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April 30, 2008 Stuttgart, Arkansas

Applied Plant Genomics Coordinated Agricultural Project

A coordinated research,

education, and extension project for the application of genomic discoveries

to improve rice in the United States

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TABLE OF CONTENTS

Agenda .......................................................................................................................................1 Attendees....................................................................................................................................2 Year 4 Project Plans of Work (September 1, 2007 – August 31, 2008) Objective 1- Summary (Breeding, Phenotyping, and Genotyping Effort) .......................3 Objective 1- Individual Plans of Work .............................................................................7 Objective 2 – Summary (Candidate Genes Effort) .........................................................23 Objective 2 – Individual Plans of Work .........................................................................25 Bioinformatics.................................................................................................................31 Scientific Advisory Boards’ Report (for Year 3).....................................................................33 RiceCAP Publications Master List (Published, Submitted, Anticipated)............................................................38 Publication Highlights (with Layman Summary & Acknowledgements) January 2007............................................................................................................44 April 2008................................................................................................................47 Abstracts and Scientific Presentations ............................................................................51 RiceCAP/CSREES Acknowledgement Language..........................................................57 Personnel Listing Through End-of-Grant (August 31, 2008)..................................................58

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RICECAP PI MEETING AGENDA Stuttgart, AR April 30, 2008

Wednesday – April 30 1:00 pm Welcome

Agenda, Meeting Objectives, USDA perspective, budget issues, moving RiceCAP into year 5, and deliverables – Jim Correll

For each of the 4 RiceCAP objectives, we will cover the following

with regard to RiceCAP deliverables: - Accomplishments to date - Specific priorities for remainder of Year 4 and for Year 5 - Specific anticipated deliverables by December 2008 and August 2009 - Prioritizing efforts and resources 1:30 Discussion by RiceCAP objective: Obj 1 Anna Bob, Jim O., Shannon, Georgia, Steve, Karen,

Yulin, Brian Obj 2 Guo-liang Yinong, Jan, Guo-liang, Pam

Database – Clare

Obj 3 Jim C. 3:30 Obj 4 Rick (Peggy)

3:45 – 4:30 Write up list of objective priorities for the following time periods: Up to August 31, 2008 Up to December 31, 2008 Up to August 31, 2009

Write up list of objective deliverables for the following time periods: Up to August 31, 2008 Up to December 31, 2008 Up to August 31, 2009 4:30 – 5:30 Presentation of priorities and deliverables to group 5:30 – 6:00 Concluding remarks

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RICECAP ATTENDEES Stuttgart, AR April 30, 2007

Principal Investigators

Steven Brooks Karen Moldenhauer Rick Cartwright Clare Nelson

Eric Christensen (telephone) Jim Oard Jim Correll Shannon Pinson

Georgia Eizenga Bishwajit Prasad Bob Fjellstrom Brian Scheffler

Melissa Jia Walter Solomon Yulin Jia Guo-Liang Wang

Peggy Lemaux (telephone) Yinong Yang (telephone) Guangjie Liu Weiqiang Zhang

Anna McClung

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YEAR 4 PROJECT PLANS OF WORK (September 2007 – August 2008)

Objective 1 – Summary Plan of Work Year 4

Breeding, Phenotyping, and Genotyping Effort

Anna McClung, Farman Jodari, Karen Moldenhauer, Jim Oard, Yulin Jia, Steven Brooks, Georgia Eizenga, Brian Scheffler, Dwight Kanter, Donn Beighley, Fernando Correa, Bob Fjellstrom, Scot Hulbert,

Yulin Jia, Sally Leong, Shannon Pinson, Herry Utomo Objective #1: Identify and use of candidate genes and other molecular markers

linked to quantitative trait loci (QTL) which control milling quality and resistance to sheath blight disease.

Experimental Approach:

1. Evaluate mapping populations to identify QTL associated with milling yield and sheath blight resistance. Validate results in subsequent populations and fine-mapping sub-populations.

2. Develop improved methods for phenotyping populations for milling and sheath blight

resistance. 3. Develop novel genetic resources possessing unique combinations of milling and

sheath blight resistance QTL. Integration into the overall project: Objective 1 continues to evaluate the original milling yield and sheath blight resistance mapping populations and fine-mapping sub-populations developed from these. Genotyping efforts on all of these are continuing. The group collaborates closely with the Bioinformatics group on the mapping analysis and closely with the Objective 2 team to identify candidate genes and new markers to fill in gaps. In addition, markers, germplasm, and genotyping and phenotyping techniques developed in this research effort are transferred directly to breeding programs. Continued evaluation of these populations and advanced materials will result in identification and mapping of QTL for milling yield and sheath blight resistance, new germplasm for use in breeding programs, and new streamlined methods for evaluation.

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Benchmarks for Year 4: Milling Yield Mapping Populations (MY1, MY2, MY3)

1. Validate putative QTL associated with components of milling yield in MY1 sub-populations: A few families from the MY1 (Cypress/RT0034) population that were segregating for QTL associated with chalkiness, green kernels, and brown spot have been advanced and increased to develop sub-populations that can be used to verify putative QTL for these traits. During year 4, these sub-populations will be phenotyped for these traits and additional markers near the putative QTL will be evaluated on selected progeny.

2. Map milling yield QTL in the MY2 population: During year 4, data collected from the

previous year on MY2 (Cypress/Lagrue) will be used for mapping analysis. Concurrently, a second year of phenotypic data will be collected in replicated trials conducted in Louisiana and Arkansas. Samples harvested at these locations will be analyzed for milling and grain dimension data in Texas and for fissuring susceptibility in California. The second year of phenotypic data will be used to strengthen the QTL analysis of MY2. Results from MY1 will be compared with findings in MY2.

3. Complete genotyping of MY 3 population and phenotype in one environment: The F7

generation of the MY3 population derived from California germplasm L204 and 01Y110 will be grown in California in a replicated trial. Since the material is poorly adapted to the southern US and very susceptible to rice blast disease, it will be grown only in California. The 265 progeny will be evaluated for milling yield and its components during 2007 and 2008. Genotypic analysis of the population will be conducted through a collaboration with Tom Tai (ARS, Davis, CA). QTL analysis will come in late 2008 and will utilize findings from MY1 and MY2.

Sheath Blight Resistance Mapping Populations (SB1, SB2, SB4, SB5)

4. Validate putative QTL associated with components of sheath blight resistance in SB1 sub-populations: Two families identified in SB1 (Rosemont/Pecos) that are segregating for the sheath blight QTL on chromosome 9 have been advanced and increased. These progeny will be used to fine map this QTL and determine if resistance associated with this QTL is independent of height and heading effects. Markers will be used to identify subpopulations of individuals for further phenotypic testing using the micro-chamber method, followed by inoculated nurseries and toxin screening.

5. Complete the mapping of SB2 population: The double haploid population of 325

individuals of SB2 will be evaluated in replicated inoculated nurseries conducted in Texas, Louisiana, and Arkansas. These data will be available shortly after the genotyping is completed in the SB2 population and will be used in mapping analysis along with phenotypic results from year 3. QTL that have been identified in SB1 and SB4 will be verified in this population.

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6. Finely map sheath blight resistance QTL in SB4 TILs: The SB4 population is the most advanced and offers the best current opportunity to finely map sheath blight QTL. Regions on chromosomes 9, 2, 4, and 12 have been associated with sheath blight resistance in several different studies. TIL populations possessing these isolated QTL will be evaluated directly or following subsequent backcrossing to the susceptible parent, Lemont. The progeny will be evaluated with markers in these regions and then seed from selected individuals will be used to verify the resistance phenotypically.

7. Complete the mapping of SB5 population: A new mapping population SB5 has been

developed from Lemont/Jasmine 85 because of the robust sheath blight resistance of Jasmine 85. The population is a wide cross and is highly polymorphic. Genotyping of some 256 families will be completed by the first few months of year 4. The population will be screened for sheath blight resistance in the field in Arkansas during 2007 and at three locations in 2008. Differentially expressed genes that have been identified through SAGE and DNA microarray analysis will be mapped in the population along with QTL identified in other mapping populations.

8. Map sensitivity to sheath blight toxin: Initial results of toxin screening indicate that

the method is robust and repeatable and capable of identifying components of sheath blight sensitivity. In year 4, toxin sensitivity genes will be mapped in two populations. Markers associated with sensitivity will then be tested in SB1, SB2, and SB4 populations and associated with resistance identified in the micro-chamber and field testing methods.

9. Identify chromosomal regions associated with sheath blight resistance derived from

wild Oryza species: Backcrossed mapping populations using wild Oryza species that have been identified as possessing resistance to sheath blight disease will be screened with markers and in inoculated disease tests to identify chromosomal regions associated with resistance. Additional wild species recently introduced into the US will be evaluated for response to sheath blight disease and the most resistant will be used to develop new mapping populations.

10. Expansion of marker assisted selection into US variety development programs:

Markers existing for key blast resistance and grain cooking quality traits will be utilized in the Mississippi and Missouri the breeding programs to a greater extent. New markers identified in the RiceCAP project will be tested in US breeding populations. New breeding lines identified in RiceCAP mapping populations will be transferred to US variety development programs for evaluation and crossing. Expertise will be gained in collecting and utilizing marker information for increasing selection efficiency in breeding programs. New genetic resources will be developed that represent an extensive survey of germplasm that has served as the foundation of US breeding programs as well as germplasm that is representative of the gene pool currently being utilized. This set of materials will be used for future studies to determine linkage disequilibrium within US germplasm and identify chromosomal regions associated with new traits of interest to breeders.

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Personnel Involved: Anna McClung, Farman Jodari, Karen Moldenhauer, Jim Oard, Yulin Jia, Steven Brooks, Georgia Eizenga, Brian Scheffler, Dwight Kanter, Donn Beighley, Fernando Correa, Bob Fjellstrom, Scot Hulbert, Yulin Jia, Sally Leong, Shannon Pinson, Herry Utomo

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Individual Plan of Work Year 4 – Objective #1

Anna McClung

USDA-ARS Stuttgart, AR

Bob Fjellstrom

USDA-ARS Beaumont, TX

Shannon Pinson USDA-ARS Beaumont, TX

Objective #1: Identify and use of candidate genes and other molecular markers

linked to quantitative trait loci (QTL) which control milling quality and resistance to sheath blight disease (Breeding Efforts 1A).

Experimental Approach: Eighteen QTLs for sheath blight resistance were previously mapped and verified in Lemont/TeQing RILs. A complimentary set of TeQing-into-Lemont introgression lines (TILs, a.k.a. SB4) provides unique opportunity to study the effect of substituting segments of chromosome from TeQing into Lemont genetic background. TILs selected as containing one or more of the QTLs selected for fine mapping (2, 4b, 9b, and 12a) were crossed with Lemont in Year 3, to provide F2 progeny for molecular and phenotypic evaluation in Year 4. Prior observation of the TILs in field plots and using the micro-chamber system suggests that at least qSB12a has ‘strong enough’ effect to be detected using the newly developed micro-chamber method. F2 plant phenotypes may thus allow fine-mapping of the qSB12a QTL. It is anticipated that field phenotyping may be required to fine-map the other SB-QTLs in both the SB1 (Rosemont/Pecos) and the SB4 populations. SB1 results can be used to verify or contrast findings from SB4 at QTLs on chromosomes 2 and 9B. Additional marker support will be provided for identifying parental polymorphisms for mapping milling yield and sheath blight resistance in the RiceCAP mapping populations. Genotyping and phenotyping efforts in the MY2 and SB2 progeny population will be completed. Proposed Benchmarks for Year 4:

1. With an order of priority set at qSB12a, qSB9b, qSB2, and qSB4b; SB-QTLs will be more finely mapped by:

a. Using markers to identify new recombination within the QTL regions among segregating SB1 and SB4 progeny.

b. Analyze the F2 and F3 recombinants phenotypically using the micro-chamber method (in TX), and/or toxin resistance (in collaboration with Steve Brooks).

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c. Collect F2:3 and F3:4 seed for further progeny analysis (GH plants), and increase seed supplies as possible for field-plot verification analysis in 2008 (in TX, AR, and/or LA – as seed supplies allow).

The precision of the mapping effort will continue to increase as numbers of progeny and newly-found recombinations increase. Our mapping precision is aimed to be 1 cM or less by the end of the project. This is finely mapped enough to support marker assisted selection and future gene cloning efforts.

2. As the location of the SB-QTLs become more finely mapped, evaluate their location

against candidate gene sequences identified by SAGE and other means (RiceCAP Obj. 2). If warranted, develop new markers to more precisely evaluate linkage between the candidate sequences and the SB-QTLs.

3. Genotype additional markers in MY2 in regions having a high QTL peak value to

better define QTL locations and identify possible candidate genes. 4. Provide additional marker support to genotyping teams for identifying

polymorphisms segregating in the RiceCAP mapping populations. 5. Test some 20 SFPs identified from Nguyen’s work in the MY2 and SB2 populations. 6. Participate in the draft of a manuscript for MY1 population for submission to journal 7. Evaluate the SB2 population in inoculated sheath blight nursery and participate in

data analysis, mapping, and manuscript preparation. 8. Participate in the MY2 data analysis, mapping, and drafting of manuscript.

