changes to be made.
Please respond. At a minimum, "good idea" or "bad idea" and why it is a
bad idea. The more input you can provide, the better.
Please discuss these proposed changes with your colleagues and funnel
community input back to the committee.
Address your responses to rosexec-list(a)bioinfo.wsu.edu.
Thanks,
Jay
John (Jay) Norelli
Research Plant Pathologist
USDA-ARS, Appalachian Fruit Research Station
telephone: (304) 725-3451 x264
email: jay.norelli(a)ars.usda.gov <mailto:jay.norelli@ars.usda.gov>
fax: (304) 728-2340
address: 2217 Wiltshire Road
Kearneysville, WV 25430
