SAES-422 Multistate Research Activity Accomplishments Report

Status: Approved

Basic Information

Participants

Officers: Chair – Carol Miles Vice Chair – Ian Ray (call in) Secretary – Joe Kuhl <b>In person (Conference Room at the National Clonal Germplasm Repository, Corvallis, Oregon):</b> Byrne, Patrick Colorado State University Fort Collins, CO, email: Patrick.Byrne@ColoState.EDU; Hu, Jinguo ARS WRPIS, Pullman, WA, email: jinguo.hu@ars.usda.gov; Hulbert, Scot Washington State University, Pullman, WA, email: j.moyer@wsu.edu; Hummer, Kim ARS NCGR, Corvallis, OR, email: Kim.Hummer@ARS.USDA.GOV; Irish, Brian ARS WRPIS, Pullman, WA, email: frank.dogan@ars.usda.gov; Jensen, Kevin ARS FRR, UT, email: Kevin.Jensen@ARS.USDA.GOV; Kinard, Gary ARS NGRL, Beltsville, MD, email: Gary.Kinard@ARS.USDA.GOV; Kuhl, Joseph University of Idaho, Moscow, ID, Email: jkuhl@uidaho.edu; Miles, Carol Washington State University, Mount Vernon, WA, email: milesc@wsu.edu; Parfitt, Dan University of California, Davis, CA, email: fzparfit@plantsciences.ucdavis.edu; Missaoui, Ali University of Georgia, email: cssamm@uag.edu Postman, Joseph ARS NCGR, Corvallis, OR, email: Joseph.Postman@ARS.USDA.GOV; Stout, Dave ARS WRPIS, Pullman, WA, email: Dave.Stout@ARS.USDA.GOV; Yerka, Melinda University of Nevada Reno, Reno, NV, email: myerka@unl.edu; <p> <b>Called In:</b> Bockelman, Harold ARS NSGC, Aberdeen, ID, email: Harold.Bockelman@ARS.USDA.GOV; Bretting, Peter ARS ONP, Beltsville, MD, email: Peter.Bretting@ARS.USDA.GOV; Chetelat, Roger C.M. Rick Tomato Genetics Resource Center, University of California, Davis, CA, email: trchetelat@ ucdavis.edu; Giroux, Michael Montana State University, Bozeman, MT, email: mgiroux@montana.edu; Greene, Stephanie ARS NLGRP, Ft. Collins, CO, email: Stephanie.Greene@ARS.USDA.GOV; Polek, Marylou ARS NCGRCD, Riverside, CA, email: Marylou.Polek@ARS.USDA.GOV; Preece, John ARS NCGR, Davis, CA, and ARS NALPGR, Parlier, CA, email: John.Preece@ARS.USDA.GOV; Ray, Ian New Mexico State University, Las Cruces, NM, email: iaray@nmsu.edu; Thro, Ann Marie USDA NIFA, Washington, DC, email: athro@nifa.usda.gov; Greene, Stephanie ARS NLGRP, Ft. Collins, CO, email: Stephanie.Greene@ars.usda.gov; Matsumoto, Tracie ARS TPGRDR, Hilo, HI, email: tracie.matsumoto@ars.usda.gov;

The meeting was called to order by Chair Carol Miles at 8:35am with brief opening remarks regarding agenda and procedure.

2017 Minutes were introduced, moved and seconded to approve without changes, unanimously approved.

Resolutions committee was discussed: Kim Hummer and Dan Parfitt agreed to co-chair. Brian Irish possible member?

Administrative Advisor report (Scot Hulbert):

Dr. Hulbert is replacing Dr. Jim Moyer, and is serving on 5 multi-state meetings. W6 5-year plan was renewed in 2016. Five-year plan reviews were very good. TAC reports need to emphasize impacts, in particular economic/commercial impacts, use bullets and keep short.

The proposed FY2019 budget of $446,257 looks appropriate. It was noted that in the proposed budget, ARS appropriations were flat year to year, while MRF funding increased 2.3% annually. Kevin Jensen moved with Dan Parfitt second to approve the FY2019 budget. Motion passed.

Moving the alfalfa germplasm program from Prosser to Central Ferry, which is estimated to cost ~$3 million, would help keep the genetic integrity of the collection. The idea was that Prosser is exposed to potential pollen drift from GE alfalfa. Brian Irish commented that currently guidelines are in place and are being followed for seed production using isolation cages.

Additional comments were made regarding W6 budget related issues.

Due to an airport expansion W6 lost 28.5 acres. State and Federal authorities are working to resolve the loss of acres, however new land may cost ~$100/acre, ~$3,000 increase to budget.

ARS National Program Office report (Peter Bretting):

Dr. Bretting presented Powerpoint slides summarizing the status, prospects and challenges facing the National Plant Germplasm System in 2018. Successes include state/federal partnerships. The number of accessions has gradually increased over the last 10 years. Germplasm distribution has remained relatively constant over the last 10 years, around 250,000 accessions disturbed annually. The ARS National Plant Germplasm System budget peaked in 2012 and has been flat since 2014. Staff retirements are projected at 30% over the next 5 years. Gayle Volk and Pat Byrne secured a USDA/NIFA planning grant for a workshop in Fort Collins in April 2018 to discuss designing and developing a training program. The workshop generated numerous insights and another grant (Higher Education Challenge) has already been submitted to extend concepts and ideas from the workshop.

National Program Leader Plant Systems-Production NIFA update (Ann-Marie Thro):

Dr. Thro presented Powerpoint slides summarizing management and utilization of plant genetic resources and associated information. In her talk, Dr. Thro noted that it is very difficult to find competitive funding for maintenance and distribution of plant germplasm.

Business meeting, NPGS Station Reports:

National Small Grains Collection, Aberdeen, ID (Harold Bockelman):

  • The National Small Grains Collection (NSGC) presently holds 146,225 accessions of the small grains (wheat, barley, oat, rye, triticale, rice, and related wild species)
  • NSGC distributed 36,868 accession samples in 727 separate requests in the past 12 months. Approximately 30% of the distributions were to foreign scientists. NSGC provided back-up samples to NLGRP totaling 470 accessions. Almost 99% of NSGC accessions have been backed-up
  • NSGC has prepared a total of 12,400 samples to be sent to Svalbard in the next shipment. More than 60,000 accessions will then be backed-up at Svalbard.