Integration into the overall project: Lead in the identification of additional polymorphic markers in the mapping populations and RIL derived from these for fine mapping purposes. Develop and phenotype fine mapping populations to identify specific QTL in MY1, SB1, and SB4. Conduct phenotyping analysis of SB2, MY2, and SB4, and participate in interpretation of data for all mapping efforts. Personnel Involved: Dr. Bob Fjellstrom serves a team leader for all of the genotyping efforts in the mapping populations. Dr. Shannon Pinson is responsible for directing the research efforts for the SB4 project. Dr. Anna McClung is responsible for RIL development and phenotyping in the MY1 and SB1 populations and coordination of phenotypic data analysis in the SB2 and MY2 populations. Funds are requested to support of one postdoctoral associate, Dr. Yueguang Wang, who is responsible for the SB4 TILs genotyping and phenotyping and will participate in the fine mapping of the SB1 RILs, and technical support for conducting the sheath blight screening assays of SB2.

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Yulin Jia

Dale Bumpers National Rice Research Center Stuttgart, AR

Fernando Correa-Victoria

CIAT Cali, Columbia, South America

Objective #1: Identify and use of candidate genes and other molecular markers linked to quantitative trait loci (QTL) which control milling quality and resistance to sheath blight disease (Breeding Efforts 1A).

Experimental approach:

1. Advance RILs of Lemont and Jasmine 85 (SB5) to the F9-10 generation with 600 RILs.

2. Genotype and phenotype 256 SB5 RILs. Phenotyping will be conducted in fields

in Arkansas (second year), Louisiana (first year with Jim Oard) and Texas (first year with Shannon Pinson).

3. QTL analysis of sheath blight resistance and fine mapping of differentially

expressed genes identified from SAGE and DNA microarrays. 4. In Colombia, the F1s of the triple crosses will be evaluated using the mist-

chamber method to identify highly resistant plants. Selected plants will be advanced to F2. At least 2000 F2 plants will be evaluated using the micro-chamber method to identify, select and harvest the seeds of the most resistant plants. Individual F2 plants will be harvested for future evaluation of the F3 lines.

Integration into the overall project: Leading a coordinated effort to develop a Lemont/Jasmine 85 RIL population and to map and pyramid the genes for sheath blight resistance. Benchmarks for Year 4:

1. March- Advance the entire SB5 population to F8-9 generations. Distribute the F6-7 seeds of SB5 to the co-PIs for field evaluation of sheath blight resistance.

2. August- Complete QTL analysis of sheath blight resistance genes and fine

mapping of differentially expressed genes identified from SAGE and DNA microarrays. Initiate the manuscripts of QTL analysis of sheath blight resistance genes, and of registration of Lemont/Jasmine 85 mapping population.

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3. August-complete the evaluation of the F1 plants of the triple cross for sheath

blight, complete the selection, harvesting F2 seeds and screening F2 plants. 4. October- Complete phenotyping of 200 RILs in fields in Arkansas and

Louisiana/Texas. Release 600 RILs of Lemont X Jasmine 85 population at F9-10 generations-no cost extension?

Personnel Involved: One postdoctoral associate Dr. Guangjie Liu will spend 100% of his time on the project in Year 4. In addition to Dr. Jia’s time, USDA-ARS, DB NRRC will provide one supporting staff scientist Melissa Jia (15% of her time) from the genomic core facility and one part time technician from Molecular Plant Pathology group.

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Farman Jodari

California Cooperative Rice Research Foundation Biggs, CA



1. Characterize fissuring resistance of parental lines and F7 progeny of Cypress/Lagrue population (MY2) using samples received from Arkansas and Louisiana for a second year.

2. Phenotype 265 RILs of L204/01Y110 (MY3) milling population grown in California

for milling yield and fissuring resistance.

3. Assist in the establishment and operation of marker analysis facility at RES, Biggs CA. Train new hires and staff in induced fissuring techniques, genotyping, and marker assisted selection procedures.

Integration into the overall project: Will provide induced fissuring characterization of the MY2 population grown in two southern environments for second year. Providing this information to the genotyping cooperators will allow development of useful markers in selection for milling yield stability. Phenotyping MY3 population for milling yield and stability under California environment allows verification of markers already found in MY2 as well as identification of new markers through this population. This population is an elite narrow based cross segregating for milling yield. Will participate in training of staff in molecular breeding techniques. Benchmarks for year 4:

1. Sep.- Complete re-calibration of hydration method and refinement of protocol for fissuring resistance characterization of MY2 and MY3 populations. – Hire technician for participation in CAP project. Initiate phenotyping 265 RILs of the 'MY3' population grown at RES, Biggs CA for milling Yield

2. Oct – Initiate processing, Hydration, and fissuring Characterization of 600 samples

from MY3. Train new hire and participate in training of staff in molecular breeding techniques. Participate in the coordination efforts for genotyping of MY3.

3. December – complete all phenotyping of MY3

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4. December - Initiate processing, Hydration, and fissuring Characterization of 1400 samples from MY2 population grown in Arkansas and Louisiana.

5. May 2008 – Complete Fissuring characterization of MY2. 6. June 2008 – Process data for use in appropriate manuscript.

Personnel Involved: One postdoctoral research associate and 3 half time technicians.

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Karen Moldenhauer

University of Arkansas Stuttgart, AR



1. Finish collecting data on the 325 RIL’s, parents and checks from the population Cypress/Lagrue (MY2) for milling quality in collaboration with the mapping groups.

2. Finish collecting the data on the 325 DH lines, parents and from the SB2 population

Cocodrie/MCR 010277 in collaboration with the mapping groups. Integration into the overall project: The University of Arkansas team will conduct extensive phenotypic characterization of the MY2 and SB2 populations grown in the AR during 2007. Data collected from the SB2 and MY2 will be utilized to discover QTL molecular markers which will be made available to the breeding group. Benchmarks for Year 4:

1. Participate in RiceCAP Workshop and meetings. 2. September -January - Finish phenotypic data collection and plot harvesting in the

field of the MY2 and SB2 populations. Prepare samples from the MY2 for milling, grain dimension and fissuring evaluation. Send data for statistical analysis

Personnel Involved: Two Agric Laboratory Technicians for completion of data collection, compilation and sample preparation, as well as a consultant to finish the sheath blight rating, in addition to Dr. Moldenhauer’s time and her breeding and staff effort.

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James Oard

Louisiana State University Baton Rogue/Crowley, LA

Herry Utomo

Rice Research Station, Louisiana State University Agricultural Center



Experimental approach: (January – August 2008)

1. Complete cleaning and milling of plot samples from 325 RIL’s of MY2 population from 2007 trial in collaboration with RiceCAP researchers.

2. Finish phenotypic and genotypic data analysis of the 325 DH lines, parents and

checks from the SB2 population for sheath blight resistance in collaboration with RiceCAP Co-PIs involved in QTL analyses.

3. Participate in development and possible field evaluation of permanent RiceCAP

association genetics mapping population(s). Brainstorm with other RiceCAP Co-PIs about future direction and funding opportunities after August 2008.

4. Participate in the summary of data analysis and write-up of final report for MY2

and SB2 research and creation of peer-reviewed journal articles. 5. Note: It is assumed that MY2 and SB2 field trials will not be conducted in 2008, but

that could change depending on 2007 field data and consensus of RiceCAP Co-PIs. Integration into the overall project:

The LSU AgCenter Co-PIs will contribute to data collection and cooperative analyses of MY2 and SB2 populations for QTL identification. RiceCAP Co-PIs will provide data, interpretation, and participation in writing peer-reviewed papers. Contributions will be also made toward the future and how to leverage RiceCAP research beyond 2008. Cooperation with other Co-PIs of Objectives 2, 3, and 4 to advance RiceCAP research will be pursued during this last year of the project.

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Benchmarks for Year 4:

1. MY2 grain samples will be prepared for milling, grain dimension and fissuring evaluation. All data collected will be sent to Clare Nelson for statistical analyses.

2. Final planning and possible evaluation of permanent association genetics mapping

population in the field will begin in cooperation with other RiceCAP Co-PIs. Additional components of future research beyond 2008 will be identified.

3. Research summaries, reports, and peer-reviewed articles will be completed by August

2008. Personnel Involved: One Postdoctoral Researcher and one Research Associate for field and laboratory research. In addition Drs. Oard, Groth, Linscombe, Utomo, and Sha will direct the research, field and laboratory work, data analysis, and write-ups of reports and journal articles.

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Steven Brooks

USDA ARS Dale Bumpers National Rice Research Center

Stuttgart, AR


Experimental approach: 1. A high-resolution gene mapping strategy will be used to fine map the first toxin

sensitivity gene. Using the framework map developed from 91 BC1F2s in year three, the gene interval will be saturated with all available SSR and InDel markers. The nearest flanking markers will be used to screen additional BC1F2s for meaningful recombinants in the gene interval. Only selected recombinants will be phenotyped, which allows for unlimited effective population size and efficiency in phenotypic evaluation.

2. Using the published rice genome sequences candidate gene(s) will be identified in the

interval delineated by the high-resolution genetic map. Integration into the overall project: The proposed research impacts RiceCAP objectives involving molecular mapping of sheath blight tolerance QTL in rice. The R. solani phytotoxin is being evaluated as an alternate approach to obtain the reliable phenotypic data necessary for mapping sheath blight tolerance loci. A toxin assay was developed to screen sheath blight populations, and toxin sensitivity loci can now be mapped and correlated with known tolerance QTL. Benchmarks for Year 4: 1. Construct a high-resolution genetic map for one of the two toxin sensitivity genes. 2. Submit a manuscript for publication detailing the mapping effort and identification of

candidate gene(s). Personnel Involved: Steven Brooks is the principle investigator for this project. One half-time Biological Science Technician is supported by RiceCAP.

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Georgia Eizenga

USDA-ARS Dale Bumpers National Rice Research Center

Stuttgart, AR



Experimental approach: (July 07 - June 08)

1. Advance the Bengal/O. nivara mapping population to BC2F2 families for genotypic and phenotypic evaluation to identify SB-QTL.

2. Initiate one new mapping population between the most resistant Oryza sp. accession

and the susceptible cultivar Lemont, and advance to at least the BC1F1. The Oryza sp. parent will be selected from the resistant accessions identified the in Yr. 3 screening effort and resistant O. rufipogon accessions received from IRRI.

Integration into the overall project: This project will identify novel QTL for SB in wild Oryza species and develop at least two new mapping populations with resistant Oryza spp. accessions. This project is fully integrated into the overall project by using Lemont, a common parent in the SB4 and SB5 populations, using selected micro-chamber SB screening method, and utilizing SSR markers being used in other RiceCAP SB populations. Benchmarks for Year 4:

1. Advance the Bengal/O. nivara IRGC 100898 population to BC2F2 families by October 2007. Genotype the selected families with SSR markers and phenotype for SB to identify QTL associated with SB resistance.

2. Advance the cross between the most resistant Oryza sp. accession identified in the

Yr. 3 screening and Lemont to at least the BC1F1 and verify with SSR markers. 3. Evaluate O. rufipogon accessions from IRRI which produce seed for SB resistance

with micro-chamber method. If shown to be more resistant than the Oryza spp. accessions identified in Yr. 3, use one of these O. rufipogon accessions to initiate the mapping population with Lemont and advance at least to the BC1F1 and verify with SSR markers for further population development.

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Personnel Involved: Bishwajit Prasad, RiceCAP funded Post-Doctoral Associate, is responsible for evaluation of SB resistance, developing mapping populations with selected Oryza spp. accessions, and analysis with SSR markers.

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Brian Scheffler

USDA-ARS Stoneville, MS

Dwight Kanter

Mississippi State University

Donn Beighley

Southeast Missouri State University Objective #1: Identify and use of candidate genes and other molecular markers

linked to quantitative trait loci (QTL) which control milling quality and resistance to sheath blight disease.

Title: Establishment of marker assisted rice breeding programs in Mississippi and Missouri Experimental Approach:

1. Screen approximately 2000 lines from the MO and MS programs for agronomic, disease and quality traits using various markers associated with these traits.

2. Continue the training of the Ph.D. candidate in molecular marker technology as it

relates to association mapping. 3. A Linkage Disequilibrium Analysis and association mapping study using in US Rice

Lines will be conducted as part of Ph.D. thesis for Solomon. This project will include some 400 cultivars that represent the US historical pedigree (100) and current US advanced breeding selections (300). The project will aim to determine linkage disequilibrium within US germplasm, which is quite unique from the rest of the world’s germplasm and identify chromosomal regions associated with new traits of interest to breeders. The on-going RiceCAP mapping efforts will provide clues as to the best markers to use for optimal genome coverage. It is estimated that this will require running 125-150 markers. Seed harvested from a replicated field increase in 2007 at Stoneville, MS will be used for phenotypic scoring of seedling vigor and cold tolerance studies.

Integration into the overall project: The scope of this project will breeding programs in Mississippi and Missouri to more fully integrate the use of molecular markers as a means to determine the absence / presence of

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particular traits in breeding populations. These breeding programs will then be positioned to use new markers for sheath blight resistance and milling quality as they become available from the RiceCAP project. The association mapping project will provide new genetic resources (a large set of purified germplasm spanning 100 years of breeding in the US) and potential markers for new traits of interest to breeders as well as identification of chromosomal regions within US germplasm that are largely fixed. This will serve as a bridge to future studies for the US rice community to further explore the US germplasm base using current and emerging genomic tools. Benchmarks for Year 4: (May 07 – August 08)

1. The molecular marker analysis and interpretation of results from each program will be summarized to provide a means for making selections for the 2007 winter nurseries and 2008 line advancement.

