F. Curator evaluations

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29 Νοε 2013 (πριν από 3 χρόνια και 10 μήνες)

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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

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 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

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.