National Germplasm Resources Laboratory, Beltsville, MD (Gary Kinard):

  • The Plant Exchange Office (PEO) supports the collection of germplasm for the NPGS through the management of a Plant Exploration and Exchange Program. The deadline for submitting proposals for explorations or exchanges to be conducted in FY 2019 is July 20, 2018
  • In 2016, ARS and the U.S. Forest Service established a new agreement to foster collaboration on conservation of crop wild relatives on U.S. National Forests
  • In 2017, 35 historical PIs were located at the former Cheyenne (Wyoming) Horticultural Station. The information on the PIs was distributed to curators for their input on the need to acquire samples of the germplasm
  • Since 2008, a project to provide thorough coverage of wild relatives of all major and minor crops in GRIN-Taxonomy has been underway
  • In 2017, 640 public orders containing a total of 55,912 samples of NPGS accessions were shipped from Beltsville to individuals in 69 countries. In addition, PEO facilitated the agricultural inspection of arriving germplasm shipments containing accessions from numerous foreign countries for researchers and curators at NPGS sites
  • At the beginning of 2018, the GRIN-Global database included the following: 584,449 active accessions representing 15,720 species and 2,533 genera, 3,023,069 inventory records, 1,973,427 germination records, 8,192,598 characteristic/evaluation records and 410,476 digitized images.

National Clonal Germplasm Clonal Repository, Corvallis, OR (Joseph Postman):

  • 12,443 accessions, 73 genera and 774 taxa of 677 species of temperate fruit, nut, and specialty crops were conserved.
  • Managed > 3,600 accessions of fruit tree and nut crops on 22 acres of orchard
  • Obtained a total of 80 new accessions and 290 new inventory items in CY 2017
  • Received 1,202 order requests and shipped 5,789 items
  • Collaborated with NGRPL, Ft. Collins, CO, on cryopreservation protocols of dormant blueberry, hazelnut, pear, currant and gooseberry
  • Collaborated with Forest Service scientists and USDA botanist and geneticist on in situ conservation of cranberry within National Forests of eastern US
  • Expanded potted greenhouse backup collections of Pyrus and Cydonia for accessions represented by a single tree and at risk of loss due to disease susceptibility, lack of hardiness or small tree size
  • Discovered a potentially novel gene for black spot resistance in rose
  • Identified Vaccinium germplasm that is slow to become infected with, and potentially resistant to Blueberry shock virus.

National Clonal Germplasm Repository, Davis, CA (John Preece):

  • In recent years, explorations were conducted in the Caucasus and Central Asian centers of diversity to fill gaps, especially in crop wild relatives. This new germplasm is clearing quarantine and will add significant diversity annually for the next 5 years and beyond. During the past year, 32 new Prunus accessions were received from APHIS. These include 10 species collected from 6 countries.

C.M. Rick Tomato Genetics Resource Center, Davis, CA (Roger Chetelat):

  • Acquisitions. The TGRC acquired 444 new accessions this year, including a large set of backcross inbred lines (BILs) from S. pennellii LA0716 in cv. M82, as well as an accession of S. pennellii used for genome sequencing, and an introgression line with a segment of S. lycopersicoides chromosome 12. The current total of number of accessions maintained by the TGRC is 4,360. For backup storage, 93 seed samples were sent to the USDA and 26 samples were sent to the Svalbard Global Seed Vault
  • A total of 5,978 seed samples representing 2,241 different accessions were distributed in response to 330 requests from 275 researchers and breeders in 31 countries. Our annual literature search uncovered 115 publications that mention use of our stocks.

Noon to 1:20pm, Working lunch

Special topic: Kim Hummer presented “Doomsday vaults, clonal style”

Business meeting, NPGS Station Reports: continued

National Laboratory for Genetic Resource Preservation Ft Collins, CO (Stephanie Greene):

  • Developing state-of-art tools to improve gene bank management
  • Status of the Base Seed Collection: 150,000 base samples have at least one monitor test: 2,885 base samples (335 taxa) have declined more than 20% since initially tested. Yet to be assessed - decline of base samples with monitor tests prior to 2014
  • We have sent 13,000 accessions representing 280 taxa to Svalbard for back up, 60% comprised of wheat, barley and soybeans.

Tropical Plant Genetic Resources and Disease Research, Hilo, HI (Tracie Matsumoto):

  • The Tropical Fruit & Nut Germplasm Repository in Hilo, HI will start the recruitment process for a new curator within the next few months
  • At the Hilo repository, we maintain 13 designated clonal germplasm collections with 1200 accessions representing 61 genera and 145 species in 33 acres of fields, greenhouses and a tissue culture laboratory
  • We also continue to serve as a backup for the ARS germplasm repositories in Miami, Florida, and Mayaguez, Puerto Rico.

National Arid Land Plant Genetic Resources Unit, Parlier, CA (John Preece)

  • Distributions from NALPGRU are in the form of seed, green cuttings/propagules, tissue or rooted plants depending on the crop and the nature of the request, and are filled and shipped year-round. The trend in distributions from NALPGRU is flat after a decrease due to a change in policy regarding distributions to home gardeners. In FY 2017, 80.5% of orders were sent to domestic co-operators, and these were splits equally between federal agencies, universities, and unaffiliated individuals
  • A significant component of the NALPGRU mission is seed regenerations of accessions from other NPGS sites that require a long growing season and/or dry conditions
  • NALPGRU was approved for funding through the Plant Exploration Office and the New Crops CGC for a collection trip targeting Parthenium in southwest Texas
  • The NALPGRU performs routine regenerations of their seed crops, and manages the rest as clonal accessions with periodic replanting.