2. The association mapping project will produce sufficient seed to conducted replicated

laboratory assays for seedling vigor, cold tolerance, and grain dimension during year 4. Some 150 markers will be evaluated on 300-400 cultivars for association mapping and linkage disequilibrium analysis.

Personnel Involved: Brian Scheffler, USDA-ARS, Rice Research Unit, Stoneville, MS Donn Beighley, Southeast Missouri State University, Malden, MO Dwight Kanter, Mississippi State University, Stoneville, MS Walter Solomon, Mississippi State University, Stoneville, MS

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RiceCAP Year 3 Progress Report

Brian Scheffler1, Gregory May 2, Robert Fjellstrom 3

1USDA-ARS, Rice Research Unit; Stoneville, MS

2 National Center for Genome Resources; Santa Fe, New Mexico 3 USDA-ARS, Rice Research Unit; Beaumont, TX

Objective #1: Identify and use candidate genes and other molecular markers linked to quantitative trait loci which control milling quality and resistance to sheath blight disease. A. Proposed Benchmarks for Calendar Year 3 (Jan 07-Dec07):

This is a newly funded project starting in 2008. The goal is to transition the US rice research community from being limited to just SSR markers to access to SNP technology. The first step in this will be to re-sequence two important US rice cultivars for genome comparison and to help in the discovery of relevant SNPs. The only significant publically available rice SNP data generated so far was done using 20 lines (Perlegen) from around the world. Two US cultivars were included, M202 and Cypress, but only Cypress is a long grain and considered key to mid-south US breeding efforts. In addition, an array based SNP discovery method was used, so although a large number of SNPs were detected among the global set of lines, the number of SNPs relevant to US efforts is limited.

B. Accomplishments on each benchmark for Year 3:

The rice cultivars LaGrue and Cypress were selected as informative and representative cultivars for mid-south US rice production. These are the parents of the MY2 project and are well known for high yield (LaGrue) and superior milling quality (Cypress). In addition, previous analysis of SSR data for these two cultivars demonstrated that they are relatively diverse considering the narrow southern US long grain germplasm base. Re-sequencing and bioinformatic strategies were selected and the Solexas platform was chosen for sequencing due to cost per bp. Dr. Gregory May at the National Center for Genome Resources was selected to lead the effort as the NCGR already has the infrastructure for the project, bioinformatics capabilities, and has performed similar projects on other species. DNA was extracted from single plants of Lagrue and Cypress; the latter using the same seed source as analyzed in the international Perlegen project.

C. Integration into the overall project:

This is the first effort to develop SNP technology that will be directly applicable to the US rice breeding community and will position US researchers to effectively utilize this platform in the future. In addition, SNPs may be discovered in regions that have been

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found to lack polymorphism in the MY2 parents that may aid in mapping efforts for milling yield.

D. Personnel involved:

Funding will support contract research conducted by NCGR. Dr. Gregory May from the National Center for Genome Resources, will head the re-sequencing effort as well as the bioinformatics. The project will be under the direction of Brian Scheffler who is in charge of the USDA ARS MSA Genomics Laboratory and will provide the necessary DNA samples. He is also involved in several of the RiceCAP mapping projects and will be utilizing the information. He will work with Dr. May on the genome comparison. Dr. Robert Fjellstrom, USDA-ARS, Beaumont, TX, will be involved in integrating the discovered SNPs in relation to known SSR markers in collaboration with Dr. Clare Nelson, Kansas State University.

E. Deliverables:

1. Refereed publications (published, in press, or submitted).

2. Refereed publications in preparation or anticipated.

May, G., Fjellstrom, R.G., and Scheffler, B.E. SNP discovery and genome characterization of US rice cultivars using a whole genome sequencing approach. The Plant Genome. December 1, 2008.

3. Abstracts/Presentations for 2007

4. Molecular markers/tools made available to the general community

A list of SNPs between the rice cultivars LaGrue and Cypress and the reference genome Nipponbare. The information will be shared and eventually used in the development of a US cultivar SNP chip.

~2.3 X genome coverage of each cultivar (LaGrue and Cypress) will be generated and made public.

5. Rice germplasm developed under RiceCAP and made available to the

community.

6. Integration

The outcome of this project will directly impact RiceCAP mapping efforts for MY2 which is based on these same cultivars, and will enhance mapping efforts in the RiceCAP MY1 (Cypress/RT0034) project, as well as others because of the pedigree association of Cypress with Cocodrie and Lemont that are used as parents in SB2, SB4, and SB5. Also, this information will identify additional candidate SNPs that can be used to develop a US SNP chip that can more fully explore the US gene pool that is being analyzed in the Linkage Disequilibrium Analysis project (Walter Soloman).

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Objective 2 – Summary Plan of Work Year 4

Candidate Genes Effort

Yinong Yang, Jan Leach, Pamela Ronald, Guo-Liang Wang Objective #2: Validate the function of candidate genes associated with sheath blight

resistance and milling quality Experimental Approach: 1. Evaluate transgenic rice lines for sheath blight resistance. Many RNAi and overexpression lines have been generated and are being analyzed for altered resistance to sheath blight. We will continue to evaluate these transgenic rice lines using the coke bottle method. In addition, Ronald lab will test several activation tagged lines for sheath blight resistance. 2. Develop molecular markers for sheath blight resistance. We have identified many differentially expressed rice genes or proteins that are associated with sheath blight disease. Some of them have been validated via transgenic analysis and shown to be involved in sheath blight resistance. We will work with Objective 1 team to develop molecular markers for introgression of sheath blight resistance genes into US cultivars. 3. Conduct bioinformatics analysis of the three milling quality MPSS libraries. The MPSS data will be further analyzed to identify candidate genes associated with grain filling and milling yield. Quantitative RT-PCR will be conducted to confirm the differential expression of candidate genes in 1, 3, 6, 9, 12, 15 day old seeds of Cypress, LaGrue and Nipponbare. 4. Conduct secretome analysis of R. solani. Analyze R. solani secretome and assess the potential role of the fungal extracellular proteins in causing rice sheath blight disease. 5. Develop new vectors and protocols for rice biotechnology toolbox. We have constructed and are evaluating new vectors that may facilitate rice functional genomics studies or enhance the transformation frequency of US rice cultivars. We will also refine other biotechnology protocols such as protoplast-based assays. Integration into the Overall Project: Identification and validation of candidate genes associated with sheath blight resistance and milling quality is an important component of the overall RiceCAP project. Secretome analysis of R. solani may lead to the identification of extracellular proteins important for the fungal virulence. As a result, the proposed work will help identify molecular markers suitable for QTL mapping and MAS for sheath blight resistance and facilitate the development of novel strategies for controlling sheath blight disease. In addition the project will enhance the

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collaboration of rice researchers, leverage additional funding and promote the outreach and education related to rice genomics. Benchmarks for Year 4: 1.Complete most of transgenic analysis and determine the role of candidate genes in sheath blight resistance.

2. Work with Objective 1 team to develop molecular markers related to sheath blight resistance for QTL mapping and MAS in US germplasm. 3. Complete bioinformatics analysis of MPSS data related to milling quality and perform quantitative RT-PCR to confirm differential gene expression. 4. Complete secretome analysis of R. solani and identify extracellular proteins potentially important for the fungal virulence. 5. Further improve biotechnology tools such as vectors for high throughput RNAi and an efficient transformation method for US rice cultivars. Personnel Involved:

Jan Stephens, Rebecca Davidson, SeWeon Lee (Leach lab), Chang Jin Park (Ronald lab), Maria Bellizzi, M. V. Sreerekha (Wang lab), Qin

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Yinong Yang

University of Pennsylvania Objective #2: Validate the function of candidate genes associated with sheath blight

resistance and milling quality Experimental approach: • Complete the disease evaluation of transgenic rice lines defective in salicylic acid (SA),

jasmonic acid (JA), ethylene (ET), and mitogen-activated protein (MAP) kinase signaling and identify specific pathway(s) important for sheath blight resistance.

• Analyze R. solani secretome and assess the potential role of the fungal extracellular proteins in causing sheath blight disease.

• Evaluate the role of validomycin in activation of rice defense response against sheath blight infection.

Integration into the overall project: The proposed work may help identify molecular markers suitable for rice breeding purpose and facilitate the development of novel strategies for controlling sheath blight disease.

Benchmarks for Year 4: • Determine the specific defense pathway(s) important for sheath blight resistance and

submit a paper. • Complete R. solani secretome analysis and submit a paper. • Evaluate additional transgenic lines (e.g., JAmyb and OsMPKs) for sheath blight

resistance. • Determine the role of validomycin in induced resistance against sheath blight disease.

Personnel Involved: Qin Wang (Senior Research Technologist, 75%) and Emily Helliwell (PhD student, 25%) will be involved in the Year 4 project.

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Pam Ronald

University of California –Davis Davis, California

Objective #2: Validate the function of candidate genes associated with sheath blight

resistance and milling quality Experimental approach: To elucidate the innate immune responses of grasses, we have generated large functional genomics data sets for rice using proteomics, transcriptomics and activation tagging. Using these datasets, and by applying careful experimental design and statistical analysis, a robust pipeline to identify defense signaling proteins with a high probability was developed. In year 4 we propose to assay activation tagged and RNAi lines altered in expression of the candidate genes for resistance to sheath blight and develop markers to sheath blight resistance genes for introgression into US varieties or for direct transformation into US varieties if more suitable. Integration into the overall project: The availability of accurate, reliable, and high-throughput screens for assessing enhanced or reduced disease resistance (and milling/yield quality) are critical to the success of the entire RiceCAP effort. Thus, we have developed a high-throughput and remarkable accurate pipeline to identify new genes involved in disease resistance- 30% of the genes identified confer resistance to bacterial blight in preliminary validation studies. In year 4, we will evaluate resistance of these lines to sheath blight in collaboration with other RiceCAP members Jan Leach and Jim Oard. Benchmarks for Year 4:

• Validate 20 newly developed rice lines for resistance to sheath blight • Identify additional candidates for sheath blight resistance • Develop markers to confirmed sheath blight resistance genes of interest for

introgression into US varieties or for direct transformation into US varieties if more suitable.

• Anticipated Deliverables: At least 3 rice lines with enhanced resistance to sheath blight At least 20 new candidate genes with resistance to sheath blight Manuscript: Chang-Jin Park, Kihong Jung and P Ronald. 2007. Generation of sheath blight resistant lines using a combined transcriptomics and activation tagging approach.

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Personnel Involved: One postdoctoral associate (Chang Jin Park). Leverage personnel: Kihong Jung (funded from a NSF grant)

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Guo-Liang Wang

Ohio State University Objective #2: Validate the function of candidate genes associated with sheath blight

resistance and milling quality Experimental approach:

1. To evaluate the resistance of five RNAi lines to sheath R. solani. Two-week old plants of the RNAi lines will be inoculated with a R. solani strain isolated from Arkansas using Coke bottle method. Plant with enhanced resistance or susceptibility will be selected for further evaluation in T3 generation.

2. To confirm the expression of selected RL-SAGE/Microarray candidate genes in

the Jasmine 85 mapping population. In collaboration with Yulin Jia’s lab, the expression of at least five candidate genes will be confirmed in the F6 mapping population using RT-PCR method.

3. To complete the bioinformatics analysis of the three milling quality MPSS

libraries. Further detailed analysis of the transcriptomes in developing seeds will be performed in Cypress, LaGrue and Nipponbare. In particularly, expression pattern of the genes involved in starch and protein synthesis pathways will be compared and analyzed.

4. RT-PCR confirmation of novel candidate genes at different stage of seed

development. Genes with differential expression among three cultivars and involved in starch and protein synthesis will be our focus. Expression level will be detected in 1, 3, 6 9 12 and 15 day old seeds of the three cultivars.

Integration into the overall project: As we have done in the previous years, we will share our RL-SAGE and MPSS results with other PIs in the consortium. We will continue to work with RiceCAP colleagues such as Yulin Jia, Clare Nelson and Bob Fjellstrom to develop DNA markers associated with sheath blight resistance or milling quality. Benchmarks for Year 4:

1. Identify lines with enhanced resistance to R. solani. 2. Identify candidate genes involved in milling quality. 3. Submit a paper on the milling quality MPSS libraries.

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Personnel Involved: Maria Bellizzi, lab technician (80%) and MV Sreerekha, Research Associate (20%).

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Jan Leach Colorado State University

Ft. Collins, CO

Objective 2: Validate the function of candidate genes associated with sheath blight

resistance and milling quality Experimental approach: • Complete screens T1 lines suppressed for candidate defense response genes (chitinase,

14-3-3, and PR1) for susceptibility to SB, rice blast, and aphid. Each plant screened must be tested for silencing of genes by RT-PCR.

• Determine variation in chr. 8 OsGLP gene family members (formerly called OsOXL) that accounts for differences in contribution to defense. (i.e., sequence information that will allow for targeted integration of the best alleles).

