Apple & Prunus Joint CGC Meeting
Sunday, September 25, 2011
ASHS Conference, Hilton Waikoloa Village, Hawaii
Apple CGC Meeting
Prunus CGC Meeting
Apple & Prunus Joint CGC Meeting
Attendees: Herb Aldwinckle (co-chair), Cameron Peace (co-chair), Nahla Bassil, Carole Bassett, Ksenija Gasic, Sally Schneider, John Clark, Randy Beaudry, Jose Chaparro, Thomas Chao, Mike Wisniewski, Gennaro Fazio, Gayle Volk, Dan Parfitt, Dario Chavez
Herb Aldwinckle and Cameron Peace explained that a joint CGC meeting will be held, followed by Apple and Prunus crop-specific CGC meetings. This is the second ever joint Apple and Prunus CGC meeting. The joint meeting has been held to encourage functional connections between the two rosaceous genera.
Introduction: Dr. ChihCheng Thomas Chao (pronounced “Zow”; call him Thomas) is the new Apple, Grape, and Tart Cherry Curator in Geneva
Discussion topic: Core Collections
Apple has multiple core collections, Prunus does not yet have core collections defined.
Apple core collections:
Main core has ~258 trees representing cultivars and wild species.
Malus sieversii cores have ~112 trees in 3 cores for wild Kazakhstan collections
Malus orientalis core has 28 trees.
Randy Beaudry requested that the apple core collection be described and documented to facilitate reference to this collection.
Increases utility of the collection
Access point for diverse materials
Possibility of having cores (panels or reference sets) for various traits of interest: disease, insect resistance, fruit quality, abscission, biochemistry
Critical to have set of basic traits evaluated for entire collection: These traits should be useful to breeders and collection users, and therefore determined by them, and ideally all accessions characterized at the same time. Some traits will require several years of evaluation, others only once.
Value of sports in the collection: Well-characterized sports serve as genetic tools, but poorly characterized sports are not highly useful. Important to differentiate “sports” from “duplicates” in a collection. Molecular markers may not differentiate.
Establishment of Core Collection Definitions: Volk will draft and circulate a document applicable to both the apple and Prunus collections that can be revised as needed.
Prunus Core Collection: Malli Aradhya used 15 SSRs to fingerprint the Davis Prunus collection (presented at last year’s Prunus CGC meeting). That SSR data could be used as the starting point to develop core collections for each of the Prunus crops. Peace suggested that ideally each core would be composed of diverse, representative individuals of that crop, as well as individuals representing species that are compatible (and thus available for breeding purposes-primary genepool) that contribute novel diversity. Volk will contact Aradhya and follow up with this strategy for developing Prunus core collections.
Conclusions: Volk will take the lead on a document that defines tree fruit core collections and considers the value of sub-cores/panels such as trait-based panels. For Prunus, development of diversity-based core collections for each crop will begin with consideration of Aradhya’s 15-SSR dataset.
Discussion topic: Genome-wide Marker Data for Collections
SNP Genome availability: SNP arrays are available through December 2011.
9K peach, 6K cherry (4.5 sweet, 1.5 tart), 9K pom (8 apple, 1 pear)
Cost for performing genome scan on core collection of apple? 45 individuals for $3500. $20K evaluation funds could be used for this purpose, if evaluation funds are awarded in 2012 (not likely). The SNP array developed for M.x domestica is likely useable for M. sieversii.
Genotyping by Sequencing Project: $19-$30/individual. Could be performed on entire collection and coordinated by Sean Miles of Nova Scotia Ag College, Kentville. Bioinformatic support supplied by Buckler’s lab.
Value of sequence data: Once you have it, it’s done. However, new technologies with lower error rates, higher quality, and lower price are always emerging. And the bioinformatics to handle the data varies according to the method used, and changes over time – no point getting stuck with a huge pile of data that we can’t adequately mine and is soon superseded by data from a less error-prone technology.
Phenotyping data is critical and expensive to obtain. It can be performed while waiting for appropriate genomic technology.
Conclusion: For the next few years at least, we should focus our attentions on phenotypic evaluation of the collections. Ultimately we want accurate whole genome sequences for each accession. We should wait until whole genome sequencing is affordable at the scale we need and highly error-free, and the bioinformatics tools are readily available for extracting full meaning from the resulting data.
Discussion topic: Databases
Critical to provide linkages between GDR and GRIN: GRIN accession data users need to be aware of available genomic data. Follow-up is needed to facilitate this process. Interoperability has been established between MaizeGDB and GRIN.