Temperate-adapted Forage Legume germplasm collection, Prosser, WA (Brian Irish)

  • Personnel: A full-time Curator (Geneticist), a full-time USDA-ARS Biological Science Technician and one ½ time USDA/WSU Technician/Farmer
  • During the 2017 summer regeneration period, alfalfa (M. sativa subsp. sativa ‘Vernal’) sentinel plots (½ covered and ½ uncovered) were established around germplasm regeneration field plots to monitor adventitious presence of genetically engineered (GE) glyphosate trait in alfalfa germplasm. Using a glyphosate-amended seedling germination assay and a seed grinding technique more than 140,000 seed was tested from 13 plots. No AP was detected from any covered (insect proof cage covers) sentinel plots, however AP was detected in five of the uncovered plots. AP detection in uncovered sentinel plots suggests transgenic gene flow to regeneration field site and extreme care must be taken to ensure timely placement of cage covers for alfalfa regenerations
  • A recent systematic review of the Lotus genus has reclassified former native North American Lotus species into two new genera: Acmispon and Hosackia. Therefore, the TFL project gained 19 Acmispon species with 63 accessions and 6 Hosackia species with 14 accessions. The number of Lotus species/accessions was adjusted correspondingly
  • Project coordinated the field planting and harvest (regeneration) of 184 Medicago, Trifolium, Lotus (Acmispon/Hosackia) germplasm accessions during the 2017 growing season. Additionally, 50 Medicago, Trifolium and Lotus species germplasm accessions were planted in the fall to be overwintered and regenerated CY 2018. The regeneration field site also included 10 sentinel plots and one faba bean (Vicia faba) accession
  • During FY 2017 project coordinated the distribution of a total of 180 (1742) requests from 154 (142) cooperators (135 U.S./19 Int.). The number of unique accessions distributed was 3,222 (2,052) and total number of items distributed was 4,407 (3,243).

Western Regional Plant Introduction Station, Pullman, WA (Jinguo Hu):

  • On December 31, 2017, there were 98,405 accessions belonging to 1,060 genera, 4,769 species (5,447 taxa) in the WRPIS collection
  • We acquired 1,499 new accessions including 1,384 native plant accessions collected by the Seeds of Success (SOS) project and 807 accessions from various sources
  • We distributed a total of 42,484 packets of seed samples to 1,060 requestors with addresses in each of the 50 domestic states and 46 foreign countries. Sixty percent (25,913 packets) were distributed to the U.S. and 40% (16,571 packets) were distributed to foreign countries. Requestors in each of the 50 domestic states received germplasm samples from WRPIS in the Year of 2017. A total of 9,682 packets from WRPIS went to the 13 Western states
  • We uploaded 17,006 observation data points on 3.515 accessions into the Germplasm Resources Information Network (GRIN)-Global database
  • We entered 2,314 seed viability records into GRIN-Global
  • We packed and stored 1,772 newly regenerated/harvested inventories of a broad range of plant species. We determined seed quantities of 6,513 inventories
  • We shipped 1,573 seed inventories to the National Laboratory for Genetic Resource Preservation (NLGRP), Fort Collins, CO and 602 inventories to the Svalbard Global Seed Vault, Svalbard, Norway for secured backup
  • We demonstrated the potential for dramatically lowering Fusarium proliferatum infestation by planting bulbils instead of seed cloves for regeneration of garlic
  • We evaluated 100 faba bean accessions with replicated small plots under organic environment on the Lundberg Family Farms, Richvale, California
  • Our genome-wide association study identified SNP markers that were significantly associated with Verticillium wilt (VW) resistance in two alfalfa populations, that were developed for mapping the disease resistance genes
  • In collaboration with USDA-ARS NWISRL, Kimberly ID, we described Penicillium cellarum sp. nov., a pathogen of stored sugar beet roots, together with demonstrating its pathogenicity and environmental preferences.

National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA (MaryLou Polek):

  • In CY 2017, 17 additional accessions were cryoprocessed in Riverside. However, due to the Hold Order placed on the repository when the HLB quarantine was implemented (see section on Distributions), these have not been sent to Ft Collins at the time of this writing. It is expected that they will be sent in June or July, 2018
  • NCGRCD acquired 3 new citrus accessions in CY 2017: Okitsu wase X Maltese ovale (RSD 2017002), Micromelum minutum (RSD 2017001), and TI (Rush) (RRUT 545). RSD 2017002 was a controlled pollination specifically intended for use at NLGRP and will not be maintained as an accession. RSD 2017001 did not establish. RRUT 545 was received as sanitized budwood from the Citrus Clonal Protection Program (CCPP)
  • In CY 2017, NCGRCD completed sanitation of 17 accessions that were released from State and Federal quarantine in November of 2017
  • During CY 2017, a total of 7988 laboratory tests were performed in support of distributions, therapy items, CVC backup and SH CTV
  • In CY 2017, NCGRCD distributed 262 items to 99 requestors. All but 6 items were citrus or related taxa, the remaining 6 being date palm materials. In recent years there was a high number of requests for date palm accessions from scientists conducting genomic research. This project is nearing completion and therefore, the number of date palm distributions has decreased
  • CY 2017 Propagations: there were 283 total propagations made from 170 genotypes
  • The Crop Germplasm Committee needs to be made aware of critical issues threatening the future of the NCGRCD. These include: 1) Budgetary shortfalls and 2) Personnel Issues.

Business meeting, State Reports:

TAC members summarized their written state reports.

California state report (Dan Parfitt)

624 requests for plant introductions from California users were filled by the NPGS in 2017, very similar to the 676 from last year, representing 341 different users, almost identical to the 342 from last year. The distributed germplasm was used for plant breeding research, testing in home gardens, and propagation of both clonal and seed propagated species. Several respondents used the germplasm for demonstration projects in school settings, researchers used materials as reference materials or checks in their experiments, and some germplasm was used as archeological reference material. Much of the germplasm continues to be used for commercial breeding research (private, university or USDA) and this category is likely highly under-reported, especially from private companies; these companies are competing with each other and are in the business to release proprietary intellectual property. There seems to be less interest to use the collections for molecular/biochemical studies. Several members of the California Rare Fruit Growers requested materials for evaluation and distribution to their members as in past years.

Colorado state report (Patrick Byrne):

Orders for germplasm from the NPGS included delivery of accessions from both clonal repositories and Plant Introduction Stations. A total of 2,450 accessions were delivered in Colorado, constituting 123 orders. This represented an increase in shipments from the previous year (1,661 accessions and 96 orders in 2016), but is similar to the numbers for 2015 (2,312 accessions and 140 orders). Orders were shipped from the following locations in 2017: COR, DAV, GEN, HILO, NC7, NE 9, NR6, NSGC, NSSL, OPGC, S9, SOY, TGRC, and W6.