• Refine Outreach materials for final publication. Integration into the overall project: • This project validates candidate genes for disease resistance, which, in turn, are marker

sets for the community to use to introgress effective QTL. Benchmarks for Year 4: • Determine roles of four candidate DR genes that are associated with QTL in broad

spectrum disease and pest resistance. • Publish papers on contributions of candidate genes (total 3 papers anticipated) • Publish outreach materials Personnel Involved: Jan Stephens Rebecca Davidson SeWeon Lee (unfunded)

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Bioinformatics Objective - Summary Plan of Work Year 4

Clare Nelson Department of Plant Pathology

Kansas State University

Bioinformatics Objective: Provide databases, interfaces, bioinformatic services

and analyses, and software to accommodate RiceCAP project data

Experimental approach: Receive and archive project data; quality-check, prepare for analysis, disseminate, conduct statistical analyses (particularly QTL analyses), report results internally on WWW and work up for publication; consult, provide ad hoc bioinformatics services as requested. Maintain WWW map displays showing markers, genes, QTLs integral to RiceCAP project. Integration into the overall project: Map displays maintained at the Data Center are the uniting feature of all RiceCAP experimental research, which aims to identify genes and markers for key rice traits. QTL analysis and interpretation of datasets with multiple-year replicate designs is essential to use of these data towards these aims. The bioinformatics lab is a clearinghouse for all datasets and provider of bioinformatics services and computer programs for data manipulation. Benchmarks for Year 4:

1. Perform data quality checks, map construction, and QTL analyses of data as received, including MY2, MY3, SB2, Eizenga, and Lemont x Jasmine 85 (Jia). This will employ multi-environment, multi-trait MIM with pleiotropy and QTLxE estimation.

2. Once Perlegen SNP data are received, identify SNPs suitable for use on RiceCAP

crosses 3. Incorporate all QTLs in map displays. 4. Lead or assist in publication preparation. 5. Continue software implementation of statistical methods: QTL shrinkage analysis,

missing-data methods, multi-trait/multi-environment methods.

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Personnel Involved: One postdoc (Xiangqiang Sun, 100% time) is responsible for running and reporting all QTL analyses including quality checks. Ph.D. student Zhigang Guo (50% time through 7/07) assists Sun.

Ph.D. student Joehanes (50% time) will continue with QTL software development, Linux system maintenance, CMap maintenance, and assistance in bioinformatics analyses.

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RICECAP SCIENTIFIC ADVISORY BOARD REPORT March 16, 2008

A RiceCAP Annual Meeting with the Advisory Boards was held in San Diego on February 18, 2008. The Scientific Advisory Board included Ron Phillips, Chair, Bill Crosby, David Mackill, Susan McCouch (by teleconference), and Melissa Fitzgerald. Absent were Gene Hookstra and Gurdev Khush (liaison member). The Scientific Advisory Board and the Stakeholder Board met together for two hours following the formal presentations and then the Boards met separately until having a review with Project Coordinator Jim Correll, followed by an oral report to the P.I.s with a following discussion period. The Boards appreciated the impressive progress report (112 pages) organized in a user-friendly and concise style. The large amount of effort devoted to this program by the P.I.s was evident and the report reflected great progress. Reports of 26 P.I.s from 19 institutions were included in the document and summarized according to each of the four major objectives of the project. Objective 1 – Identify and use candidate genes and other molecular markers linked to quantitative trait loci which control milling quality and resistance to sheath blight disease – was presented by Anna McClung on behalf of the entire objective 1 group. Objective 2 – Validate the function of candidate genes associated with sheath blight resistance and milling quality- was presented by Yinong Yang on behalf of that subgroup. Clare Nelson presented a summary of the Bioinformatics component. Objective 3 – Develop technical training programs and resources to ensure implementation of molecular marker and gene validation technologies to solve rice problems – was presented by Jim Correll on behalf of the group. Objective 4 – To effectively communicate the science and potential of rice plant genomics, including progress and description of the RiceCAP, to the U.S. rice industry – was presented by Rick Cartwright on behalf of that subgroup. This approach to reporting progress had been previously recommended by the Advisory Boards, and we appreciated their adoption of this efficient and effective approach. From the standpoint of the Scientific Advisory Board, we wish to highlight that this project has extended the application of genomic discoveries to improve rice in the U.S. to the point that all rice breeding programs in the U.S. now are using molecular markers. The workshops have been very effective and the attitudes and communication among molecular geneticists and breeders are noticeably positive. Many useful mapping populations have been developed serving specific purposes in the project. Germplasm from the mapping populations with valuable phenotypes has been released to the community. Lines with recombinations around regions controlling milling yield, sheath blight, and other traits currently being developed will be even more valuable. Significant progress has been made for resistance to sheath blight, a very difficult breeding objective considering the relatively low level of tolerance in the germplasm. Five mapping populations have been developed and are being used to identify QTLs and candidate genes. In SB1, two QTLs independent of plant height and heading date have been mapped and fine-mapping of a QTL on chromosome 9 is proceeding. More detailed studies are being conducted in SB2 using 325 DH lines. The population has been carefully phenotyped at several locations both in the field and in the “coke bottle” screening. This population should provide the most detailed analysis of sheath blight resistance to date.

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The Teqing/Lemont TILs (SB4) are proceeding nicely, and these should provide useful materials for fine-mapping of QTLs in Lemont background. This should allow better measurement of tolerance in materials with a cleaner background. Sensitivity to toxin is also being mapped in this population, and there seems to be an association of this trait with resistance, although there are exceptions (Bengal is resistant to the toxin but susceptible to sheath blight). Toxin sensitivity is also being mapped in a new population (SB6, Cypress/Jasmine 85//Jasmine 85). SB5 (Lemont/Jasmine 85) looks like a very promising population, considering the higher level of tolerance of Jasmine 85. Milling yield is definitely the more challenging trait, and accurate phenotyping of the trait is a major bottleneck. For MY1, at least a brown spot resistance QTL has been mapped. MY2 has been phenotyped at AR and LA for two seasons each. It is disappointing that the reactions at the two locations are not correlated. However, the Board did not see the individual location data, and the distribution of the means for the four locations looks good, with a normal distribution and the parents on the two extremes. This suggests that the families with extreme phenotypes could be used for genotyping and QTL discovery analogous to the bulked segregant analysis approach. In any case, the data should be nearly complete for QTL mapping in the next few months. MY3 is being used for QTL analysis of head rice yield and fissuring. The flexibility in the management of the project has allowed the project to initiate efforts to adopt newer and more efficient marker technologies, beyond the SSR technology considered the most efficient approach at the commencement of the program. We were pleased to learn the amount of leveraging influenced by RiceCAP funds to access technology platforms, analysis strategies and training opportunities supported by NSF and other funds. The Oryza SNP discovery project laid the foundation for the emerging Illumina Golden Gate Assay (1,536-SNP chip) being developed as part of McCouch’s NSF-funded project on Rice Diversity (NSF #0606461). An Association Mapping Project on US Rice Germplasm also is underway in collaboration with the NSF-funded Rice Diversity project. P.I.s from the RiceCAP project have authored a preproposal to fully sequence the sheath blight organism, Rhizoctonia solani, by the DOE-Joint Genome Institute which has been approved and from which a full proposal has been invited. Interestingly, rice crops have historically been sprayed with the drug Validamycin to control the pathogen. This drug prevents the breakdown of trehalose in both the pathogen and the host, and may be a strong inhibitor of pathogen growth. Ideas are being generated as to how to modify the rice plant to interfere with trehalose breakdown in the pathogen and/or the host may be involved in mitigating the destructive effects of the pathogen. The traits chosen for emphasis in the program were ones identified as important to the producers and quite retractable by conventional methods. Although this reflects the importance of this program to the industry, it also makes it a highly difficult project. The huge GxE interaction in milling yield where standard phenotyping results in low correlations across years and environments (i.e. between States), makes reaching broad conclusions difficult. Although this was known at the outset, there was not a highly documented scientific base to reach that conclusion; the standard phenotyping procedure especially for

35

milling quality is now viewed as quite inadequate and approaches are being generated to allow RiceCAP participants to make a more hypothesis-driven approach. The bioinformatics program provides archiving, displaying of data, analysis by various means, aid in publication, and an important data quality control feature. We were pleased to note the operational integration of bioinformatics-based analysis to project decision-making (e.g. the QTL resident on chromosome 9) which has served to focus project efforts on relatively profitable research directions. Phenotype and genotype data for the different mapping populations will be flowing to the bioinformatics program at a much accelerated rate this coming year. The various populations will allow considerable validation of results from one population to another, and with QTLs previously reported in the literature. This in turn, will facilitate the identification of candidate genes from the various approaches relative to milling yield and sheath blight resistance. Many candidate genes have been identified, but the real power of QTL mapping and forward genetics in general, is that it allows for the discovery of genes that would never be identified as candidates because their contribution to the target phenotypes is currently unknown. In addition, even where there are clear candidates (i.e., for sheath blight resistance) the validation depends on considerable related data from QTL analysis, mutant analysis, and transgenic approaches such as RNAi or over-expression studies. Transgenic experiments to investigate the phenotypic impact of several candidate genes are underway and should prove useful in understanding how they contribute to sheath blight resistance in specific genetic backgrounds and in identifying molecular markers for use in the breeding program. To date, the criteria for candidate gene selection have been somewhat geneal; we would encourage the development and deployment of criteria for future pursuit of selected candidate genes, with particular emphasis on associated genetic data. In order to speed the identification of QTLs with large effect, the Scientific Advisory Board encourages more effort devoted to Bulk Segregant Analysis where phenotyping can reliably identify the extreme segregants. Especially with the new SNP technology, markers associated with traits should be much easier to identify. We would recommend that a strong effort in this direction with the sheath blight trait be forthcoming. We also would recommend that many more recombinants be chosen among progeny of heterozygous markers at loci showing an association with the trait. Because sheath blight has a heritability of about .75, rather distinct regions controlling this trait should be more rapidly identified. Candidate gene validation then should be much easier with the recombinational analysis more complete. BSA could also be appropriate for milling yield studies, where the more extreme phenotypes may represent lines that more stably express the trait and have accumulated QTLs in one direction. Comparison of extreme phenotypes across years and environments might allow the identification of a relatively small number of lines in each population that could be reliably used in a BSA approach. If this is possible, it would help reduce the noise associated with the large majority of lines having intermediate phenotypes, which is what we expect to be the source of much of the GXE interactions associated with milling yield. If there are no lines that are consistently in the extremes of the phenotypic distribution (top 10% and bottom 10%), then this approach will not be useful. We would recommend in this final year of the grant, that additional methods be employed for phenotyping the milling quality trait, again because of huge GXE interaction. Because Cypress is now recognized as a unique cultivar that does not have breakage after extended

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times in the field, a careful laboratory look at Cypress seems reasonable. Does it have a different expression pattern for starch synthase, or does it have more densely packed grains due to a starch-protein complex, or does it have more tightly adhering hulls? Scoring for such traits might reduce the observed GXE interactions, and this project has highlighted that these are some of the pathways that could be followed to understand the contribution of each of these factors to its milling yield. Cypress is a unique cultivar, and the project has developed really good populations for milling yield, and genotyping of those populations is underway. However, it seems that there is not expertise in the RiceCap project for identifying exactly what Cypress has, and developing that into a phenotyping tool. Is it to do with the hull or the grain? For the final year, and no cost extension,of this project, is it possible to use some funding for a Masters Student at IRRI’s post-harvest group to carry out a project to define the special trait of Cypress? Since you already have the populations and have the genotyping data, this could be a productive and important step. There is enormous interest in Asia in ways to maximize head rice yield.. IRRI has the equipment, expertise and capacity to define the tolerance of Cypress. The cost of a student at IRRI is about $10 000 USD/year. This does not include university fees. If a student can be enrolled in a university in their own country, fees could be avoided. Such a student could be co-supervised by Anna McClung (at a distance) and Dr Adoracion Resurreccion (at IRRI). This would provide the phenotyping tool, and could then provide a US student with a very nice project to associate genotype with phenotype, spring-boarding directly from the RiceCAP project. This project has enabled the formulation of a number of hypotheses. One of the most promising findings last year was the early expression of the genes of starch synthesis in Cypress. Intuitively, this could lead to densely filled grains that are hard to crack and break. It would be useful to follow this up, and test if it is a real association using a selection of the progeny in the populations. Perhaps take a few of the low millers and high millers and see if expression of starch synthase 1 associates with milling yield. This is unlikely to present an opportunity for a phenotyping tool, but perhaps the outcome of early expression – packing of the grain – could be. This, of course, depends on whether the milling yield of Cypress is due to factors of the grain. The effort on studying the wild rices appears to be quite useful. Several of the wild species have sheath blight resistances nearly equal to the best U.S. materials, yet the genes are perhaps different and may provide an opportunity to enhance the level contributed by those QTLs identified in the cultivated rice resistance sources. The wild species may also have novel alleles at loci identified in the cultivars that provide a higher level of resistance. Crosses with certain species have been made and are undergoing testing. In the long term, this should be an exciting approach. It has the advantage of introducing novel genetic variation into US rice cultivars that may result in improvements in other traits. Looking ahead we recommend:

1) Phenotyping be more of a hypothesis-driven activity, particularly with respect to milling yield

2) Gather information on breeder’s opinion of the potential value of the germplasm provided through this RiceCAP project

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3) Enhance the development of high-throughput marker technology 4) Look for more breakthrough publications based mostly on RiceCAP funding 5) Develop an economics component illustrating the importance of improved U.S. rice 6) Find ways of reducing the apparent GXE interactions with milling quality, using

genetic noise-reduction techniques (i.e., BSA as described above), statistical noise-reduction techniques and new approaches to phenotyping

7) Examine grain quality characteristics of Cypress leading to its late seasonal drop off in milling quality

8) Employ Bulk Segregant Analysis more extensively to speed up the identification of QTLs with major effect

9) Explore the development of additional user-friendly breeder-based informatics 10) Focus on a few candidate genes that are associated with QTLs identified in the project

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RICECAP PUBLICATIONS (DELIVERABLES)

Master List

Category

Includes RiceCAP

Acknowledgement (Yes / No)

PDF on RiceCAPweb page

(Yes / No)

Citation

Published refereed papers and book chapters (total to March 2008 = 18)

Published No Yes Bart R, Chern, M., Park, C-J., Bartley, L., and Ronald, P. 2006. A novel system for gene silencing using siRNAs in rice leaf and stem-derived protoplasts. Plant Methods 2:13.

