Brief Summary of Minutes of Annual Meeting

Kevin Jensen (W6 Chair)

Kevin welcomed everyone, particularly, Marilyn Warburton who was recently hired as the Research Leader at the Western Regional Plant Introduction Station (WRPIS). This was followed by a brief introduction of everyone since there were many new state representatives present. The agenda had changed significantly from previous meeting with the State Reports in the morning followed by a working meeting in the afternoon to discuss ways that the W6 RTAC can help meet current and foreseen needs of W6 Regional Multistate Project.

Scot Hulbert (WSU W6 Administrative Advisor)

• Scot provided a report, remarks, and discussed budget
• 5-year project was approved (2022-2026) – thanks to everyone who worked on it.
• Report was given on the new construction of the 100,000 sq ft USDA ARS building on the WSU campus in Pullman, WA. Concerns were raised over possible cost overruns (~$17,000,000) in the construction, which will likely result in the sharing of equipment and controlled environmental rooms. Stakeholders, including Washington State University, are speaking with their representatives in Congress to get additional funding to complete the project.
• Wendy Powers would assume Dean of Agriculture August 15, 2022.
• Concerns over increased wages and flat budgets were discussed, in the context of the W6 multistate project and personnel supported by it.
• 2023 budget was presented by Scot Hulbert which requested a $49,352 increase in W6 funding. The W6 budget routinely covers 6 full-time people, wages for summer help and some supplies. A concern discussed was that, due to increased wage requirements, project might have to do with less workers.
• Shaun Mehlenbacher made the motion to approve the budget
• Charlie Brummer seconded the motion
• Discussion … State Representatives need to visit with their respective Experiment Station Directors to support this and other increases to the W6 program.
• W6 2023 proposed budget was approve unanimously.

Peter Bretting (USDA ARS National Programs Leader)

Peter Bretting presented slides entitled: The National Plant Germplasm System: 2022 Status, Prospects, and Challenges. A map of the gene banks nationwide was presented. NPGS accessions have increased over the last several years up to 600,092 in 2021. From 2018 to 2021, the number of accessions is not increasing significantly. The big increase was associated with the Seeds of Success program submitting their native plant collections. NPGS distributed 219,000 accessions in 2021 up 14% from 2020. During the Pandemic, some genebanks are finding it difficult to hire temporary, often student labor, because of the low unemployment rate and demographic changes. As in the past, most of these distributions are to public research institutions (e.g., Land-Grant and USDA) with about 1/3 for private usage. Two thirds to three quarters of distributions are domestic and the remainder international. Acknowledged the passing of David Spooner, long-time USDA ARS successful plant geneticist/breeder.

Budget wise, NPGS saw a $2.5 million increase in its 2021. Specifically, the increases went to Small Grains PGR, Aberdeen, ID ($190,000); Vaccinium PGR, Corvallis, OR ($150,000); Hemp PGR, Geneva, NY ($1.35 million); and Pecan PGR, College Station, TX ($400,000). Challenges facing the NPGS include:

• Expanding the NPGS operational capacity and infrastructure to reduce PGR management backlogs and meet increased demand for PGR and associated information.
• Increased operation costs (labor, inputs, overall inflation, etc.). Reference the Economic Research Service (ERS) Amer Waves online magazine article on “Investment in U.S. Public Agricultural Research and Development Has Gallen by a Third Over Past Two Decades, Lags Major Trade Competitors”.
• NPGS personnel transitions – hiring, training, etc. In the next few years over 1/3 of the germplasm managers will likely retire.
• Developing and applying cryopreservation and/or in vitro conservation methods for clonal and some seed PGR.
• BMPs and procedures for managing accessions (and breeding stocks) with increased diversity of GE traits in more crops, the occurrence of adventitious presence (AP, and the products of gene editing.
• Acquiring and conserving additional PGR, especially of crop wild relatives.

Christian Tobias (USDA NIFA Representative) 

Christian is representing the Institute of Food Production and Sustainability with programmatic authority over Plant Breeding with over $2 million available and will be taking over the potato breeding research programs within the next year. The agency lost ~80% of their work force in the move to Kansas City, MO with 80% of the time teleworking. Encouraged conventional plant breeding for new cultivars with a deadline of September 2^0, 2022 for submission.

2021 W6 RTAC meeting minutes, changes, discussion, and approval

The virtual floor was opened for any discussions, questions, or comments about the 2021 meeting minutes. Brian Irish reported identifying two to three grammatical corrections. Those suggestions were sent to Ian Ray, past W6 RTAC Chair for correction. Ian Ray moved that the minutes be approved, and Kevin Jensen seconded the motion. The motion was approved unanimously.