GDR is developing features that are relevant to NPGS Germplasm users. This includes a breeder toolbox module and reference genome alignments.
Crop Wild Relatives Initiative (see attachment): Hannes Demplewolf (Global Crop Diversity Trust, Rome) and ARS Systamatics Lab (John Wiersema) are proposing establishment of primary, secondary, and tertiary wild relatives for each major crop, including apple and Prunus genera. This information will be documented within GRIN.
National Program Staff update: ARS budgets will be tight next year. ARS closures are imminent. This is already threatening availability of FY12 CGC Evaluation funds.
Apple CGC Meeting 10:00-11:30
In the future, conference call capability will be requested. Many Apple CGC members were unable to attend or call-in for this meeting. It is often difficult to solve the logistics at anonymous conference venues, unlike when hosted at institutions of members.
New Candidates for CGC Membership: Thomas Chao will be added as an Ex-officio member.
Curator Comments, Vision, and Priorities (Chao):
Put local data into the GRIN database.
Receive input from stakeholders regarding high priority traits for phenotyping
Increasing budgetary efficiencies
Find better ways to manage seedling collections
Sieversii orchard options
~200 trees (core + those of interest) have been/are being grafted to add to the main collection
Removal of trees
Graft onto alternative rootstocks
Partial removal of trees (thin rows vs leave 2 rows for demonstration plot)
Explore possibilities for future collection trip(s)
Revision of Vulnerability and Priority Statement for the Apple CGC: This effort will be coordinated by Chao, with help from Fazio.
Quarantine status of cider apple accessions? Merwin report has some information.
Inclusion of landrace varieties in collection: These may provide pre-breeding materials that have selection for key traits without as many undesirable traits as the wilds species. Once characterized for fruit quality and disease resistance under an ongoing project, Turkish village varieties could be valuable additions to the NPGS collection:
Molecular Scientist position at PGRU: Exploring the possibility of hiring a SCEP graduate student to focus on molecular aspects of a PGRU clonal collection. This minority person would then have to commit to the program for 1 year (probation) after completing their degree. PGRU RL will coordinate effort.
Future of the Apple Collection: Aldwinkle suggested revamping the main core. Core collection (4x copy) needs to be replanted if it is to be continued in Geneva. The demonstration “forest” of sieversii and oreintalis only has 3-4 viable years left in its current state. The long-term future of the 7 mapping populations will be addressed in emails and teleconferences-no time now.
Comprehensive and systematic phenotyping: A huge comprehensive and systematic phenotypic project is needed (a la RosTRAIT). We need to first define the traits and protocols and number of seasons of evaluation for each trait.
New planting: to facilitate systematic evaluation, a new planting would be ideal
Keep in mind:
-the need for replanting the core (mentioned above)
-Volk’s new diversity data
-the inclusion of the apple Crop Reference Set as painstakingly defined and under characterization by the RosBREED project.
-a systematic system of key individuals together is needed for effective evaluation
-a robust phenotypic evaluation is of highest priority for understanding and utilizing apple germplasm (over any genotyping needs, as mentioned in the preceding joint meeting).
Wild species in the Geneva collection: Aldwinckle asked Volk to provide the CGC with a paragraph or two summary of the wild species currently available in Geneva.
Volk collaborations involving Geneva Apple collection (brief summary, as requested by Aldwinckle):
Summer buds can be successfully cryopreserved for some apple species that are not amenable to dormant bud techniques.
Manuscript has been submitted to Tree Genetics & Genomes describing differentiation among M. domestica, M. orientalis, M. sieversii, and M. sylvestris.
Performing chloroplast sequencing to differentiate Chinese apple species.
Using SSR data to compare cider and dessert apples.
Preparing manuscript that describes Malus collection using SSR markers.
Fazio has provided data for 3 SSRs for the main collection so that it can be compared to the French and Brogdale collections. Data analyses underway.
Follow-up Meeting: A teleconference will be held in the near future so that all committee members can be included in follow-up discussions.
Additional Reports (see attachments)
National Plant Germplasm System Program Report
National Germplasm Resource Laboratory Report
Jurick and Janisiewicz Report
Minutes submitted by Gayle Volk (Gayle.Volk@ars.usda.gov), and edited by Herb Aldwinckle and Cameron Peace
Prunus CGC Meeting 11:30am-1:00pm
Future CGC meetings – joint with Malus or separate? Nahla Bassil recommended joint meetings and involving pear CGC as well. Members agreed we should try to have joint meetings as much as possible.