Published No

Boza, E.J., Moldenhauer, K.A.K., Gibbons, J.W., Lee, F.N., Cartwright, R.D., and Blocker, M.M. 2007. Phenotypic analysis of the 2006 MY2 mapping population in Arkansas. In R.J. Norman, J.F. Meullenet and K.A.K. Moldenhauer (eds.) Rice Research Studies 2006. University of Arkansas Agricultural Experiment Station Research Series.

Published Yes Yes Brooks, S.A. 2007. Sensitivity to a host-selective toxin from Rhizoctonia solani correlates with sheath blight susceptibility in rice. Phytopathology 97:1207-1212.

Published Yes Yes Chu, Q.R., Linscombe, S.D., Rush, M.C., Groth, D.E., Oard, J., Sha, X., and Utomo, H.S. 2006. Registration of a C/M Doubled Haploid Mapping Population of Rice. Crop Science 46:1416.

Published Yes Yes

Davidson, R., Manosalva, P., Vera Cruz, C., Leung, H., Leach, J. 2006. Expression patterns of oxalate oxidase-like genes associated with blast resistance QTL on chromosome 8 of Oryza sativa. Pages 148-152 in Biology of Plant-Microbe Interactions, Vol 5, eds. F. Sanchez, C. Quiton, I. Lopez-Lara, and O. Geiger. IS-MPMI Press, Minneapolis.

Published Yes Yes

Gowda, M., Venu, R.C., Jia, Y., Stahlberg, E., Pampanwar, V., Soderlund, C., and Wang, G-L. 2007. Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions. In "Methods in Molecular Biology: Plant-Pathogen Interactions” Vol. 354:131-44. Ed. P. Ronald, Humana Press.

Published Yes Yes

Jia, Y., Correa-Victoria, F., McClung, A., Zhu, L., Liu, G., Wamishe, Y., Xie, J., Marchetti, M.A., Pinson, S.R.M., Rutger, J.N., and Correll, J. C. 2006. Rapid determination of rice cultivar responses to the sheath blight pathogen Rhizoctonia solani using a micro-chamber screening method. Plant Disease 91: 485-489.

Published No No Jung, K., An, G., and Ronald, P. Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nature Genetics (Feb 2008; doi:10.1038/nrg2286)

Published No No

Kadaru, S.B., Yadav, A.S., Fjellstrom, R.G., and Oard, J.H. 2005. Alternative Ecotilling protocol for rapid, cost-effective SNP discovery and genotyping in rice (Oryza sativa L.). Plant Mol Biol Reporter 24:1-20.

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Category

Includes RiceCAP



(Yes / No)

Citation

Published No Yes Kumar, R., Qiu, J., Joshi, T., Valliyodan,B., Xu, D., and Nguyen, H. (2007) Single Feature Polymorphism Discovery in Rice. PLoS ONE 2(3): e284. doi:10.1371/ journal.pone.0000284

Published Yes Yes

Leach, J.E., Davidson, R., Liu, B., Manosalva, P., Mauleon, R., Carrillo, G., Bruce, M., Stephens, J., Maria Genaleen Diaz, Nelson, R., Vera Cruz, C., and Leung, H. 2007. Understanding Broad-Spectrum, Durable Resistance in Rice. Pages 191-209 in Rice Genetics V, D S Brar, D Mackill & B Hardy, eds. World Scientific Publ. Co.

Published No No

Lee, J., Bricker, T. M., Lefevre, M., Pinson, S. and Oard, J.H.. 2006. Proteomic and genetic approaches to identifying defense-related proteins in rice challenged with the fungal pathogen Rhizoctonia solani. Molecular Plant Pathology 7:405-416.

Published No Yes

McNally, K., Bruskiewich, R., Mackill, D., Buell, C., Leach, J., and Leung, H. 2006. Sequencing multiple and diverse rice varieties: connecting whole-genome variation with phenotypes. Plant Physiol. 141:26-31.

Published Yes Yes

Mei, C., Zhou, X., and Yang, Y. 2006. Use of RNA interference to dissect defense signaling pathways in rice plants. In “Methods in Molecular Biology: Plant-Pathogen Interactions” Vol. 354: 161-171. Ed. P. Ronald, Humana Press.

Published Yes Yes Park, D.-S., Sayler, R. J., Hong, Y.-G., Nam, M.-H., and Yang, Y. 2008. A method for inoculation and evaluation of rice sheath blight disease. Plant Dis. 92:25-29.

Published Yes Yes Sayler, R. J., and Yang, Y. 2007. Detection and quantification of Rhizoctonia solani AG-1 IA, the rice sheath blight pathogen, in rice using real-time PCR. Plant Dis. 91:1663-1668.

Published Yes Yes

Venu, R.C., Jia Y, Gowda, M., Jia, M.H., Jantasuriyarat, C., Stahlberg, E., Li, H., Rhineheart, A., Boddhireddy, P., Singh, P., Rutger, N., Kudrna, D., Wing, R., Nelson, J.C., and Wang, G-L. 2007. RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Molecular Genetics and Genomics (2007) 278:421–431.

Published Yes Yes

Zhou, X., Bailey, T.A. and Yang, Y. 2006. Signal transduction and pathway interactions in rice disease resistance. In “Model Plants, Crop Improvement”, pp207-225. Eds. R.M.D. Koebner and R.K. Varshney, CRC Press.

Submitted publications (total to March 2008 = 5)

Submitted Yes No Guo, Z., and Nelson, J.C. Multiple-trait QTL analysis with missing phenotypic data . BMG Genetics (Mar 2008)

Submitted Yes No

Nelson, J.C., Sun, X., McClung, A., Fjellstrom, R., Moldenhauer, K., Boza, E., Jodari, F., Oard, J., Linscombe, S., and Guo, Z. QTL mapping for milling-quality traits in a U.S. japonica x indica rice cross. Euphytica (Mar 2008 submitted)

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Category

Includes RiceCAP



(Yes / No)

Citation

Submitted No

Park, C.J., Peng, Y., Bart, R., Chen, X., Ruan, D., Canlas, P., Dardick, C., and Ronald, P. Rice XB15, a protein phosphatase 2C, negatively regulates programmed cell death and XA21-mediated innate immunity. PLos Biol (Mar 2008 submitted)

Submitted Yes No Prasad, B., and Eizenga, G.C. 2008. Rice sheath blight resistance identified in Oryza spp. accessions. Plant Disease 92: (Feb 2008 accepted with revisions)

Submitted No

Sharma, A., McClung, A.M., Pinson, S.R.M., Kepiro, J.L., Shank, A.R., Tabien, R.E., Wang, Y., and Fjellstrom, R.G.. Genetic Mapping of Sheath Blight Resistance QTLs within Tropical Japonica Rice Cultivars. Crop Science (Mar 08 submitted)

Anticipated Publications (total to project completion: 18 + 5 + 38 = 61)

Anticipated na Bellizzi, M., Venu, R.C., and Wang, G.. Disease resistance of RNAi lines to sheath blight pathogen. Phytopathology (Nov. 2008)

Anticipated na Boddhireddy, P., Jannink, J.-L., and Nelson, J.C. Selective advance for accelerated development of recombinant inbred QTL mapping populations. Crop Science (May 2008)

Anticipated na Brooks, S.A. High-resolution mapping of a gene conferring necrotic sensitivity to a Rhizoctonia solani phytotoxin in rice. Phytopathology (Dec 2008)

Anticipated na Brooks, S.A. High-resolution mapping of a gene conferring chlorotic sensitivity to a Rhizoctonia solani phytotoxin in rice. Phytopathology (June 2009).

Anticipated na

Davidson, R., Manosalva, P., VeraCruz, C., Leung, H., and Leach, J.E. Expression patterns of oxalate oxidase-like genes associated with disease resistance QTL on chromosome 8 of Oryza sativa. Molecular Plant-Microbe Interactions (Apr 2008)

Anticipated na Eizenga, G.C. and B. Prasad. Registration of the Bengal/ O. nivara (IRGC 100898) mapping population. Journal of Plant Registrations (Dec 2008)

Anticipated na Eizenga, G.C. and B. Prasad. Registration of the Bengal/O. nivara (IRGC 104705) mapping population. Journal of Plant Registrations (Apr 2009)

Anticipated na Fjellstrom, R., McClung, A., Nelson, J.C., and Lacaze, X. Fine mapping of chalk in MY1. Plant Breeding (Jun 2009)

Anticipated na

Fjellstrom, R., McClung, A., Oard, J., Linscombe, S., Moldenhauer, K., Boza, E., Jodari, F., Roughton, A.I., Dinu, Scheffler, B., Wang, G., Nelson, J.C., Correll, J., Lacaze, X., Rutger, J., Leong, S., and Nguyen, H. Mapping of milling yield QTL in MY2. TAG (Jun 2008)

Anticipated na

Groth, D., Oard, J., Boza, E., Lee, F.N., Zhang, and Moldenhauer, K. Consistency of multiyear phenotypic expression of sheath blight severity rating at different locations. Crop Science (Jun 2008)

41

Category

Includes RiceCAP



(Yes / No)

Citation

Anticipated na

Groth D., Oard, J., Zhang, W., Linscombe, S., Moldenhauer, K., McClung, A., Jia, Y., Correa, F., Liu, G., Fjellstrom, R., Scheffler, B., Dinu, Nelson, J.C., Lacaze, X., Correll, J.C., Utomo, H., Rutger, N., and Leong, S. Identification of SBR QTL in SB2. Theoretical and Applied Genetics (Nov 2008)

Anticipated na Guo, Z., Joehanes, R., and Nelson, J.C. Shrinkage interval mapping for quantitative-trait locus analysis. TAG (May 2008)

Anticipated na

Jia, Y., Liu, G, and McClung, A., and Rutger, N. Registration of a recombinant inbred line population of the cross of Lemont X Jasmine 85 (January 2009). Journal of Plant Registration (Mar 2009)

Anticipated na Jia, Y., Liu, G., Zhou, E., Lee, S., Dai, Y., and Singh, P. Rice diseases: Interactions of rice with pathogens. In a book on “Rice”, Edited by Paul Counce , Blackwell Publishing (May 31 2008).

Anticipated na Jodari, F, Roughton, A., McKenzie, K.S., Moldenhauer, K., and Linscombe, S. Changes in fissuring susceptibility of rice genotypes due to environment. Crop Science (Jun 2009)

Anticipated na Jodari, F, Roughton, A., Andaya, V.C., and McKenzie, K.S. Registration of MY3 mapping population. Journal of Plant Registrations (Jun 2009)

Anticipated na

Jodari, F, Roughton, A., Andaya, V.C., and McKenzie, K.S., Scheffler, B., Dinu, Fjellstrom, R., Nelson, J.C., and Lacaze, X. Mapping of MY QTL in a elite temperate japonica cross (MY3). Crop Science (Jun 2009)

Anticipated na Joehanes, R., Guo, Z., Boddhireddy, P., and Nelson, J.C. QGene 4.0, an extensible QTL analysis software platform. Bioinformatics (May 2008)

Anticipated na Joehanes, R., and Nelson, J.C. Multiple-trait MIM and shrinkage interval mapping. Genet Res Camb (May 2008)

Anticipated na

Lacaze, X., Nelson, J.C., McClung, A., Fjellstrom, R.G., Moldenhauer, K., Jodari, F., Oard, J., and Linscombe, S. Combined QTL analysis of rice milling quality [all MY crosses, Panda x Cypress, etc]. Crop Science (Jul 2008)

Anticipated na

Lee, S.W., Davidson, R., Snelling, J., Oard, J., and Leach, J. Roles of candidate defense response genes in broad spectrum disease resistance contributed by quantitative trait loci. Physiological and Molecular Plant Pathology or Phytopathology (Jul 2008)

Anticipated na

Lee,S.W., Davidson, R., Snelling, J., and Leach, J. Contribution of chitinase to a disease resistance quantitative trait locus in rice. Physiological and Molecular Plant Pathology or Phytopathology (Jul 2008)

Anticipated na Li, L.-C., Wang, Q., and Yang, Y. The secretome of Rhizoctonia solani, the rice sheath blight pathogen. Proteomics (Jun 2008)