Idaho state report (Joe Kuhl):

In 2017, 3,024 accessions were requested in Idaho from the National Plant Germplasm System in a total of 83 orders. As observed in past years orders were fairly evenly divided among state, federal and private groups, 31, 20, and 32 orders, respectively. The major user groups in 2017 were USDA scientists accounting for 66% of total accessions, while state entities accounted for 25% of total accessions, together accounting for ~91% of the total accessions requested in Idaho. University researcher requests made up the vast majority of requests from state agencies. While there were 32private orders requesting 276 accessions. The top two private requests were from companies, Crookham Company with 67 accessions and Mountain River Kirby, 52 accessions.

Montana state report (Michael Giroux):

Thirty-three recipients received 1941 plant germplasm accessions in Montana during 2017. Twenty of the recipients responded to inquiry. About 1/3 of the accessions were for bread or durum wheat, 1/3 for barley and 1/3 for pulse crop accessions. The biggest increase over previous years was for barley and pulse crop accessions which reflects the fact that Montana State hired a pulse crop breeder who began work in January 2017 and several years ago hired a new barley breeder who is screening barley accessions for traits of interest. We also continue to have a number of individuals requesting accessions of various species including tree fruit to screen for those that may tolerate MT winters.

New Mexico state report (Ian Ray):

Twenty-five individuals from New Mexico placed 52 orders and received 945 accessions from the NPGS in 2017. In general, these materials were utilized for agronomy, botany, genetics, physiology, taxonomy, and plant pathology research (51%); educational and demonstration programs (29%), varietal development (10%), and undeclared use (10%).

Nevada state report (Melinda Yerka):

Ten individuals from Nevada placed 17 orders and received 91 accessions from the NPGS in 2017. Plant materials were used for chemistry/molecular genetics (40%), plant pathology (18%), anthropology (3%), breeding/varietal development (10%), public educational (19%), and undeclared (11%) efforts. Researchers at the University of Nevada, Reno (UNR) continue to be the primary users (54%), which accounts for the significant reduction in requests made in 2017 as opposed to previous years (large projects are initiated when new plant science faculty are hired or obtain significant grant funding). Users reported that materials would be used for research (70%), education (19%), or other/unspecified (11%) use.

Oregon state report (Present by Carol Miles in place of Shawn Mehlenbacher):

Oregonians continue to use the PI system extensively. Users include state and federal researchers as well as private seed companies and private individuals. Oregon is a major user in the western region, along with California and Washington. 23 publications utilizing NPGS germplasm were published in 2017 and the first part of 2018.

Utah state report (Kevin Jensen):

Dr. Kevin Jensen sent out three rounds of emails to 2017 germplasm users. Their responses are documented in the 2017 Utah report.

Washington State report (Carol Miles):

In 2017, 126 Washington State residents requested a total of 6,032 germplasm samples from the National Plant Germplasm System (NPGS). Recipients were with universities (37, 32 at WSU), USDA (17), private research groups (10), commercial firms, seed companies and nurseries (27), and non-profit organizations (8), as well as 27 private individuals. Recipients received germplasm (in the form of seeds and cuttings) from 17 NPGS repositories or stations in 239 orders. The germplasm material was used in diverse scientific disciplines such as agronomy, anthropology, archaeology, botany, genetics, horticulture, plant pathology, entomology, and soil science, and contributed significantly to scholastic and economic activity in the State of Washington. Several recipients stressed the importance of the NPGS service, and mentioned in particular the value of NPGS as a system for acquiring material for research work. Some recipients wrote of the increasing difficulty of obtaining germplasm for breeding uses from private sources, so that the NPGS is globally important for the development of new breeding programs.

Alaska, Arizona, Hawaii and Wyoming do not have state representatives. Dave Stout summarized the information from these states.

Alaska State report (Dave Stout):

During 2017 NPGS there shipped 14 orders with a total of 102 items (18 from WRPIS) to 10 people in Alaska. Eleven orders were submitted over the GRIN-Global Website and others were through emails or other means. We received three responses to our email questionnaire from requestors.

Arizona state report (Dave Stout):

During 2017 NPGS there shipped 62 orders with a total of 1,936 items (83 from WRPIS) to 41 people in Arizona. Fifty-three orders were submitted over the GRIN-Global Website and others were through emails or other means. We received eight responses to our email questionnaire from requestors.

Hawaii state report (Dave Stout):

During 2017 NPGS there shipped 28 orders with a total of 320 items (only one from WRPIS) to 19 people in Hawaii. Sixteen orders were submitted over the GRIN-Global Website and others were through emails or other means. We received four responses to the questionnaire from Rebecca Canevali, Priscilla Carbajal, Ken Love and Nancy Redfeather, respectively.

Wyoming state report (Dave Stout):

During 2017 NPGS shipped 38 orders with a total of 886 items (494 from WRPIS) to 10 people in Wyoming. All the orders were submitted over the GRIN-Global Website. Only one person, Saleh Osama, responded to my email questionnaire.

Open discussion:

The W6 TAC has discussed how state representative prepare state reports over the years. This year the topic came up and there was interest in possibly coordinating the questions asked to germplasm users. A standardize set of questions might be agreed upon by all members so that there is greater uniformity between state reports and increased ability to summarize all state reports into a single annual review. It was also discussed how to address the issue that many germplasm users that request germplasm in the previous year do not necessarily have results in time for the report, and in many cases the impact of germplasm use may not be realized for many years after received. How many years back should germplasm use be assessed? How do we get an accurate assessment of germplasm use when it may take years to collect results and determine utilization?

A brief discussion revised the issue of GM traits contaminating alfalfa germplasm.

A motion to adjourn for the day was made and seconded, unanimously approved.

Tuesday, June 26, 2018

In person: Kim Hummer, Jinguo Hu, Dan Parfitt, Brian Irish, Pat Byrne, Dave Stout, Kevin Jensen, Carol Miles

Called In: Anne-Marie Thro and Ian Ray

Challenges of the W-6 Station (Jinguo Hu)

Farmland issue – WRPIS lost 4 parcels of land, 28.5 acres, when Pullman Airport expanded; 5 yr rotation needed to rotate by crop species, disease cycle and hard-seeded issue

Action item: The tac wrote a resolution to request this issue is resolved by 2019

Central Ferry and alfalfa issue – at Central Ferry 37 acres WSU and 100 A long-term lease to ARS from U.S. Army Corps of Engineers; so plenty of land to accommodate the alfalfa program

Action item: Jinguo and Brian plan to meet to discuss and decide if move is viable, report back to the group next year

The greenhouse is being constructed at Central Ferry, should be ready by winter, for Phaseolus program

Staff – technician resigned, WSU position, 3 months until rehire is complete

Dave Stout’s position in process of being refilled, position description is complete, will be advertised soon

Vicky Bradley retired last week, may be 1 yr until rehire; Jesse acting curator temporarily for now, working well

Impact (Pat) – we have to demonstrate impact for what we are doing, good anecdotal reports in state reports

Create a narrative of 1-2 success stories for each state; economic impact good to show but hard to demonstrate

Kevin: Oregon hazel nuts and Shawn’s work a big impact story, so is Utah wheat breeding

Anne-Marie: each state creates a table highlighting impacts

Can we coordinate efforts with other regions?