State Reports: See the details of all the reports, charts, and graphs by loading the PDF in the attached file. 

Budget

The total federal ARS budget for the PGITRU was $3,257,476 and includes the budgets for the Pullman-based germplasm ($2,539,778), the Prosser-based temperate-adapted forage legume germplasm ($275,939) and alfalfa genetics research ($441,759) projects. After indirect costs are assessed, net balance was $2,903,622 with $2,563,900 dedicated to salaries and the remainder for supplies, equipment, repairs, and extramural agreements. The discretionary dollar amount per SY (7 in the Unit in 2020), an indicator of the financial health of the Unit, was $36,228; an improvement from last year due to the abolishment of one of the SY positions. The ‘in kind’ support from the W6 Western Regional Multistate Research Project, through Washington State University, was $477,301.

W6 RTAC Business Meeting

RTAC discussion on how we can make the W6 project sustainable.

• Stakeholder group – currently WRPIS/W6 does not have a stakeholder group. Discussion was had on who should be (commodity groups) on the stakeholder committee.  Besides research guidance, one of the main reasons for a stakeholder group is to advocate on the WRPIS’s behalf in efforts to remain fiscally sustainable. Possible commodity groups mentioned include alfalfa, American Seed Trade Association, sugar beets, legumes, and The Plant Conservation Alliance.
  

Each State Representative was tasked with sending some potential stakeholder names to Marilyn before the end of the year. It was decided that the W6 RTAC Chair would invite several stakeholders to the next W6 RTAC meeting in 2023.

• Discussion on how to improve ways to collect impact data – One advantage of working with a good stakeholder group is to be able to document the impact that germplasm distributions from the NPGS are having. The W6 RTAC does a good job reporting on current year’s seed distribution and potential use, but there is little follow up in years to come. How can we better hold germplasm users accountable for the germplasm received? In efforts to document impacts, state representatives were asked to contact 2018 germplasm users for publications and impact. Peter Bretting indicated that in the past he had used the ERS to estimate economic impact of NPGS.

• Possibly looking on the national level to use Artificial Intelligence to collect data – using a set of key words to search publications.
• Could USDA NIFA funded proposals utilizing NPGS germplasm be require to report impacts of the germplasm?

• White Paper Development – Demonstration of economic impact.
  • Private sector – statement of support (look to commodity groups)
  • Public sector (Land Grant U., USDA, non-profit, etc.)
  • State Representative Specialty (i.e., Kevin Jensen – grasses)
  • Utilize Crop Science Sub-Divisions

It was agreed upon that the state representatives would develop a 1-to-2-page document in their area of specialty, describing the economic impact of NPGS collections. A good example is the “Use of Plant Introduction or Cultivar Development Part I and II”.  This is due by December 20^th, 2022.

• Budget Increase – W6 portion
• Proposed increase
• State Reps Responsibility Discussion/Working with Ag. Exp. St. Dir. …Contact Wyoming and Arizona to identify a state representative.
• Other ways – discussion on funding

W6 RTAC Nominations for Vice-Chair (Matt Lavin) and Secretary (Amjad Ahmad)

2023 meeting date/site – Prosser, WA after July 4^th   

Motion to adjourn the meeting at 5:07 PM, seconded by Ian Ray.

Outputs:

• A total of 36 publications, including one durum wheat cultivar and five bean germplasm releases, were reported for FY 2021. This includes a book entitled “The Alfalfa Genome” (co-edited by Long-Xi Yu) published by Springer in 2021. It contains 16 chapters covering history, classical and molecular breeding as well as advances in genomics associated with the alfalfa crop.

• Chickpea (Cicer arietinum), lentil (Lens culinaris) and pea (Pisum sativum) genetic resources were screened for resistance to the pea aphid (Acrythosiphon pisum). The chickpea (Cicer arietinum) resources were screened for resistance to Pythium seed rot caused by Pythium ultimum.  Out of 188 lentil accessions screened for resistance to the pea aphid, twenty were determined to be resistant and fifteen candidate genes were identified as being associated with the resistance.  Out of 301 pea accessions screened for resistance to the pea aphid, 48 were determined to be resistant and seventeen candidate genes were identified as being associated with the resistance.