Anticipated na Linscombe, S., Oard, J., and Groth, D. Registration of MY2 CPRS/LGRU mapping population. Journal of Plant Registrations (Dec 2008)

42

Category

Includes RiceCAP



(Yes / No)

Citation

Anticipated na

Liu, G., Jia, Y., Correa-Victoria, F., Wang, G., Jia, H. M., McClung, A., Correll, J. C., and Rutger, N. Identification of sheath blight resistance QTLs and mapping candidate genes using a recombinant inbred line population of the cross of Lemont X Jasmine 85 (in preparation). Euphytica (Dec 2008)

Anticipated na

Manosalva, P., Davidson, R., Hulbert, S., Leung, H., and Leach, J.E. Germin-like protein genes contribute to rice blast disease resistance governed by quantitative trait loci. Proceedings of the National Academy of Sciences (Apr 2008)

Anticipated na May, G., Fjellstrom, R., and Scheffler, B.E. SNP discovery and genome characterization of US rice cultivars using a whole genome sequencing approach. The Plant Genome (Dec 2008)

Anticipated na

McClung, A., Kepiro, J., Linscombe, S., Moldenhauer, K., Nelson, J.C., Jodari, F., Oard, J., and Yeater, K. Use of the Winseedle method for evaluating grain dimension and other milling yield traits. Crop Science (Nov 2008)

Anticipated na

McClung, A., Moldenhauer, K., Jodari, F., Linscombe, S., Boza, E., Yeater, K., Fjellstrom, R., and Nelson, J.C. Identification of which sub-component traits are important for milling in several mapping populations. Crop Science (Jun 2009)

Anticipated na Park, C.J., Jung, K., and Ronald, P. Generation of sheath blight resistant lines using a combined transcriptomics and activation tagging approach. Mol. Plant-Microbe Interact. (Nov 2008)

Anticipated na

Pinson, S.R.M., Liu, Wang, G.-L., Jia, Y., Jia, H. M., Fjellstrom, R. G., Sharma, A., and Li, Z. Release of a Population of ‘TeQing’-into-‘Lemont’ Backcross Introgression Lines as a Molecularly Characterized Gene-Mapping Population. Journal of Plant Registrations (May 2008)

Anticipated na

Prasad, B., Eizenga, G.C., and Nelson, J.C. Identification of sheath blight quantitative trait loci in a Bengal/O. nivara (IRGC 100898) BC2F2 population. Theoretical and Applied Genetics (Aug 2008)

Anticipated na

Prasad, B., Eizenga, G.C., and Nelson, J.C. Exploring sheath blight quantitative trait loci in a Lemont/O. meridionalis advanced backcross population. Theoretical and Applied Genetics (Jun 2009)

Anticipated na

Prasad, B., G.C. Eizenga, G.C., Nelson, J.C, and H.A. Agrama. Mapping blast and sheath blight quantitative trait loci in an advanced backcross Bengal/O. nivara (IRGC 104705) population. Crop Science (Jan 2009)

Anticipated na Singh, P, Jia, Y., and et al. Identification of specific differentially expressed genes from rice after infection by the sheath blight pathogen. MPMI (Dec 2008).

Anticipated na

Sreerekha, M.V., Venu, R.C., Nobuta, K., Nelson, J.C., Fjellstrom, R., Meyers, B., and Wang, G-L. Deep transcriptome analysis of developing seeds of rice using massively parallel signature sequencing. Mol. Plant-Microbe Interact. (Apr 2008)

43

Category

Includes RiceCAP



(Yes / No)

Citation

Anticipated na Solomon, W., Scheffler, B., McClung, A., Kanter, D., Oard, J., Zhang, W., Fjellstrom, R., Nelson, J.C., and Rutger, N. Association mapping of US germplasm pool. Crop Sci (Jun 2009)

Anticipated na Wang, Q., Lee, M. W., and Yang, Y. A host cell death-associated Myb transcription factor promotes rice sheath blight susceptibility. Mol. Plant-Microbe Interact. (Jan 2009)

Anticipated na Wang, Y., McClung, A., Pinson, S., Fjellstrom, R. Fine mapping of SBR QTL in RSMT/PCOS cross. TAG (Dec 2008)

Anticipated na

Wang, Y., Pinson, S.R.M., Fjellstrom, R.G., Brooks, S.A., and Jia, Y. Isolation of Two Rice Sheath Blight Resistance QTLs as Mendelian Factors and Development of Molecular Tags to Support MAS. Journal of Plant Registrations (Feb 2009)

44

PUBLICATION HIGHLIGHTS – JANUARY 2007

Bart R, Mawsheng Chern, Chang-Jin Park, Laura Bartley and P Ronald. 2006. A novel system for gene silencing using siRNAs in rice leaf and stem-derived protoplasts. Plant Methods. 2:13.

In dicotyledonous plants, protoplasts have been used for high-throughput studies of gene function. This paper describes development of a protoplast assay for rice, a model monocotyledonous plant. We report a system for isolation, transformation and gene silencing within rice protoplasts. This system provides a powerful tool for rapid in vivo functional studies of large numbers of rice genes.

Brooks, S.A. 2006. Sensitivity to a host-selective toxin from Rhizoctonia solani 2 correlates with sheath blight susceptibility in rice. Phytopathology (in press) The purpose of the work presented in this manuscript is to describe a new method to screen for sheath blight resistance in rice, a disease which results in over $50 M in yield loss and control expenses in the southeastern rice growing areas in the U.S. Limited improvement in disease resistance has been achieved through traditional breeding and screening methods. A primary limitation to any analysis of sheath blight resistance has been accurate disease ranking. The disease is highly influenced by unrelated plant traits (such as plant height) and the environment. The new method exploits a known virulence factor produced by the pathogen, which is a host-selective toxin. By using the purified toxin in place of the pathogen, many confounding disease factors are circumvented and a more accurate phenotype can be obtained. Sensitivity to the toxin is positively correlated with disease susceptibility, allowing the toxin to be used for eliminating susceptible germplasm and mapping toxin sensitivity genes. In this manuscript we describe the new method directly, and its utility for identifying disease susceptible germplasm. Furthermore, we describe the genetic regulation of toxin sensitivity and the ability to identify the corresponding genes. Chu, Q.R., S.D. Linscombe, M.C. Rush, D.E. Groth, J. Oard, X. Sha, and H.S. Utomo. 2006. Registration of a C/M Doubled Haploid Mapping Population of Rice. Crop Sci. 46:1417. Sheath blight disease, caused by the fungus Rhizoctonia solani, is a major impediment to high grain yield and quality for rice producers in the southern U.S. All major commercial varieties are susceptible to this disease and over $50 M is expended annually on chemical control in the southeastern U.S. The RiceCAP Project has dedicated considerable effort in that last three years to discover genes or chromosomal regions that confer resistance to sheath blight disease. The ultimate goal is to breed new varieties by conventional means that carry and express these disease resistant genes.

Toward that effort, the RiceCAP Project has developed the SB2 genetic mapping population derived from crossing or hybridization of a popular commercial variety that is susceptible to sheath blight with a second strain that is highly tolerant. Hybrid or F1 plants from this cross

45

were planted in the greenhouse until the “boot stage” where anthers with pollen grains were removed from young developing flowers and placed on medium in the laboratory containing hormones, sugars, vitamins and other ingredients. After a period of three weeks on the medium, the anthers produced small clumps of cells that later gave rise to roots, shoots, and eventually 325 adult fertile plants. This “anther culture” procedure was important because there was considerable variation for sheath blight resistance and other traits among the 325 plants, while at the same time, each of the 325 plants grown to the next generation was genetically pure.

Field observation of the SB2 population in 2004 revealed substantial variation for different agronomic traits such as seedling vigor, plant height, and heading date. Available data on each of the 325 lines can be accessed of the GRIN web page (www.ars-grin.gov) as GSOR 200001 to 200325. SB2 has been placed in the GSOR collection at Stuttgart, AR. Limited amounts (ca. one quarter gram or 10 seeds of each line) may be obtained by contacting the GSOR, Dale Bumpers National Rice Research Center, USDA-ARS, P.O. Box 1090, Stuttgart,

AR 72160. Jia, Y., Correa-Victoria, F., McClung, A., Zhu, L., Liu, G., Wamishe, Y., Xie, J., Marchetti, M. A., Pinson, S. R. M., Rutger, J. N., and Correll, J. C. 2007. Rapid determination of rice cultivar responses to the sheath blight pathogen Rhizoctonia solani using a micro-chamber screening method. Plant Dis. 91:485-489. Sheath blight disease of rice, caused by the fungus Rhizoctonia solani, is one of the most important diseases of rice in the United States. The disease causes over $ 50 million in losses to rice growers annual in the southeastern U.S.. Losses occur as a direct impact of the disease on yield as well as the cost of management practices that are required such as fungicide application. Sheath blight disease is favored by many factors used in commercial rice production practices such as high nitrogen inputs. Environmental conditions in the southeast also typically favor disease development. Traditionally, breeders have had limited success in improving commercial rice varieties for resistance to sheath blight because of the difficulty in getting consistent conditions for screening and evaluating germplasm for resistance. In this study, a standardized greenhouse screening method was developed to evaluate rice germplasm for resistance to this disease. Furthermore, disease reactions in the greenhouse screening method were consistent with those observed under field conditions. The standardized screening protocol will allow breeders to make more accurate and faster selections for sheath blight resistance and thereby expedite the improvement of sheath blight resistant commercial rice varieties.

Venu, R.C., Yulin Jia, Malali Gowda, Melissa H. Jia, Chatchawan Jantasuriyarat, Eric Stahlberg, Huameng Li, Andrew Rhineheart, Prashanth Boddhireddy, Pratibha Singh, Neil Rutger, David Kudrna, Rod Wing, James C. Nelson, Guo-Liang Wang. 2007. RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Molecular Genetics and Genomics (in press) Sheath blight caused by the fungal pathogen Rhizoctonia solani is an economically important problem in the US and other rice producing countries. Breeding resistant rice cultivars is challenging due to the quantitative nature of host resistance to R. solani and the lack of highly effective germplasm. To elucidate the mechanisms by which the rice plant defends

46

itself from the pathogen, RNA isolated from R. solani-infected leaves of Jasmine 85 was used for both RL-SAGE library construction and microarray hybridization. RL-SAGE sequence analysis identified 20,233 and 24,049 distinct tags from the control and inoculated libraries, respectively. Nearly half of the significant tags (>2 copies) from both libraries matched TIGR annotated genes and KOME full-length cDNAs. Among them, 42% represented sense and 7% antisense transcripts, respectively. Interestingly, 60% of the library-specific (>10 copies) and differentially expressed (>4.0 fold change) tags were novel transcripts matching genomic sequence but not annotated genes. About 70% of the genes identified in the SAGE libraries showed similar expression patterns (up or down-regulated) in the microarray data obtained from three biological replications. Some candidate RL-SAGE tags and microarray genes were located in known sheath blight QTL regions. The expression of ten differentially expressed RL-SAGE tags was confirmed with RT-PCR. The defense genes associated with resistance to R. solani identified in this study are useful genomic materials for further elucidation of the molecular basis of the defense response to R. solani and fine mapping of target sheath blight QTLs.

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PUBLICATION HIGHLIGHTS – APRIL 2008

Jung, K., An, G., and Ronald, P. Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nature Reviews Genetics 9, 91-101 (February 2008) | doi:10.1038/nrg2286

This publication presents a comprehensive review on the methodologies available to examine and validate the function of the estimated 41,000 genes hypothesized to be present in rice. A wide range of genomic tools, many of which are being employed by the RiceCAP project, are discussed that can be used to facilitate and determine the function of various rice genes and the effect they have on particular agriculturally important traits. The tools and approaches discussed have broad practical implications for developing a thorough understanding of how rice genes function and the impact they have on important complex traits. Many new molecular tools, some of which are being developed and utilized by the RiceCAP effort, are beginning to provide valuable information toward our understanding of the rice genome. Acknowledgements for this publication: We thank B. C. Meyers, L. Bartley, C. Dardick, L. Comai,D. Neale, J. Schroeder, J. Leach, G. L. Wang, K. Shimamoto,V. Sundaresan and R. C. Buell for comments and discussions. We also thank S. Ouyang, Y. S. Lee and P. Cao for helping to generate tables and figures. This work was supported by National Institutes of Health grants 5R01GM055962-0 United States Department of Agriculture grant 2004-63560416640 and National Science Foundation grants DBI-0313887 to P. R., the 21st Century Frontier Program CG1111 and Biogreen 21 Program to G. A, Korea Research Foundation grant 2005-C00155 to K. H. J.

