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Case Study: pea phenotyping

Case Study: pea phenotyping. Cooperators Funded evaluations Publication data mining Funded research projects Survey germplasm users (NCRPIS) Curator evaluations Publishable using augmented designs Data from other genebanks. A. Cooperators – CORE studies.

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Case Study: pea phenotyping

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  1. Case Study: pea phenotyping • Cooperators • Funded evaluations • Publication data mining • Funded research projects • Survey germplasm users (NCRPIS) • Curator evaluations • Publishable using augmented designs • 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 resourcesPacific 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.

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