• Activities:

• The Phaseolus program developed a near-infrared spectroscopy (NIR) calibration curve for bean seed protein, which was used to measure the seed protein of the BeanCap genomewide association panel. With this data and the sequencing data publicly available for the BeanCap population, protein levels can be associated with genomic locations and genes. This will lead to information on genes for future marker aided improvement of this important trait.
• The Cool Season Food Legume program published a collaborative pea evaluation study promoting genomic selection's potential. A set of 482 pea accessions genotyped with 30,600 SNP markers and phenotyped for seed yield and yield-related components highlighted the best genomic prediction model. This was then used to evaluate all USDA pea accessions that were genotyped but not phenotyped, sparing the unit the expense of having to phenotype.
• A collaborative team led by Long-Xi Yu mapped genetic loci associated with drought and high salinity, two abiotic stressors affecting alfalfa production worldwide. Associated genes were identified that can be used for gene pyramiding, gene editing and developing markers for marker-assisted selection for drought and salt tolerant alfalfa once they are validated.
• All alfalfa and wild relative germplasm (Medicago spp.) were screened for disease reaction to Phoma medicaginis, the causal agent of spring blackstem and leaf spot of alfalfa.
• Phenotypic data for resistance to Phytophthora megasperma were collected from 150 seedlings each of 250 half-sib families derived from an elite NMSU breeding population. The study was repeated twice. GWAS analyses of these data, in conjunction with >10,000 DNA markers, are being conducted to identify alfalfa genome regions that are associated with P. megasperma resistance. The data are also being analyzed using multiple genomic selection models to identify superior models for accelerating improvement of alfalfa resistance to this disease.

• Milestones:
  • Washington State University’s Johnson Hall, which housed 8 offices and 4 laboratories used by WRPIS staff, has been vacated prior to the demolition of the building and the construction of the new Plant Biosciences Building. This new building will be funded by the USDA ARS, and house USDA and WSU Units/Departments, faculty offices and laboratories. It will house Pullman-based WRPIS scientific and technical staff and include six modern Unit-shared laboratory spaces. The new building will be built on what is the current Johnson Hall footprint. Johnson Hall is now vacated, and all WRPIS moved into adjacent (and smaller) Clark Hall until the new building is finished. Johnson Hall is scheduled for demolition in January 2023, following asbestos abatement. The new building is scheduled to be completed in l2026 and WRPIS will occupy new facilities at that time.

Abbasi J, Dehghani H, Dvorak J, McGuire PE. 2020. Perennial growth and salinity tolerance in wheat×wheatgrass amphiploids varying in the ratio of wheat to wheatgrass genomes. Plant Breeding 139(6):1281–1289. https://doi.org/10.1111/pbr.12856

Al Bari, M., Zheng, P., Worral, H., Szwiec, S., Ma, Y., Main, D., Coyne, C.J., McGee, R.J., Bandillo, N. 2021. Harnessing genetic diversity in the USDA pea (Pisum sativum L.) germplasm collection through genomic prediction. Frontiers in Genetics. 12:707754. https://doi.org/10.3389/fgene.2021.707754

Boots-Haupt, L., Brasier, K., Saldivar-Menchaca, R., Estrada, S., Prieto-Garcia, J., Jiang, J., Riar, R., Hu, J., & Zakeri, H. (2022). Exploration of global faba bean germplasm for agronomic and nitrogen fixation traits. Crop Science, 00, 1– 12. https://doi.org/10.1002/csc2.20794

Brasier, K, Smither-Kopperl, M, Bullard, V, Young-Matthews, A, Bartow, A, Friddle, M, Bernau, C, Humphrey, M, Dial, H, Wolf, M, Hu, J, & Zakeri, H. A multi-environment analysis of winter faba bean germplasm for cover crop traits. Agronomy Journal.  2021; 113:3051−3064. https://doi.org/10.1002/agj2.20717

Brown, M.M., J.M. Martin, E.M. Jobson, A.C. Hogg, P.M. Carr, and M.J. Giroux. (2022).   Evaluating the impact of Rht hypomorphic mutations in durum wheat.  Crop Science 62, 247-258. https://doi.org/10.1002/csc2.20672

Chandel, A., Khot, L., Yu, L. 2021. Alfalfa (Medicago sativa L.) crop vigor and yield characterization using high resolution aerial multispectral and thermal infrared imaging technique. Computers and Electronics in Agriculture. 182. Article 105999. https://doi.org/10.1016/j.compag.2021.105999

Cox, A., Boots-Haupt, L., Brasier, K., Riar, R., & Zakeri, H. (2022). Using δ¹⁵N to screen for nitrogen fixation: Reference plant position and species. Agronomy Journal, 114, 1842-1850. https://doi.org/10.1002/agj2.21032