Kumar, R., Qiu, J., Joshi, T., Valliyodan,B., Xu, D., and Nguyen, H. (2007) Single Feature Polymorphism Discovery in Rice. PLoS ONE 2(3): e284. doi:10.1371/ journal.pone.0000284

A commercially produced microchip array, originally designed to study rice gene expression changes, was tested as a way to discover genetic markers between unsequenced rice varieties. DNA from three rice parents used in gene mapping studies was fluorescently labeled and carefully annealed to a microchip array containing 49,824 gene probe sites. With each probe site being 24 DNA nucleotides in length, analyzing the chip to detect the presence or absence of a perfect match at each probe allowed the high-throughput comparison of DNA sequences at ~630,000 sequence points. The presence of a perfect match is estimated from the degree of fluorescence detected at each probe site on the microchip. Non-perfect matches between the probe DNA sequence (on the chip) and the fluorescently labeled DNA sequence (from the varieties tested) result from a DNA nucleotide deletions, insertions, or substitutions, collectively called “single feature polymorphisms” (SFPs), between the chip and tested variety sequences being compared. The accuracy of this method was seen to be dependent on the sequence match sensitivity level chosen in the analyses, such that many SFPs were detected at a relatively relaxed level of fluorescence intensity and fewer SFPs found at higher fluorescence intensity levels, but with higher error rates seen at relaxed SFP detection levels. At an expected 90% success rate, 6,865 candidate SFPs were identified between closely

48

related varieties and 63,420 candidate SFPs between distantly related varieties. This expansive comparison technique provided a new way to identify genetic markers for complex gene mapping studies throughout the rice genome, including areas where marker polymorphisms were not previously found. This approach will allow RiceCAP to more accurately develop markers linked to economically important traits such as sheath blight resistance and milling yield.

Acknowledgements for this publication: We are thankful to DNA Core facility; University of Missouri-Columbia for performing microarray and sequencing. The help from Tonya Mueller, Division of Plant Science, University of Missouri-Columbia in preparing figures is highly appreciated. We thank to staff of Sears Green house facility at University of Missouri-Columbia for growing rice plants.

Leach, J.E., Davidson, R., Liu, B., Manosalva, P., Mauleon, R., Carrillo, G., Bruce, M., Stephens, J., Maria Genaleen Diaz, Nelson, R., Vera Cruz, C., and Leung, H. 2007. Understanding Broad-Spectrum, Durable Resistance in Rice. Pages 191-209 in Rice Genetics V, D S Brar, D Mackill & B Hardy, eds. World Scientific Publ. Co.

A major limitation to traditional breeding efforts is the development of resistant cultivars of a given crop that, upon widespread cultivation, are soon overcome by new strains of a pathogen. This short-term resistance continues to be problematic in many crops including rice. In order to develop long-term, or durable resistance in rice, it is important that a comprehensive understanding of the genes that are involved in disease resistance be developed. There are several major groups involved in disease resistance including genes which recognize invasion, defense response genes, or those that respond to infection, and genes that regulate the defense response genes. The identification of such genes and the complex interaction of such genes is the focus of extensive investigation. One of the RiceCAP goals is to identify which defense response genes are involved in sheath blight resistance, where they are located, and how they work in concert with other defense related genes. Efforts have identified regions, or large sections of the rice genome that contain disease response genes or loci. Currently, molecular markers that are linked to these regions are being utilized to develop rice germplasm that contains various regions with these particular traits in order to assess what effect they will have on disease resistance. Thus, the tools being developed could have broad applicability to disease resistance in general.

Acknowledgements for this publication: This work was supported by the USDA-CSREES-NRI, Rockerfeller Foundation, USAID, Generation Challenge Program, and Colorado State University Agricultural Experiment Station.

Note: Correspondence from Dr. Jan Leach on 11/16/07 confirms that the USDA-CSREES-NRI support was provided specifically through the RiceCAP grant.

Park, D.S., Sayler, R.J., Hong, Y.G. and Yang, Y. 2008. A method for inoculation and evaluation of rice sheath blight disease. Plant Dis. 92:25-29.

Sheath blight disease of rice remains one of the most important diseases of rice worldwide occurring in over up to 50% of all global rice production areas. This disease is favored by an increased intensification of global agricultural practices such as increase nitrogen rates,

49

higher planting densities, etc. Quantifying resistance to sheath blight continues to present challenges to researchers and breeders trying to screen for resistance to this disease. An improved greenhouse screening method was developed that can consistently and accurately quantify disease reactions in this host-pathogen system. Such an improved screening method could potentially save months, or even years in the ability to develop rice cultivars that have enhanced levels of sheath blight resistance under commercial production practices.

Acknowledgements for this publication: This study was supported by Korea Research Foundation oversea training fellowship (M01-2005-000-10120-0 to D.-S. Park) and the United States Department of Agriculture (USDA)/NRI Rice Coordinated Agricultural Project grant (2004-35317-14867 to Y. Yang). We thank Y. Jia at SDA–Agricultural Research Service Dale Bumpers National Rice Research Center for providing R. solani isolate RR0140 and R. McNew at the University of Arkansas for assistance with the statistical analysis.

Prasad, B., and Eizenga, G.C. Sheath blight resistance identified in Oryza spp. accessions. Plant Disease (Feb 08; accepted with revisions)

Sheath blight is a major disease of rice in the USA and worldwide. Some rice cultivars, found in various rice growing areas of the world, have been identified as moderately resistant to sheath blight but no resistant cultivars have been discovered to date. Wild relatives of rice (Oryza species) are another source of novel sheath blight resistance genes. Two of these species, Oryza rufipogon and Oryza nivara, are the ancestors of cultivated rice. In other words, these are plant species that humans domesticated in prehistoric times to select what is now known as cultivated rice (Oryza sativa). Rice wild relatives are often a source of new pest resistance genes that can be incorporated into our currently grown rice varieties to improve pest resistance. Most all testing of rice cultivars for their reaction to the sheath blight disease is done in the field. Because the rice wild relatives drop seed very easily (shatter) and cannot be grown in the field, a different method is needed to evaluate them for sheath blight resistance. Three different methods were used to evaluate the reaction of 73 Oryza species accessions originating from different areas of the world to the sheath blight disease. Seven accessions were identified as moderately resistant to sheath blight. These accessions represent the species Oryza barthii, Oryza meridionalis, Oryza nivara and Oryza officinalis. Efforts are now underway to further identify the sheath blight resistance gene(s) and incorporate this resistance into rice varieties adapted to the United States. These U.S. adapted, sheath blight resistant lines will eventually be used by rice breeders to develop new and improved rice varieties that are resistant to the sheath blight disease.

Acknowledgements for this publication: The work was supported in part by the USDA Cooperative State Research, Education and Extension Service – National Research Initiative – Applied Plant Genomics Program entitled “RiceCAP: A coordinated research, education, and extension project for the application of genomic discoveries to improve rice in the United States” (USDA/CSREES grant 2004-35317-14867).

Venu, R.C., Jia Y, Gowda, M., Jia, M.H., Jantasuriyarat, C., Stahlberg, E., Li, H., Rhineheart, A., Boddhireddy, P., Singh, P., Rutger, N., Kudrna, D., Wing, R., Nelson, J.C., and Wang, G-L. 2007. RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Molecular Genetics and Genomics (2007) 278:421–431.

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Sheath blight caused by the fungal pathogen Rhizoctonia solani is an economically important problem in the US and other rice producing countries. Breeding resistant rice cultivars is challenging due to the quantitative nature of host resistance to R. solani and the lack of highly effective germplasm. To elucidate the mechanisms by which the rice plant defends itself from the pathogen, RNA isolated from R. solani-infected leaves of Jasmine 85 was used for both RL-SAGE library construction and microarray hybridization. RL-SAGE sequence analysis identified 20,233 and 24,049 distinct tags from the control and inoculated libraries, respectively. Nearly half of the significant tags (>2 copies) from both libraries matched TIGR annotated genes and KOME full-length cDNAs. Among them, 42% represented sense and 7% antisense transcripts, respectively. Interestingly, 60% of the library-specific (>10 copies) and differentially expressed (>4.0 fold change) tags were novel transcripts matching genomic sequence but not annotated genes. About 70% of the genes identified in the SAGE libraries showed similar expression patterns (up or down-regulated) in the microarray data obtained from three biological replications. Some candidate RL-SAGE tags and microarray genes were located in known sheath blight QTL regions. The expression of ten differentially expressed RL-SAGE tags was confirmed with RT-PCR. The defense genes associated with resistance to R. solani identified in this study are useful genomic materials for further elucidation of the molecular basis of the defense response to R. solani and fine mapping of target sheath blight QTLs.

Electronic supplementary material: The online version of this article (doi:10.1007/s00438-007-0260-y) contains supplementary material, which is available to authorized users.

Acknowledgements for this publication: We thank CuWanda Flowers for excellent technical support. Financial support for this project came from the RiceCAP project of the USDA-NRI, National Program NP301 on “Genomic characterization of rice germplasm”, the University

of Arkansas Rice Research and Promotion Board on “Development of molecular strategies to control rice sheath blight disease” and the NSFPlant Genome Research Program (#0115642

and #0321437).

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RICECAP MEETING ABSTRACTS AND SCIENTIFIC PRESENTATIONS

(Master List; total to December 2007 = 64)

Boza, E.J., Moldenhauer, K.A.K., Gibbons, J.W., Lee, F.N., Cartwright, R.D., Jia, Y., Boyett, V., and Blocker, M.M. 2006. RiceCAP (MY1) Mapping Population in Arkansas. Field day. Rice Research and Extension Center, Stuttgart, AR. August 9, 2006. Boza, E.J., Moldenhauer, K.A.K., Gibbons, J.W., Lee, F.N., Cartwright, R.D., Jia, Y., Boyett, V., and Blocker, M.M. 2006. Field and milling quality analysis of the MY1 mapping population in Arkansas. 31st RTWG. The Woodlands, TX. Feb. 26-28, 2006. Brooks, S.A. “Genomic Research for Rice Improvement”. RiceCAP outreach program (Korth), Agriculture Extension Center, University of Arkansas, Lonoke, AR, 2006. Brooks, S.A. 2006. Cultivar specific response to the host-selective toxin produced by Rhizoctonia solani, the causal pathogen of sheath blight disease of rice. Phytopathology 96:S16. Brooks, S.A. Differential response of rice cultivars to RS toxin, a pathogenicity factor in Sheath Blight disease of rice. 31st RTWG. The Woodlands, TX. Feb. 26-28, 2006. Davidson, R., Manosalva, P., Vera Cruz, C., Leung, H., Leach, J. 2006. Expression patterns of oxalate oxidase-like genes associated with blast resistance QTL on chr. 8 of O. sativa. Pp. 148-152 in Biology of Plant-Microbe Interactions, Vol 5, eds. F. Sanchez, C. Quiton, I. Lopez-Lara, and O. Geiger. IS-MPMI Press, Minneapolis. Davidson, R., Manosalva, P., Vera Cruz, C., Leung, H., Leach, J. 2006. Expression patterns of oxalate oxidase-like genes associated with blast resistance QTL on chromosome 8 of Oryza sativa. 5th International Rice Genetics Symposium and the 3rd International Rice Functional Genomics Symposium, Manila, Philippines, November 2005. Davidson, R., Manosalva, P., Vera Cruz, C., Leung, H., Leach, J. 2006. Expression patterns of oxalate oxidase-like genes associated with blast resistance QTL on chromosome 8 of Oryza sativa. Selected oral presentation at the XII International Congress on Molecular Plant-Microbe Interactions in Merida, Mexico, December 2005. Eizenga, G.C., Agrama, H.A., and Lee, F.N. Mapping R-genes in rice wild relatives (Oryza spp.) Proc. Rice Technical Working Group. The Woodlands, Texas. 26 Feb.-1 Mar. 2006. Eizenga, G.C., Agrama, H.A., Prasad, B., Bryant, R.J., Neves, P.F., Mackill, D.J. 2007. Developing mapping populations between U.S. rice cultivars and selected O. nivara accessions. 5th International Symposium of Rice Functional Genomics, Tsukuba, Japan, Oct. 15-17, 2007.

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Fjellstrom R. 2005. How to Map a Marker Associated with a Major Gene. Markers Unleashed: An overview of DNA marker technology as it applies to rice improvement. RiceCAP Marker Assisted Breeding Workshop, June 14-16, 2005, Stuttgart, AR. Fjellstrom, R. G., Linscombe, S., Oard, J., Moldenhauer, K.A.K., Boza, E., Jodari, F., Nelson, J.C., Yeater, K. and McClung, A. 2007. RiceCAP: Identification Of QTL Associated With Rice Milling Yield In A Long Grain Cross. Plant and Animal Genome Conf. Poster, Abstract for Plant and Animal Genome XV Conference, Jan 13-17, 2007, San Diego, CA Guo, Z., Nelson J. C. 2007. Shrinkage interval mapping for QTL and QTL epistasis analysis in line crosses. Poster, Plant and Animal Genome XV Conference, Jan 13-17, 2007, San Diego, CA. Jia, Y., Rutger, J.N. and Xie, J. 2005. Development and characterization of rice mutant populations for functional genomics of host-parasite interactions. Phytopathology 95:S48. Jia, Y., Singh, P., Jia, M.H., Wang, G., Wamishe, Y., Zhu, L and Zhou, E. Development of molecular strategies to control rice sheath blight disease. 31st RTWG. The Woodlands, TX. Feb. 26-28, 2006. Jia, Y. Wang, G. - L., and Valent, B. Compare and contrast invasive growths and global gene expressions of rice after infections with rice blast and sheath blight pathogens. Proc. 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Jodari, F. and Y. Roughton. California Rice Field Day, 2006. ‘ RiceCAP efforts in California; The Focus on Fissuring resistance.’ Biggs, CA. Jodari, F., Roughton, A.I., Fjellstrom,R.G., Scheffler, B., and Nelson, J.C. 2008. Factors contributing to milling quality differences in MY3, a ‘RiceCAP’ project milling population. Proc. 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Korth, K.L. (2006). An overview of the RiceCAP goals, outreach efforts, and the teacher workshop, was presented in a poster at the annual meeting of the American Society of Plant Biologists. Education and Outreach Efforts of the Rice Coordinated Agriculture Project – RICECAP. August 3rd -6th, 2006, Boston, MA. Leach, J. 2007. Durable Disease Resistance in Plants. First RR Nelson Memorial Lecture, Department of Plant Pathology, Penn State University, April 15-16. Leach, J. Approaches to Broad-Spectrum Durable Disease Resistance. Seminar speaker, Department of Botany, University of Sao Palo, Brazil. March 2, 2007. Leach, J. Associating genomic variation of diverse rice varieties to understand disease resistance. Invited Symposium speaker, Stadler Genetic Symposium, Columbia, MO October 2-4, 2006.

