Source: LOUISIANA STATE UNIVERSITY submitted to
DEVELOPMENT OF RICE GERMPLASM USING MOLECULAR AND CONVENTIONAL GENETIC APPROACHES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0216107
Grant No.
(N/A)
Project No.
LAB93929
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2008
Project End Date
Sep 30, 2013
Grant Year
(N/A)
Project Director
Oard, J.
Recipient Organization
LOUISIANA STATE UNIVERSITY
202 HIMES HALL
BATON ROUGE,LA 70803-0100
Performing Department
School of Plant, Environmental, and Soil Sciences
Non Technical Summary
Dr. Oard has recently developed DNA markers for imazethapyr (Newpath) herbicide resistance and grain aroma in rice. Different combinations of these markers could facilitate breeding efforts for U.S. rice. All public U.S. breeding programs are now using DNA marker technology. The use of markers has shown promise during the development of new populations for Dr. Sha's breeding program. Dr. Oard is a Co-PI in the USDA-funded RiceCAP project to identify DNA markers for sheath blight resistance and whole-grain milling yield. Candidate markers have been identified from RiceCAP that will be evaluated by Dr. Oard against different lines, varieties, and populations. The production of hybrid rice varieties with higher yields over standard inbred varieties is one approach that is gaining momentum in the U.S. rice industry. Dr. Oard has initiated exploratory research for development of certain inbred lines adapted specifically to Louisiana that would be used for development of hybrid rice. New statistical approaches that increase power and precision in data mining and analyses will be part of the proposed research effort in 2008-2012. Sheath blight disease is considered, along with rice blast, as the most economically significant constraint for high yield and quality of rice in Louisiana. The proposed research will combine multiple sources of resistance by both traditional methods and DNA marker technology as described above to develop disease resistant germplasm.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011530108040%
2021530108020%
2041530108110%
2121530108110%
9012410108020%
Knowledge Area
202 - Plant Genetic Resources; 901 - Program and Project Design, and Statistics; 204 - Plant Product Quality and Utility (Preharvest); 212 - Pathogens and Nematodes Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1530 - Rice; 2410 - Cross-commodity research--multiple crops;

Field Of Science
1080 - Genetics; 1081 - Breeding;
Goals / Objectives
1. Identification and application of DNA markers for enhancement of aroma, amylose content, gelatinization temperature, rice blast resistance, sheath blight resistance and grain quality in U.S. rice germplasm 2. Development of adapted germplasm for Louisiana hybrid rice 3. Development of new statistical approaches for association genetics in rice 4. Development of sheath blight resistant rice by conventional breeding methods
Project Methods
Dr. Oard's laboratory has recently initiated cooperative research with Dr. Sha to evaluate the potential of SNP markers for development of new Louisiana aromatic varieties with disease resistance and acceptable cooking characteristics. Future work will involve expanded use of markers and screening of additional breeding lines. When the final analyses are complete, Dr. Oard will evaluate the candidate markers in his sheath blight resistance crossing program described in Objective 4. The SVR and RFR non-linear approaches described in Objective 3 will be applied to the raw SB2 data to confirm RiceCAP results. The same approach used for sheath blight markers will also be applied to candidate makers for whole-grain milling from the RiceCAP MY2 mapping population derived from the parents Cypress and LaGrue. The strategy for development of the adapted germplasm will follow that from China - namely the introgression of adapted germplasm, in this case from Louisiana, into the A, B, and R lines. A pilot study will be initiated in the first phase where a collection of 100-150 elite inbred Louisiana and Arkansas lines will be evaluated in replicated plots in at least two different environments for certain agronomic traits on an individual plant basis to include height, maturity, panicle length, panicles/plant, and 1000 grain weight. DNA markers identified by GLM Select in the first study described above would be evaluated for their association with the measured traits. If the first phase successfully validated the markers detected by GLM Select, then a second phase would involve the hybridization of two to five elite inbred lines to create two recombinant inbred line (RIL-F5 or F6) association mapping populations by standard generation advance. To improve the SVR methodology, step-wise regression will be incorporated into the SVR procedure using the R software package to reduce Type I errors vs. the forward regression approach. Dr. Oard will evaluate and select potential lines developed by Dr. Rush as parents in crossing for sheath blight resistance. A vigorous effort to backcross sheath blight-resistant lines with commercial varieties will be implemented. New sources of sheath blight resistance from indica subspecies or other "wild" sources will be introgressed as they become available into local adapted germplasm. Candidate sheath blight markers such as those detected from the RiceCAP Project as described above will be evaluated using the selfed and backcrossed material produced from the proposed research