Das, S, Porter, LD, Ma, Y, Coyne, CJ, Chaves-Cordoba, B & Naidu, RA (2022) Resistance in lentil (Lens culinaris) genetic resources to the pea aphid (Acyrthosiphon pisum). Entomologia Experimentalis et Applicata 170: 755– 769. https://doi.org/10.1111/eea.13202

Hogg, A. C., Carr, P., Eberly, J., Chen, C., Kowatch-Carlson, C., Crutcher, F., Lamb, P., McNamara, K., Haney, E., Kephart, K., Smith, V., Dykes, L., Chen, X., Huang, , & Giroux, M. (2022). Registration of ‘Lustre’ durum wheat. Journal of Plant Registrations, 16, 576– 584. https://doi.org/10.1002/plr2.20214

Irish, B.M., Greene, S.L. 2021. Germplasm collection, genetic resources, and gene pools in alfalfa. In: Yu LX., Kole C., editors. The Alfalfa Genome. Compendium of Plant Genomes. Springer. Cham, Switzerland. p.43-64. https://doi.org/10.1007/978-3-030-74466-3_4

Lin, S., C.A. Medina, S. Norberg, D. Combs, G. Wang, G. Shewmaker, S. Fransen, D. Llewellyn, Long-Xi Yu. 2021. Genome-Wide Association Studies Identifying Multiple Loci Associated with Alfalfa Forage Quality. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.648192

LoPresti EF, Pan V, Goidell J, Weber MG, Karban R. (2019) Mucilage-bound sand reduces seed predation by ants but not by reducing apparency: a field test of 53 plant species. Ecology. 2019 Oct;100(10):e02809. https://doi.org/10.1002/ecy.2809

Jobson, E.M., J.M. Martin, R. Sharrock, A.C. Hogg, and M.J. Giroux. (2021a). Identification and molecular characterization of novel Rht-1 alleles in hard red spring wheat. Crop Science. 61:1030–1037. https://doi.org/10.1002/csc2.20375

Jobson, E.M., J-B. Ohm, J.M. Martin, and M.J. Giroux. (2021b) Rht-1 semi-dwarfing alleles increase the abundance of high molecular weight glutenin subunits.  Cereal Chemistry 98:337-345.  https://doi.org/10.1002/cche.10371

Medina, C., Samac, D.A., Yu, L. 2021. Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). Scientific Reports. 11:17203. https://doi.org/10.1038/s41598-021-96712-x

Medina, C., Yu, L. 2021. Developing SNPs and strategies for genomic analysis in alfalfa. In: Yu LX., Kole C., editors. The Alfalfa Genome. Compendium of Plant Genomes. Springer. Cham, Switzerland. pp.159-175. https://doi.org/10.1007/978-3-030-74466-3_10

Pan, VS, M McMunn, R Karban, J Goidell, MG Weber, EF LoPresti. (2021) Mucilage binding to the ground protects seeds of many plants from harvester ants: a functional investigation. Functional Ecology, 35: 2448-2460. https://doi.org/10.1111/1365-2435.13881 

Pan, VS, C Girvin, EF LoPresti. (2022) Attachment strength of seed mucilage prevent seed dislodgement in high surface flow: a mechanistic investigation. Annals of Botany, mcac045, https://doi.org/10.1093/aob/mcac045

Parajuli, A., Yu, L., Peel, M., See, D.R., Wager, S., Norberg, S., Zhang, Z. 2021. Self-incompatibility, inbreeding depression, and potential to develop inbred lines in alfalfa. In: Yu LX., Kole C., editors. The Alfalfa Genome. Compendium of Plant Genomes. Springer. Cham, Switzerland. p.255-269. https://doi.org/10.1007/978-3-030-74466-3_15

Parker, T. A., Berny Mier y Teran, J. C., Palkovic, A., Jernstedt, J., & Gepts, P. (2020). Pod indehiscence is a domestication and aridity resilience trait in common bean. New Phytologist, 225(1), 558-570. https://doi.org/10.1111/nph.16164

Parker, T., & Gepts, P. (2021), Population genomics of Phaseolus spp.: A domestication hotspot. In: Rajora OP (ed) Population Genomics: Crop Plants. Springer Nature Switzerland.