Every few years a meeting of the 4 regions, we can discuss then, last meeting was in CO 2 years ago

Action item: Form a subgroup of the tac to: determine what is done with the state reports and W6 annual report; ask other regions what they are doing; ask each state representative in W6 to share annual request letter; maybe we need to ask recipients who received germplasm several/3 years ago (Kevin); subgroup volunteers: Pat, Kevin, Carol, others let Pat know if you are interested

More states participated this year than in the past (Dan), how do we keep state representatives engaged?

Distribution of germplasm (Kim) – need to restrict distribution next year due to lack of resources (budget is not adequate to maintain current samples or ship requests)

Dan: it’s a quandary, we are promoting importance of NRGS to public, so public wants to use it

Kevin: exposure is good, there is a genetic diversity movement

Missy: they have a letter letting people know they won’t receive material, could update it so people understand the lack of resources

Kim: some people are asking for germplasm so they can sell it, can recognize some names and screen them out

Missy: people asking for hops germplasm (a few 100) so they can start a commercial production operation

Kevin: create a core set of germplasm for general requesters?

Kim: homeowners would see a small set in GRIN, scientists see whole set

Action item: 2019 annual meeting will be hosted by W6-WRPIS in Pullman in mid-June, will have a webinar connection with WebX; 2020 annual meeting tentatively to be held in Logan UT

Resolutions:

Resolution 1. The W-6 Technical Advisory Committee thanks Dr. Kim Hummer, Joseph Postman and the staff of the USDA ARS National Clonal Germplasm Repository in Corvallis for their efforts in organizing and hosting the 2018 W-6 meeting with teleconference options.

Resolution 2. The W-6 Technical Advisory Committee thanks Dr. Jim Moyer for his many years of service as Administrative Advisor for the W-6 Regional Technical Advisory Committee.

Resolution 3. The W-6 Technical Advisory Committee thanks Dave Stout and Vicki Bradley for their many years of service at the W-6 station and their contributions to NPGS.

Motion to adjourn the meeting by Kevin, Dan seconded, passed unanimously.

Meeting minutes for Tuesday, June 26, 2018 recorded by Carol Miles.

W6 TAC Secretary: Joe Kuhl

To view all the complete state reports, please follow these instructions: Log in to NIMSS at https://www.nimss.org/   Click on "WEST" in the Sort by Region section, then the "W," then on "W6." When the project homepage comes up, go to the left hand side and click on "Attachments." Here you will see all the individual 2018 State reports.

 

 

 

Accomplishments

This project manages a diverse collection of important agricultural crop genetic resources and associated information and makes them accessible to plant breeders around the world to develop new cultivars with improved quality and increased productivity, which are critical for global food security. Crop genetic resources are also used by scientists in basic research to increase our knowledge of plant sciences. To fill the gaps in our collection, we acquired 1,499 new accessions including 1,384 native plant accessions collected by the Seeds of Success (SOS) project and 807 accessions from various sources. As of August 6, 2018, the WRPIS held 100,979 accessions that belong to 1,065 genera and 5,356 taxa including 4,687 identified species. We uploaded 17,006 observation data points on 3.515 accessions into the Germplasm Resources Information Network (GRIN)-Global database. These data points are on 97 established descriptors for 13 different crop species. Our collaborators contributed 7% and WRPIS staff provided 93% of the evaluation data. The database is accessible by researchers worldwide via the internet. We distributed a total of 42,484 packets of seed samples to 1,060 requestors with addresses in each of the 50 domestic states and 46 foreign countries. Sixty percent (25,913 packets) were distributed to the U.S. and 40% (16,571 packets) were distributed to foreign countries. Requestors in each of the 50 domestic states received germplasm samples from WRPIS in the Year of 2017. A total of 9,682 packets from WRPIS went to the 13 Western states.

We entered 2,314 seed viability records into GRIN-Global in 2016. The WRPIS tested 985, the National Laboratory for Genetic Resource Preservation (NLGRP), Fort Collins, CO tested 1,329 accessions. We packed and stored 1,772 newly regenerated/harvested inventories of a broad range of plant species. We determined seed quantities of 6,513 inventories. We shipped 1,573 seed inventories to the National Laboratory for Genetic Resource Preservation (NLGRP), Fort Collins, CO and 602 inventories to the Svalbard Global Seed Vault, Svalbard, Norway for secured backup.

  • Cool season food legume germplasm curator Clarice Coyne co-directed a Ph.D. dissertation project of Dr. Md Nurul Amin, a native of Bangladesh, who was conferred doctoral degree by Washington State University. This project discovered 10,052 Single Nucleotide Polymorphism (SNP) markers in the USDA lentil core collection using Genotyping-By-Sequencing (GBS) and identified markers that are significantly associated with some important agronomic traits including early flowering and high yield in the genome-wide association study (GWAS).
  • Research Plant Pathologist Frank Dugan and horticultural crops germplasm curator Barbara Hellier demonstrated that garlic bulb rot caused by Fusarium proliferatum infestation can be dramatically lowered by planting bulbils instead of seed cloves for regeneration of garlic.
  • Research Geneticist Long-Xi Yu identified SNP makers associated with resistance to Verticilium wilt in alfalfa. A couple of these markers could be from the functional genes since their sequences show homology to the conserved components of plant disease resistant genes.
  • Horticultural crops germplasm curator Barbara Hellier finished characterization of the USDA table beet collection. The data and images are being uploaded to GRIN-Global database.
  • Agronomy and native plants germplasm curator Vicki Bradley selected and released a new tef germplasm line ‘Crimson Torch’ for ornamental crop development.
  • Phaseolus bean germplasm curator Theodor Kisha analyzed 120 Heirloom Beans for protein, extractable phenolics and non-extractable proanthocyanidins. There were 2 to 3-fold differences even within market classes of Red and Black beans. Data is being entered into the GRIN Global database for plant breeders to select desirable parental accession in developing varieties with the optimal polyphenolic compound contents for consumers.
  • On May 18, 2018, the Central Ferry research farm hosted a field trip of the 5th grade class from La Crosse, WA. Four plant science technicians (Lisa Taylor, Jessica McGowan, Dawn Tachell and Saber Glass) and the farm crew (Kurt Tetrick and Jennifer Morris) showed the kids different plants in the field and greenhouse, methods of harvesting and cleaning seeds and farm equipment. The class late rated the field trip the best in the school year.