Approval of last year’s minutes. C. Peace commented on the necessity to have a designated person to take minutes at CGC meetings. Whether to have a volunteer or elect a secretary was discussed. The person that would type minutes in the computer during the meeting and has to be able to type quickly. C. Peace mentioned that last year his student Sanchita Haldar who passed last summer took notes. She was also working on cherry CGC project. K. Gasic agreed to take the minutes for this year’s meeting and pass them to C. Peace.
Membership issue – membership subcommittee K. Gasic and J. McFerson and everyone is welcome to participate. Prior to the meeting C. Peace sent an email with membership list. Members that were rotating off the committee had an option of continuing their membership. Tom Beckman, Margaret Pooler, K. Gasic and J. Chaparro expressed willingness to stay on the committee. K. Gasic and J. Chaparro commented that Prunus community has a big issue with many people retiring and positions closing. C. Peace suggested that K. Gasic contact J. McFerson to talk about future actions to stop membership attrition.
Crop subcommittee chairs – need to make sure they are elected and active. All the positions are now vacant except the recently appointed sweet cherry one – N. Oraguzie. C. Peace stressed the need for annual reports/updates for each crop regarding current status, what has happened in the last year, new positions, new data acquired, update crop reports in the Rosaceae White Paper etc. Subcommittees are: Apricot, Almond, Sweet cherry, Tart cherry, Peach, Plum and Rootstock. The problem of having crop subcommittee chairs is that there are not enough members to fill each position. For some crops in USA there are no breeding programs or only one. Suggestion is to have “crop representatives” instead of subcommittee chairs – e.g. CGC plum representative. Need to suggest new members, or those that should be CGC members but are not yet. Use American Pomological Society membership to attract new members. Contact them and ask if they would agree to serve on Prunus CGC. Question was raised about having graduate students as members – the problem is that members need to be involved in breeding/be experts and graduate students are still not and the time is an issue.
Prunus Vulnerability Statement update – very useful to add germplasm gene pools when knowledge becomes available for different crops. Update evaluation priority traits per crop. We really need to update them for all crops. Sweet cherry is up to date and Tart cherry is getting there. Other crops urgently need update of Priority Evaluation traits. C. Peace compiled the statement soon after last year’s meeting and sent them to GRIN and CGC members in July 2010. There was a delay before the updated statement was posted on GRIN but that has been taken care of.
Crop report – C. Peace had asked all crop subcommittee chairs for crop reports but didn’t get much response. There is a need to find a way that contributors can get credit for CGC work like preparing crop reports. N. Bassil suggested publishing them in Journal of American Pomological Society for (JAPS) – Current status of crop, opinions, how to deal with climate change in the future etc. C. Peace will send an email in mid-October with explanation what is expected in the report for each crop and a separate email for updating the Vulnerability Statement.
NGRL Report –A. Malli started a breeding program in mixing all Prunus and reported success in acquiring hybrid seeds and plants. Clay Weeks has retired, and is unlikely to be replaced anytime soon.
Geneva Repository Report – Tart cherry collection is held at Geneva - nothing new since last year. Amy Iezzoni had recommended last year that tetraploid cherry should not be held in NGR in Davis.
APHIS Report– very detailed report with numbers of samples in the process and how many are released. John Preece and Joseph Postman are on a collection trip to Albania for Prunus and other material.
Rationalizing the collection – for core collection need to start with peach, come up with the objective and develop strategy. Gayle Volk asked if the peach collection should have separate wild and cultivar merged core sets – or to have separate Prunus wild collection and crop specific collections. C. Peace mentioned that this is where application of the gene pool concept comes in place, in case of core set for peach collection it should include everything that could readily be crossed with peach (including other crops like almond, apricot, diploid plum etc.) but as it gets further away there should be separate collections that have some joint and unique accessions. Will it be based on diversity? There was a question how to determine the diversity to be sure that it really reflects accurate diversity of the collection. There is need to have accurate pedigree information to help with decisions what goes in the core collection. Gayle Volk expressed interest to be involved in the planning and design of future core collections.
New acquisition and collections – need to know what is coming in from quarantine to decide what type of work would be needed from Malli to decide accessions that would fill the gaps in the collection. Gayle Volk reported about success of cryopreservation initiative with shoot tip buds of Prunus.
Additional Reports (see attachments)
Prunus CGC Membership committee and chairs
PGOC Report (same as that for Apple)
NGRL Report (same as that for Apple)
APHIS Report (same as that for Apple)
Crop Wild Relatives Report
Minutes submitted by Ksenija Gasic (email@example.com), and edited by Gayle Volk and Cameron Peace