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Leach, J. Gene Candidates for Broad-Spectrum Durable Resistance in Rice. Invited Symposium speaker 4th International Symposium on Rice Functional Genomics, Montpellier, France, October 9-11, 2006. Leach, J. Understanding Durable Resistance. Invited Symposium speaker, Northeast Division Meetings of the American Phytopathological Society, Burlington, VT November 7-9, 2006. Leach, J., P. Manosalva, R. Davidson, S. Lee, M. Bruce, M. Genaleen Diaz, B. Liu, C. Vera Cruz, H. Leung. Approaches to Durable Resistance in Rice. Invited Symposium Speaker, Cold Spring Harbor Symposium: Plant Genomics. Cold Spring Harbor, NY March 13-15, 2007. Leach, J., P. Manosalva, R. Davidson, S. Lee, M. Bruce, M. Genaleen Diaz, B. Liu, C. Vera Cruz, H. Leung. Gene Candidates for Broad-Spectrum Durable Resistance in Rice. Invited Symposium Speaker, Cold Spring Harbor Symposium: Plant Genomics. Leach, J., P. Manosalva, R. Davidson, S. Lee, M. Bruce, M. Genaleen Diaz, B. Liu, C. Vera Cruz, H. Leung. Gene Candidates for Broad-Spectrum Durable Resistance in Rice. Invited Symposium Speaker, International Symposium in Brazil on Molecular Genetics of Plants , Natal, Brazil. March 5-7. Leach, J.E. 2006. Understanding Broad-Spectrum, Durable Resistance in Rice. Symposium speaker at the 5th International Rice Genetics Symposium and the 3rd International Rice Functional Genomics Symposium, Manila, Philippines, November 2005. Leong, S. A., Tian, S., and Splinter BonDurant, S. Discovery of Genomic DNA Polymorphisms using Oligonucleotide Arrays. 31st RTWG. The Woodlands, TX. Feb. 26-28, 2006. Liu, G., Y. Jia, M.H. Jia, R.G. Fjellstrom, A. Sharma, Z. Li, and S.R.M. Pinson. 2007. Molecular Characterization of a Population of Backcross Introgression Lines Derived from Crossing the US Japonica Rice Cultivar ‘Lemont’ as the Recurrent Parent with the Chinese Indica Cultivar ‘TeQing’. Plant and Animal Genome XV, January 13-17, 2007, San Diego, CA; http://www.intl-pag.org/15/abstracts/PAG15_P05b_240.html Liu, G., Jia, Y., Correa, V.F., Jia, M.H., McClung, A., and Correll, J.C.. Identification of Sheath Blight Resistance QTLs in Rice Using Recombinant Inbred Line Population of Lemont�Jasmine 85. Proc. 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Liu, G., Jia, M.H., Jia, Y., McClung, A., Correll, J.C and Rutger, J.N. Molecular Characterization of the Recombinant Inbred Line Population of the Cross of Lemont with Jasmine 85. Proc. 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. McClung, A., Boza, E., Fjellstrom, R.G., Guo, Z., Jodari, F., Linscombe, S., Moldenhauer, K.A.K., Nelson, J.C., Oard, J.H., Scheffler, B. and Sun, X. 2007. RiceCAP: Development of

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molecular markers associated with long grain milling. AACC International Annual Meeting Oct.7-10, 2007, San Antonio, TX. McClung, A.M., Groth, D.E., J. H. Oard, H. Utomo, Moldenhauer, K.A.K., Boza, E., Scheffler, B., Jia, Y., Liu, G., Correa, F., and Fjellstrom, R.G. 2007. Development and Characterization of RiceCAP QTL Mapping Population for Sheath Blight Resistance. ASA Meeting New Orleans, LA Nov. 3-9. Mysore, S., Venu, R.C., Nobuta, K. Meyers, B.C., Wang, G-L. Analysis of Developing Seed Transcriptomes of Rice Using Massively Parallel Signature Sequencing. Poster presented at the ASPB Annual meeting in Chicago, July 7-11, 2007. Nelson J. C. 2006. Basic data relations for markers, traits, and genotypes. Markers, Mapping, and Beyond: RiceCAP second annual marker workshop, June 4-9, 2006, Ardmore, OK. Nelson J. C. 2006. Constructing linkage maps in plants: theory and practice. Markers, Mapping, and Beyond: RiceCAP second annual marker workshop, June 4-9, 2006, Ardmore, OK. Nelson, J.C. 2005. Basics of QTL analysis. Markers Unleashed: An overview of DNA marker technology as it applies to rice improvement. RiceCAP Marker Assisted Breeding Workshop, June 14-16, 2005, Stuttgart, AR. OryzaSNP Discovery Workshop held at The 5th International Symposium of Rice Functional Genomics, Oct 16, Tskuba, Japan. Coordinated by J. Leach with presentations by K. McNally (IRRI), K. Childs (MSU), R. Davidson (CSU), Mashiro Yano (NIAS), H. Leung (IRRI). The 3 h workshop purpose was to introduce the rice research community to the OryzaSNP data set. RiceCap funded travel for Rebecca Davidson and Kevin Childs, who presented at the workshop. Park, D.S., Sayler, R.J., Hong, Y.G., and Yang, Y. 2006. An improved method for the inoculation and evaluation of sheath blight. The 31st Meeting of Rice Technical Working Group, Woodlands, Texas, Feb. 26- Mar.1, 2006. Pinson SRM. 2005. Development and handling of plant materials for marker analysis. Markers Unleashed: An overview of DNA marker technology as it applies to rice improvement. RiceCAP Marker Assisted Breeding Workshop, June 14-16, 2005, Stuttgart, AR. Pinson SRM. 2005. Putting sheath blight resistance genes to work in the rice field. Texas Rice, July 2005 edition, Special section, pp. VIII-IX;http://beaumont.tamu.edu/eLibrary/Newsletter/2005_Highlights_in_Research.pdf Pinson, S.R.M. New Molecular Tools For Breeders. Rice Field Day, Beaumont, TX - July 13, 2006. (Oral)

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Pinson, S.R.M. Incorporating Foreign Sheath Blight Resistance Genes into US Rice Germplasm. Texas Rice, July 2006 edition, Special section, pp. VI-VII; http://beaumont.tamu.edu/eLibrary/Newsletter/2006_Highlights_in_Research.pdf. 2006. Pinson, S.R.M., J.H. Oard, D. Groth, R. Miller, G. Liu, Y. Jia, M.H. Jia, and R.G. Fjellstrom. 2007. New Breeding Parents Containing Novel QTL for Rice Sheath Blight Resistance Identified by Combining Phenotypic and Molecular Characterizations. Poster Abstract for Plant and Animal Genome XV Conference, Jan 13-17, 2007, San Diego, CA Pinson, S.R.M., Jia, Y., Oard, J.H., Fjellstrom, R.G., Jia, M.H., Hulbert, S., Liu, K. and Nelson, C. Bringing Quantitative Traits Under Breeder Control by Combining QTL Mapping with Candidate Gene Approaches: A Case Study of Rice Sheath Blight Resistance Proc. 31st Rice Tech. Work. Group Meet., The Woodlands, TX in press Feb. 26 - March 1, 2006. Pinson, S. R.M., Wang, Y., Liu, G., Jia, M.H., Jia, Y., Sharma, A. and Fjellstrom, R.G. 2008. Using a Set of TeQing-into-Lemont Chromosome Segment Substitution Lines for Fine Mapping QTL: Case Studies on Sheath Blight Resistance, Spreading Culm, and Mesocotyl Elongation. Oral presentation for 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Prasad, B. and Eizenga, G.C. Developing a Bengal / O. nivara advanced backcross mapping population to identify sheath blight QTL. Proc. 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Prasad, B. and Eizenga, G.C. Development of mapping populations using sheath blight resistant wild species. Field day. Rice Research and Extension Center, Stuttgart, AR. August 8, 2007. Ronald, P. Candidate genes for sheath blight resistance. RiceCAP Annual Meeting, Feb 23-25, Houston Texas Ronald, P. Candidate genes for sheath blight resistance. RiceCAP Annual Meeting, June 12-16, Little Rock, Arkansas Ronald, P. Genetic engineering and agriculture. Rice technical working group. Houston, Feb 25, 2006. Roughton, A.I., Jodari, F., Moldenhauer, K.A.K., Linscombe, S.D., and McClung, A.M. Refining induced fissuring procedures used in characterization of ‘RiceCAP’ milling populations. Poster, 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Sharma, A., Kepiro, J., R.G. Fjellstrom, S.R.M. Pinson, A.R. Shank, A.M. McClung, R.E.Tabien. Mapping sheath blight resistance QTL(s) in rice. Plant and Animal Genome XIV, San Diego, CA; http://www.intl-pag.org/pag/14/abstracts/PAG14_P244.html . Jan.14-18, 2006.

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Sharma, A., J. Kepiro, S.R.M. Pinson, R.G. Fjellstrom, R.E. Tabien, R. Shank, and A.M. McClung. RiceCAP - Mapping Sheath Blight Resistance QTL(s) in Tropical Japonica Rice. Proc. 31st Rice Tech. Work. Group Meet., The Woodlands, TX in press Feb. 26 - March 1, 2006. Scheffler, B.E. SNP discovery and utilization: Are we finally looking at the holy grail of blending plant breeding and molecular biology? Proc. 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Snelling, J., R. Davidson, J. E. Leach. 2007. Hydrogen peroxide accumulation and oxalate oxidase activity correlate with quantitative disease resistance in rice. Annual Mtg of the American Society of Plant Biologists, Chicago, Ill. July 8. Poster Presentation. Utomo, H.S. 2005. RiceCAP update. Rice Research Station News Vol. 2(2). p.4. Utomo, H.S., I. Wenefrida, S.D. Linscombe, D. Groth, X. Sha, and J. Oard. 2006. Preliminary marker genotyping of sheath blight mapping population SB2. Rice Research Station Field Day (poster). Wang, Y., Pinson, S.R.M., Fjellstrom, R.G., Sharma, A., Brooks, S., Tabien, R.E. 2008. Using TeQing-into-Lemont Introgression Lines (TILs) to Dissect Sheath Blight Resistance QTLs and Fine-Map a Spreading Culm Gene. Poster at 32nd Rice Technical Working Group. San Diego, California. 18-20 Feb. 2008. Wang GL. SAGE and microarray analysis of the rice defense transcriptome during Rhizoctonia solani infection. Invited oral presentation at the APS/CPS/MSA Joint meeting, Quebec, Canada 7/28-8/2, 2006. Wang, G.-L. Deep Transcriptome analysis of the rice and rice blast genomes using LongSAGE and MPSS Technologies. International Conference on the Frontier of Plant Molecular Biology, Oct. 26-29, Shanghai, China. Wang, G.-L. SAGE and MPSS profiling of sheath blight resistance and milling quality. RiceCAP Annual Meeting, June 12-16, Little Rock, Arkansas Zhou, Y., Bailey, T.A. and Yang, Y. 2006. Antigonistic interaction of ethylene and abscisic acid signaling modulates disease resistance and abiotic stress tolerance in rice. The 31st Meeting of Rice Technical Working Group, Woodlands, Texas, Feb. 26- Mar.1, 2006.

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RICECAP/CSREES ACKNOWLEDGEMENT LANGUAGE

Please continue to acknowledge RiceCAP (USDA-CSREES NRI) funding in posters, presentations, and publications. This should include the RiceCAP logo along with the CSREES logo which can be located on the RiceCAP website at http://www.uark.edu/ua/ricecap/ .

Also, publications resulting from RiceCAP support should acknowledge that support as follows:

The work was supported (in part?) by the USDA Cooperative State Research, Education and Extension Service – National Research Initiative – Applied Plant Genomics Program entitled “RiceCAP: A coordinated research, education, and extension project for the application of genomic discoveries to improve rice in the United States” (USDA/CSREES grant 2004-35317-14867)

CSREES would like to continue to publicize high impact results from its funded projects. A brief 250 word “non-technical” write up of the project results is most useful. Copies of publications, public relations material, brochures, newspaper articles, abstracts, high quality photographs or images that depict your research or other funded activities are always welcome. Please email this information to me as a WORD, PDF or jpg file if possible. Also, please make sure this info is communicated to Yinong Yang who is collating this for the RiceCAP project.

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PERSONNEL LISTING THROUGH END-OF-GRANT

(AUGUST 31, 2008)

ricecap year 4 setting priorities, response to boards, … · ricecap year 4 setting priorities,...

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