On June 19, 2018, the W6 station hosted 21 High School Students with the Omak/Okanogan County Upward Bound Program in Pullman, WA as part of their WSU visit. ARS volunteers showcased many aspects of plant science education and USDA careers through discussion, worksheets and hands-on activities. The students rotated through 4 stations, each focusing on a different aspect. These stations included: ‘Botany/Mendelian Genetics’, ‘Fungal Pathogens/Microscopy’, ‘Seed Cleaning/Identification’ and ‘Molecular Research Tools/Phenotypic Variation’.

Impacts

  1. The rich genetic diversity managed by WRPIS contributed significantly to the more than five-fold expansion of the U.S. production of pulse crops (dry bean, Pea, chickpea, lentil) in terms of planted acreage and total production in the past twenty years. A substantial portion of the pulse crop is exported.
  2. NPGS germplasm has contributed to plant genome, biochemistry and ecology research needed to support the state's food industry and conservation efforts. During the past calendar year, researchers in the western region published 73 scientific papers that were resulted from use of the NPGS genetic resources.
  3. The NPGS system has provided educators and private citizens with access to crop plant resources for small business development and teaching that they otherwise would not have had access to. One recipient in Washington State noted that the availability of unique and rare varieties has allowed growers to begin the process of re-establishing viable local commercial farms that can compete at a very small scale. Another described it as “an invaluable resource.”