Parker, T., Palkovic, A., Brummer, E. C., & Gepts, P. (2021). Registration of ‘UC Sunrise’heirloom‐like orange and white mottled bean. Journal of Plant Registrations, 15(1), 43-47. https://doi.org/10.1002/plr2.20096

Parker, T., Palkovic, A., Brummer, E. C., & Gepts, P. (2021). Registration of ‘UC Southwest Red’ heirloom‐like red and white mottled bean. Journal of Plant Registrations, 15(1), 21-27.   https://doi.org/10.1002/plr2.20092

Parker, T., Palkovic, A., Brummer, E. C., & Gepts, P. (2021). Registration of ‘UC Southwest Gold’ heirloom‐like gold and white mottled bean. Journal of Plant Registrations, 15(1), 48-52.   https://doi.org/10.1002/plr2.20117

Parker, T., Palkovic, A., Brummer, E. C., & Gepts, P. (2021). Registration of ‘UC Rio Zape’ heirloom‐like dry bean. Journal of Plant Registrations, 15(1), 37-42.  https://doi.org/10.1002/plr2.20095

Parker, T., Palkovic, A., Brummer, E. C., & Gepts, P. (2021). Registration of ‘UC Tiger's Eye’ heirloom‐like dry bean. Journal of Plant Registrations, 15(1), 16-20.  https://doi.org/10.1002/plr2.20084

Parker, T.A., Cetz, J., de Sousa, L.L., Kuzay, S., Lo, S., Floriani, T.d.O., Njau, S., Arunga, E., Duitama, J., Jernstedt, J., Myers, J.R., Llaca, V., Herrera-Estrella, A. and Gepts, P. (2022), Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion and overexpression of PvIND. New Phytol, 235: 2454-2465. https://doi.org/10.1111/nph.18319

Rajendran, K., Coyne, C.J., Zheng, P., Saha, G., Main, D., Amin, N., Ma, Y., Kisha, T.J., Bett, K., Kumar Agrawal, S., McGee, R.J. 2021. Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection. Plant Genetic Resources. 1-10. https://doi.org/10.1017/S147926212100006X

Samac, D.A., Yu, L., Missaoui, A.M. 2021. Identification and characterization of disease resistance genes in alfalfa and Medicago truncatula for breeding improved cultivars. In: Yu, X. and Kole, C., editors. The Alfalfa Genome, Compendium of Plant Genomics. Springer, Cham: Switzerland. p. 211-233. https://doi.org/10.1007/978-3-030-74466-3_13

Soler-Garzón, A., A. Oladzad, J. Beaver, S. Beebe, R. Lee, J. Lobaton, E. Macea, P. McClean, B. Raatz, J. C. Rosas, Q. Song, P. N. Miklas. 2021. NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean. Front. Plant Sci. 12:628443. https://doi.org/10.3389/fpls.2021.628443

Tang, Z., Parajuli, A., Chen, C., Hu, Y., Revolinski, S., Medina, C., Lin, S., Zhang, Z., Yu, L. 2021. Validation of UAV-based alfalfa biomass predictability using photogrammetry with fully automatic plot segmentation. Scientific Reports. 11(1). Article 3336. https://doi.org/10.1038/s41598-021-82797-x

Vetch JM, Tillett BJ, Bruckner P, Martin JM, Marlowe K, Hooker MA, See DR, Giroux MJ. TAMFT-3A and TAMFT-3B2 homeologs are associated with wheat preharvest sprouting. Plant Genome. 2022 Aug 16:e20250. https://doi.org/10.1002/tpg2.20250. Epub ahead of print. PMID: 35971881

Volk, G.M., Byrne, P.F., Coyne, C.J., Flint Garcia, S.A., Reeves, P.A., Richards, C.M. 2021. Integrating genomic and phenomic approaches to support plant genetic resources conservation and use. Plants. 10(11). Article e2260. https://doi.org/10.3390/plants10112260

Volkman, M.M., J.M. Martin, A.C. Hogg, L. Wright, C. Hale, P.M. Carr, and M.J. Giroux. (2022) Teosinte Branched 1 mutations increase tillering.  Crop Science 62:1522-1530. https://doi.org/10.1002/csc2.20775

Weeden, N., Coyne, C., Lavin, M., McPhee, K. E. (2021) Distinguishing among Pisum accessions using a hypervariable intron within Mendel’s green/yellow cotyledon gene. no. Genetic Resources and Crop Evolution: v. 68 p. 2591-2609.

Yu, L., Medina, C., Peel, M. 2021. Genetic and genomic assessments for improving drought resilience in alfalfa. In: Yu LX., Kole C., editors. The Alfalfa Genome. Compendium of Plant Genomes. Springer. Cham, Switzerland. p.235-253. https://doi.org/10.1007/978-3-030-74466-3_14