Case Study: pea phenotyping
A. CooperatorsB. Funded evaluationsC. Publication data miningD. Funded research projectsE. Survey germplasm users
(NCRPIS)F. Curator evaluations
A. Publishable using augmented designsG. Data from other genebanks
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
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.
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
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
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
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
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
Field evaluations-ARS resourcesPacific West Region example
PWA Statistical Support• Bruce E. Mackey, PWA & WHNRC
[email protected] (510) 559-6078
• Linda C. Whitehand WRRC & PGEC, [email protected] (510) 559-6077
Services offered in order of priority:1. Training in Statistics 2. Experimental Design3. Statistical Inference 4. Statistical Models and Methods 5. Data Analysis6. 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
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
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.
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
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.