Publications

  1. Arkwazee, Haidar A. 2018. Quantitative trait loci and genome wide association study for resistance to white mold in common (snap) bean. Ph.D. dissertation, Oregon State University.
  2. Bhattarai, G. and S. A. Mehlenbacher. 2018 Discovery, characterization and linkage mapping of simple sequence repeat markers in hazelnut (Corylus avellana ). J. Amer. Soc. Hort. Sci. 143: (accepted).
  3. Bhattarai, G. and S.A. Mehlenbacher. 2017. Development and mapping of new tri-nucleotide repeat simple sequence repeat markers from the hazelnut genome sequence. PLoS ONE 12(5): e0178061.
  4. Bhattarai, G., S.A. Mehlenbacher, and D.C. Smith. 2017. Eastern filbert blight disease resistance from Corylus americana ‘Rush’ and selection 'Yoder #5' maps to linkage group 7. Tree Genetics and Genomes 13:45 doi.org/10.1007/s11295-017-1129-9
  5. Bhattarai, G., S.A. Mehlenbacher, and D.C. Smith. 2017. Inheritance and mapping of eastern filbert blight resistance from 'Uebov' hazelnut. J. Amer. Soc. Hort. Sci. 142:289-297.
  6. Bushakra, J.M., M. Dossett, K.A. Carter, K.J. Vining, J.C. lee, D.W. Bryant, R. VanBuren, J. Lee, T.C. Mockler, and N.V. Bassil. 2018. Characterization of aphid resistance loci in black raspberry (Rubus occidentalis ). Mol. Breed. (in press). DOI: 10.1007/s11032-018-0839-5.
  7. Byrne PF, Gardner C, Gore MA, Simon PW, Smith S, Volk GM. 2018. Sustaining the Future of Plant Breeding: The Critical Role of the USDA-ARS National Plant Germplasm System. Crop Science 58:451-468. doi: 10.2135/cropsci2017.05.0303
  8. Carpenter M.A., M Shaw, R. Cooper, T.J. Frew, R.C. Butler, S.R. Murray, L. Moya, J. Coyne, G.M Timmerman-Vaughan. 2017. Association mapping of variation in starch chain length distribution in pea (Pisum sativum L.) using carbohydrate and starch metabolism candidate genes. BMC Plant Biology 17:132. DOI 10.1186/s12870-017-1080-9
  9. Colburn, B.C., S.A. Mehlenbacher and V.R. Sathuvalli. 2017. Development and mapping of microsatellite markers from transcriptome sequences of European hazelnut (Corylus avellana ) and use for germplasm characterization. Molecular Breeding 37:16.
  10. Dandurand, LM, Morra, MJ, Zasada, IA, Phillips, WS, Popova, I, and C Harder. 2017. Control of Globodera spp. Using Brassica juncea seed meal and seed meal extract. Journal of Nematology. 49:437-445.
  11. DOI:10.1371/journal.pone.0160941
  12. Dugan, F.M., J. Landry, and J. Hu. 2017 Ascochyta blight of faba bean. Washington State University Cooperative Extension Fact Sheet.
  13. Dugan, F.M., S.L. Lupien, and J. Hu. 2017. Fungal plant pathogens associated with emerging crops in North America: A challenge for plant health professionals. Plant Health Progress 18: 221-229.
  14. Dugan, F.M., S.L. Lupien, C.M. Vahling-Armstrong, G.A. Chastagner, and B.K. Schroeder. 2017. Host ranges of Penicillium species causing blue mold of bulb crops in Washington State and Idaho. Crop Protection 96: 265-272.
  15. Elias, G.E. and Y. Wu. 2017. Grow-out test to distinguish different amaranth species. Seed Technol. 38 (2): 153-154. (Abstract)
  16. Elwan, EA, Aleem, EEA, Fattouh, FA, Green, KJ, Tran, LT, and AV Karasev. 2017. Occurrence of diverse recombinant strains of Potato Virus Y circulating in the potato fields in Egypt. Plant Disease. 101:1463-1469.
  17. Feng, X, Guzman, P, Myers, JR, and AV Karasev. 2017. Resistance to bean common mosaic virus conferred by the bc-1 gene affects systemic spread of the virus in common bean. Phytopathology. 107:893-900.
  18. Feng, X., G.E. Orellana, J.R. Myers, and A.V. Karasev. 2018. Recessive resistance to bean common mosaic virus conferred by the bc-1 and bc-2 genes in common bean (Phaseolus vulgaris ) affects long distance movement of the virus. Phytopathology doi.org/10.1094/PHYTO-01-18-0021-R.
  19. Feng, X., P. Guzmán, J.R. Myers and A.V. Karasev. 2017. Resistance to bean common mosaic necrosis virus conferred by the bc-1 gene affects systemic spread of the virus in common bean. Phytopathology 107:893-900. org/10.1094/PHYTO-01-17-0013-R.
  20. Finn, C.E., T.A. Mackey, J.D. Postman, and R.R. Martin. 2017. Identifying blueberry germplasm that is slow to get Blueberry shock virus in the Pacific Northwest United States. Acta Hortic. (in press).
  21. Funke, CN, Nikolaeva, OV, Green, KJ, Tran, LT, et al. 2017. Strain-specific resistance to potato virus Y (PVY) in potato and its effect on the relative abundance of PVY strains in commercial potato fields. Plant Disease. 101:20-28.
  22. Green, KJ, Brown, CJ, Gray, SM, and AV Karasev. 2017. Phylogenetic study of recombinant strains of Potato Virus Y. Virology. 507:40-52.
  23. Green, KJ, Chikh-Ali, M, Hamasaki, RT, Melzer, MJ, and AV Karasev. 2017. Potato virus Y (PVY) isolates from Physalis peruviana are unable to systemically infect potato or pepper and form a distinct new lineage within the PVYc strain group. Phytopathology. 107:1433-1439.
  24. Holdsworth W.L., E. Gazave, P. Cheng, J. Myers, M.A. Gore, J. Coyne, R.J. McGee, M. Mazourek. 2017. A Community Resource for Exploring and Utilizing Genetic Diversity in the USDA Pea Single Plant Plus Collection. Horticulture Research 4;17017; doi:10.1038/hortres.2017.17.
  25. Ingwell, LL, Lacroix, C, Rhoades, PR, Karasev, AV, and NA Bosque-Perez. 2017. Agroecological and environmental factors influence Barley yellow dwarf viruses in grasslands in the US Pacific Northwest. Virus Research. 241:185-195.
  26. Jibran, R., H. Dzierzon, N. Bassil, J.M. Bushakra, P.P. Edger, S. Sullivan, C.E. Finn, M. Dossett, K.J. Vining, R. VanBuren, T.C. Mockler, I. Liachko, K.M. Davies, T.M. Foster and D. Chagné. 2018. Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis ) genome based on chromatin interaction data. Hort. Res. 5:8-, DOI 10.1038/s41438-017-0013-y
  27. Kahraman A, Pandey A, Khan MK, Lindsay D, Moenga S, Shin M-G, Molano G, Carrasquilla-Garcia N, Vance L,Bergmann E, vonWettberg E, Chang P, Taran B, Cook DR, Penmetsa RV(2017).Distinct subgroups of Cicer echinospermum are associated with hybrid sterility and breakdown in interspecific crosses with cultivated chickpea. Crop Science 57:3101-3111. doi: 10.2135/cropsci2017.06.0335.
  28. Kim, W., J.-J. Park, M. Dugan, T.L. Peever, D.R. Gang, G. Vandemark, and W. Chen. 2017. Production of the antibiotic secondary metabolite solanapyrone A by the fungal plant pathogen Ascochyta rabiei during fruiting body formation in saprobic growth. Environmental Microbiology 19: 1822-1835.
  29. Lafta, A., T. Turini, G. Sandoya, and B. Mou. 2017. Field evaluation of green and red leaf lettuce genotypes in the Imperial, San Joaquin, and Salinas Valleys of California for heat tolerance and extension of the growing seasons. HortScience 52: 40-48.
