1. Case Study: pea phenotyping A.Cooperators B.Funded evaluations C.Publication data mining D.Funded research projects E.Survey germplasm users (NCRPIS) F.Curator evaluations A.Publishable using augmented designs G.Data from other genebanks

2. A. Cooperators – CORE studies Examples of published data in GRIN Usually a subset of the pea CORE –McPhee K.E. 2005. Variation for Seedling Root Architecture in the Core Collection of Pea Germplasm. Crop Sci. 45:1758-1763. –McPhee K.E. and F.J. Meuhlbauer. 2000. Biomass production and related characters in the core collection of Pisum germplasm. Genetic Resources and Crop Evolution 48: 195-203

3. B. CGC funded evaluations Aphanomyces –Malvick DK and J.A. Percich. 1999. Screening of Pea Plant Introduction Collection for Resistance to Aphanomyces Root Root 1990-1994. Biological and Cultural Tests, Vol 11. Ascochyta blight –Kraft, J.M., Dunne, B., Goulden, D., and Armstrong, S. 1998. A Search for Resistance in Peas to Mycosphaerella pinodes. Pl Dis. Plant Dis 82:251-253. Fusarium root rot –Grunwald NJ., Coffman VA., Kraft JM.. 2003. Sources of partial resistance to fusarium root rot in the Pisum core collection. Plant Disease 87:1197-1200. Fusarium wilt race 2 –McPhee KE, Tullu A, Kraft JM, Muehlbauer FJ 1999. Resistance to Fusarium wilt race 2 in the Pisum core collection. J. Amer. Soc.Hortic.Sci. 124:28-31. Mineral nutrients in seed –Grusak, M.A. et al., 2004. Novel approaches to improve legume seed mineral nutrition. Proceedings of the 5th AEP- 2nd ICLGG Conference, pgs. 37-38.

4. C. Data mining from publications Crop Registrations –from JASHS and Crop Science –high quality peer-reviewed & replicated data Literature review –WEB of Science dbf –AGRICOLA dbf Sign up for Digitop https://d2.nal.usda.gov/login

5. D. Funding evaluation research projects USDA – FAS ($15,000/year, 3 yrs) –Seed weight and number in pea –www.fas.usda.gov/icd/grants/scrp.htm Organization for Economic Co-operation and Development – funds scientific exchange visits –www.oecd.org/home/0,2605,en_2649_201185_1_1_1_1_1, 00.html ARS Post-doctoral funding: pea SNPs –2 years, $50,000/year = $100,000 –www.npstaff.ars.usda.gov/ARIS/Manual/chapt15g.pdf NRI (rejected so far, but they fund germplasm projects) –http://www.csrees.usda.gov/funding/rfas/pdfs/06_nri.pdf

6. E. Survey stakeholders Ad hoc (polite for random): Large germplasm requests-ask if you may enter the data into GRIN after publication Systematic: once/year mail survey Western Region Advisory committee Systematic: Survey each germplasm order (NCRPIS) Discussion

7. F. Curator evaluations – design for publication Advantages: scientists will know the data is available with the experimental details – two examples Protein (cooperator ground seed, paid for gases for nitrogen analyzer) – core only –Coyne CJ, Razai L, Baik B-K, Grusak M.A. 2005. Variation for pea seed protein concentration in USDA Pisum core collection. Pisum Genetics 37: (in press). Seed weight and seed number – core only –Replicated field trial, two locations, two years, too much Solution to too much –Work with statistician –Augmented designs

8. Field evaluations-design resources Book: Agricultural Field Experiments: Design and Analysis. RG Peterson. 1994. Marcel Dekker, NY. IPGRI. 2001. The design and analysis of evaluation trials of genetic resources collections. A guide for genebank managers. IPGRI Technical Bulletin No. 4. International Plant Genetic Resources Institute, Rome, Italy. USDA ARS Area Office Statisticians Ex. Western Regional, Albany, CA

9. Field evaluations-ARS resources Pacific West Region example PWA Statistical Support Bruce E. Mackey, PWA & WHNRC bmackey@pw.ars.usda.gov (510) 559-6078 Linda C. Whitehand WRRC & PGEC, lcw@pw.usda.gov (510) 559- 6077 Services offered in order of priority: 1. Training in Statistics 2. Experimental Design 3. Statistical Inference 4. Statistical Models and Methods 5. Data Analysis 6. Data Salvage PC SAS - Distribution of the SAS software is through the statisticians. Yearly licensing fees, are paid out of PWA funds and then charged back to each user

10. Field evaluations-6.4 Augmented designs Augmented designs are appropriate for evaluation stages when hundreds or even thousands of accessions are being studied in the same experiment, using a limited amount of sowing material perhaps enough for one replicate only. They cope with environmental heterogeneity by placing replicates of controls systematically in the experiment. As control plots may be said to keep a check on environmental variation, they have been called checks, and in this section we use check for control”. From IPGRI Technical Manual 4. http://www.ipgri.cgiar.org/publications/pubselect.asp

11. Augmented designs: data analysis Manuals & Programs: Several programs, users manuals, and data examples can be downloaded: AMMI contains a manual, SAS codes, and data examples for performing the analysis of the Additive Main Effects and Multiplicative Interaction (AMMI) model of multi-environment trials and for constructing the biplot. UNREPLICATE includes a manual, SAS macro, and data for analyzing unreplicated trials where the repeated checks are arranged in incomplete blocks. SPATIAL has a manual and data for using the ASREML method for spatial analysis of field trials. BIPLOTS contains a manual, data, SAS codes, and examples for constructing GE biplots and GGE biplots obtained from AMMI and SREG models, respectively. These biplots delineate subsets of environments and genotypes with positive interaction. From www.cimmyt.org/english/wps/biometrics/index.htm Other Reference book: Kang MS (ed) 2003. Handbook of Formulas and Software for Plant Geneticists and Breeders. Haworth Press, New York.

12. Data analysis and presentation GRIN –Design descriptors during experimental design phase –Think about software for your analysis –SAS, TASSEL, GERMINATE Publication options –Crop Science –Genetic Resources and Crop Evolution –Euphytica –Plant Breeding –Plant Genetic Resources: Characterization and Utilization

13. G. Data from other genebanks Australia example: –Used IRRI’s ISIS database format –Downloaded all available data from SINGER and GRIN on lentil and chickpea –www.iris.irri.org/ranjanweb/SiteMain.jsp Have not done in pea yet, but in discussion with other pea genebanks Funded project with ICRISAT- exchange chickpea data-failed.