  30. Landis, JB, A Guercio, CF Fiscus, and D Koenig. Elucidating the genetic control of long-term success in a near century long study of barley (Hordeum vulgare). (Oral). Evolution 2017 Conference, June 23-27, Portland, OR.
  31. Landis, JB, A Guercio, CF Fiscus, and D Koenig. Phenotypic variation and genetic control of long-term success in a near century long study of barley (Hordeum vulgare). (Oral). Botany 2018 Conference, July 21-25, Rochester, MN.
  32. Landry E., C.J. Coyne, R. J. McGee and J. Hu. 2017. A modified mass selection scheme for creating winter-hardy faba bean (Vicia faba ) lines with a broad genetic base. Euphytica 213: 72. doi:10.1007/s10681-017-1843-2
  33. Liu X-P, Yu L-X (2017) Genome-wide association mapping of loci associated with plant growth and forage production under salt stress in alfalfa (Medicago sativa ). Front. Plant Sci. doi: 10.3389/fpls.2017.00853.
  34. Lupien, S.L., F.M. Dugan, K.M. Ward, and K. O'Donnell. 2017. Wilt, crown and root rot of common rose mallow (Hibiscus moscheutos) caused by a novel Fusarium sp. Plant Disease 101: 354-358.
  35. Ma Y., C.J. Coyne, D. Main, S. Pavan, S. Sudheesh, S. Kaur, J.W. Foster, J. Leitão, S. Sun, Z. Zhu, X. Zong, R.J. McGee. 2017. Development and validation of breeder-friendly KASPar markers for er1, a powdery mildew resistance gene in pea (Pisum sativum ) Molecular Breeding 37:151 https://doi.org/10.1007/s11032-017-0740-7
  36. Ma, Y., Coyne, C.J., Grusak, M.A., Mazourek, M., Cheng, P., Main, D. and McGee, R.J., 2017. Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum ). BMC Plant Biology, 17:43. DOI: 10.1186/s12870-016-0956-4
  37. Mathey, M.M., S. Mookerjee, L.L. Mahoney, K. Gunduz, U. Rosyara, J.F. Hancock, P.J. Stewart, V.M. Whitaker, N.V. Bassil, T.M. Davis, and C.E. Finn. 2017. Genotype by environment interactions and combining ability for strawberry families grown in diverse environments. Euphytica 213:112. DOI 10.1007/s10681-017-1892-6.
  38. Mehlenbacher, S.A., D.C. Smith, and R.L. McCluskey. 2018. 'Burgundy Lace' ornamental hazelnut. HortScience 53:387-390 https://doi.org/10.21273/HORTSCI12623-17
  39. Mehlenbacher, S.A., D.C. Smith, and R.L. McCluskey. 2018. 'York' and 'Felix' hazelnut pollenizers. HortScience 53: (in press).
  40. Pincot DDA, Poorten, Hardigan. Harshman, Acharya, Cole, Gordon TR, Stueven M, Edger PP, Knapp SJ (2018) Genome-Wide Association Mapping Uncovers Fw1, a Dominant Gene Conferring Resistance to Fusarium Wilt in Strawberry. G3:  Genes, Genomes, Genetics 8: 1817-1828.  https://doi.org/10.1534/g3.118.200129.
  41. Price, R. A., P. Woods, and D. Meyer. 2017. Seed identification from ITS DNA sequencing-an update. Seed Technology 38: 152-153.
  42. Price, R. A., T. Bartling, J. Kaste, P. Woods, D. Thiede, D. Meyer, and F. Ghavami. 2017. Palmer amaranth: identification from ITS DNA sequencing. Seed Technology 38: 151-152.
  43. Qin, J., A. Shi, B. Mou, G. Bhattarai, W. Yang, Y. Weng, and D. Motes. 2017. Association mapping of aphid resistance in USDA cowpea (Vigna unguiculata Walp.) core collection using SNPs. Euphytica 213: 36. doi:10.1007/s10681-016-1830-z
  44. Qin, J., A. Shi, B. Mou, M.A. Grusak, Y. Weng, W. Ravelombola, G. Bhattarai, L. Dong, and W. Yang. 2017. Genetic diversity and association mapping of mineral element concentrations in spinach leaves. BMC Genomics 18: 941. DOI 10.1186/s12864-017-4297-y
  45. Ravelombola, W., A. Shi, Y. Weng, B. Mou, D. Motes, J. Clark, P. Chen, V. Srivastava, J. Qin, L. Dong, W. Yang, G. Bhattarai, and Y. Sugihara. 2018. Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages. Theoretical and Applied Genetics 131: 79-91. doi:10.1007/s00122-017-2987-0
  46. Ruas, M ., Guignon, V., Sempere, G., Sardos, J., Hueber, Y., Duverhey, H., Andrieu, A., Chase, R., Jenny, C., Hazekamp, T., Jelali, K., Adeka, J., Ayala Silva, T., Chao, C., Daniels, J., Dowlya, B., Effa Effa, B., Gueco, L., Kempenaers, E., Herradura, L., Ibobondji, L., Irish, B.M., Kilangi, J., Muhangi, S., Ngo Xuan, P., Paofa, J., Pavis, C., Sandoval Jorge, Sutanto, A., Thiemele, D., Tossou, C., Vangu Paka, G., Ganjun, Y., Van Den Houwe, I., Roux, N., Rouard, M. 2017. MGIS: Managing banana (Musa ) genetic resources information and high-throughput genotyping data. Database: The Journal of Biological Databases and Curation. doi:10.1093/database/bax046.
  47. Salinas, N.R., J.D. Zurn, M. Mathey, S. Mookerjee, B. Denoyes, J. Perrotte, A. Potier, C.E. Finn, J.F. Hancock, P. Stewart and N.V. Bassil. 2017. Validation of molecular markers associated with perpetual flowering in octoploid Fragaria Mol. Breeding 37:70-82. DOI 10.1007/s11032-017-0672-2
  48. Sathuvalli, V., S. Mehlenbacher, and D. Smith. 2017. High-resolution genetic and physical mapping of the eastern filbert blight resistance region in 'Jefferson' hazelnut (Corylus avellana ). The Plant Genome 10(2) doi:10.3835/plantgenome2016.12.0123
  49. Shi, A., J. Qin, B. Mou, J. Correll, Y. Weng, D. Brenner, C. Feng, D. Motes, W. Yang, L. Dong, G. Bhattarai, and W. Ravelombola. 2017. Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing. PLoS ONE 12(11): e0188745. https://doi.org/10.1371/journal.pone.0188745
  50. Smýkal P, I. Hradilová, O. Trněný, J. Brus, A. Rathore, M. Bariotakis, R. Rani Das, C. Richards, C.J. Coyne, S. Pirintsos. 2017. Macroecological patterns of wild relatives of domesticated pea in the Mediterranean Region and the Fertile Crescent. Scientific Reports 7:17384 DOI:10.1038/s41598-017-17623-4
  51. Strausbaugh, C.A., and M. Dugan. 2017. A novel Penicillium sp. causes rot in stored sugar beet roots in Idaho. Plant Disease 101: 1781-1787.
  52. Thavarajah D., A. Abare, I. Mapa, J. Coyne, S. Kumar, P. Thavarajah. 2017. Selecting lentil accessions for global selenium biofortification. Plants 6 (3), p.34.
  53. Thompson, JR, Dasgupta, I, Fuchs, M, Iwanami, T, Karasev, AV, et al. 2017. ICTV Virus taxonomy profile: Secoviridae. Journal of General Virology. 98:529-531.
  54. VanBuren, R., C. Man-Wai, M. Colle, J. Wang, S. Sullivan, J.M. Bushakra, I. Liachko, K.J. Vining, M. Dossett, C.E. Finn, R. Jibran, D. Chagne, K. Childs, P.O. Edger, T.C. Mockler, and N.V. Bassil. 2018. A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. GigaScience (accepted)
  55. Verma, S., J.D. Zurn, N. Salinas, M. M. Mathey, B. Denoyes, J.F. Hancock, C.E. Finn, N.V. Bassil, and V.M. Whitaker. 2017. Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in strawberry (Fragaria ×ananassa) breeding populations using pedigree-based QTL analysis. Hortic. Res. 4:17062 doi:10.1038/hortres.2017./62.
  56. Vining KJ., Johnson SR., Ahkami A., Lange I., Parrish AN., Trapp SC., Croteau RB., Straub SCK., Pandelova I., Lange BM. 2017. Draft genome sequence of Mentha longifolia and development of resources for mint cultivar improvement. Molecular Plant 10:323–339. doi: 10.1016/j.molp.2016.10.018.
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