Progress 10/01/08 to 09/30/13

Outputs
Target Audience: 1. Louisiana rice producers and millers. 2. Louisiana, national, and international rice researchers. 3. National and international scientists involved in rice genetic improvment and disease resistance. Effort: Research results obtained from this Project disseminated through formal classroom instruction at LSU and the March 2009 RiceCAP Workshop. Research results and practical impact transmitted throughout the course of this Project via extension and outreach to LSU Agcenter rice extension agents and Louisiana rice producers’ meetings. Research progress also was reported at different regional and national scientific conferences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? During this project six Ph.D. students were trained inresearch, data analysis, and dissemination of new knowledge in the form of reports, publications, and presentations in both oral and poster forms. How have the results been disseminated to communities of interest? Research results were disseminated by referred publications, oral and poster presentations at research conferences, popular press articles, field days, growers’ meetings, and classroom lectures. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. Co-development and registration of two new Louisiana aromatic rice varieties using DNA markers for aroma, amylose content, gelatinization temperature, and rice blast resistance. 2. Co-development of seven sheath blight-resistant germplasm lines. 3. Identification of new sheath blight-resistant DNA markers. 4. Identification of new markers for rice grain quality. 5. Development ofnew male-sterile (A) lines adapted to Louisiana conditions. Identification of new hybrid combinations with advances in grain yield and grain quality approaching those of commercial hybrids grown in Louisiana.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Silva, J., B. Scheffler, Y. Sanabria, C. DeGuzman, D. Galam, A. Farmer, J. Woodward, G. May, J. Oard. 2012. Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing. Theor. Appl. Genet. 124:63-74.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Sha, X.Y., S.D. Linscombe, D.E. Groth, J.H. Oard, D.L. Harrell, L.M. White, C.C. Grimm, S.J. Theunissen and B.J. Henry. 2013. Registration of Jazzman-2 aromatic long-grain rice. J. Plant Registration 7: 1: 26-30.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Liu, G., Jia, Y., McClung, A., Oard, J. H., Lee, F. N., and Correll, J. C. 2013. Confirming QTLs and finding additional loci responsible for resistance to rice sheath blight disease. Plant Dis. 97:113-117.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Jia, Y., G. Liu, F. J. Correa-Victoria, A. M. McClung, J. H. Oard, R. J. Bryant, M.H. Jia, J. C. Correll. 2012. Registration of four rice germplasm lines with improved resistance to sheath blight and blast diseases. Plant Registration. 6:95-100.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Nelson JC, Oard JH, Groth D, Utomo, HS, Jia Y, Liu G, Moldenhauer KAK, Correa-Victoria FJ, Fjellstrom RG, Scheffler B, Prado GA (2012) Sheath-blight resistance QTLs in Japonica rice germplasm. Euphytica 184:2334.


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Information generated by this project was disseminated in 2012 via a total of 3 refereed research publications, 4 presentations at national, regional, commodity board, and ACE meetings. Specific research outputs include: Development and registration of four genetic rice lines resistant to disease in cooperation with USDA, Stuttgart, AR; identification of genes and genetic loci for resistance to rice sheath blight disease; and of development and genetic characterization of a mapping population for rice disease resistance.The significance and impact of the research were discussed with regional, national, and international rice researchers, members of the rice industry, and farmer commodity boards. PARTICIPANTS: J. Oard (PI), X. Sha, D. Groth, S. Linscombe, and PhD students (Silva, Sanabria, DeGuzman, and Galam), LSU AgCenter. Collaborators include: Nelson, Kansas State University, Drs. Jia (USDA-Stuttgart), Liu (USDA-Stuttgart), Correa-Victoria (RiceTec), Bryant (USDA-Stuttgart), and Correll (Univ. AR); Scheffler (USDA) Farmer, Woodward, and May (NCGR). TARGET AUDIENCES: Target audiences for the results of this project include U.S. and international rice breeders, geneticists, and pathologists, rice commodity federations, groups, and research boards, individual U.S. rice producers, country agents, and consultants. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Disease resistant varieties are a major priority for the US rice industry. This is especially true for Louisiana and Texas varieties that suffered a severe outbreak of blast disease in 2012. Development of four germplasm lines provide critical new genetic stocks that will lead to creation of new elite varieties resistant to sheath blight and blast fungal diseases. The USDA-funded RiceCAP project generated whole genome sequences for 13 lines currently used to develop new elite U.S. varieties. Analysis and filtering of the genomic sequences resulted in identification of candidate disease resistance genes that were validated in different breeding stocks and in the RiceCAP SB2 mapping population. Breeding new, disease resistant varieties will reduce input cost and increase margins for U.S. rice producers. This research has recently identified new genomic regions in adapted U.S. germplasm that will aid plant breeders in their quest to develop sheath blight resistant varieties.

Publications

  • Nelson JC, Oard JH, Groth D, Utomo, HS, Jia Y, Liu G, Moldenhauer KAK, Correa-Victoria FJ, Fjellstrom RG, Scheffler B, Prado GA (2012) Sheath-blight resistance QTLs in Japonica rice germplasm. Euphytica 184:23-34.
  • Silva, J., B. Scheffler, Y. Sanabria, C. DeGuzman, D. Galam, A. Farmer, J. Woodward, G. May, J. Oard. 2012. Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing. Theor Appl Genet 124:63-74
  • Silva, J., Scheffler, B., Sanabria, Y., De Guzman, C., Galam, D., Farmer, A., Woodward, W., May, G., and Oard, J. 2012. Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing. Proc. Rice Tech. Wrkg. Grp., 34:37.
  • Silva, J., Scheffler, B., Sanabria, Y., De Guzman, C., Galam, D., Farmer, A., and Oard, J. 2012. Diversity of elite inbred lines of rice as revealed by whole-genome sequencing. Proc. Rice Tech. Wrkg. Grp., 34:41.
  • Sha, X.Y., Li, W.K., Linscombe, S.D., Oard, J.H., Groth, D.E., Theunissen, S.J., and Henry, B.J. 2012. Development of hybrid rice in Louisiana - A progress report. Proc. Rice Tech. Wrkg. Grp., 34:50.
  • Sha, X.Y., Li, W.K., Linscombe, S.D., Oard, J.H., Theunissen, S.J., and Henry, B.J. 2012. Restoring abilities of U.S. long-grain rice genotypes to selected Chinese cytoplasmic male sterile lines. Proc. Rice Tech. Wrkg. Grp., 34:64-65.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Information generated by this project was disseminated in 2011 via a total of six refereed publications, four presentations at national, regional, commodity board, and ACE meetings. Specific outputs included: Release of a new aromatic Louisiana rice variety "Jazzman" assisted by DNA marker technology; development and registration of four genetic rice lines resistant to disease in cooperation with USDA-ARS, Stuttgart, AR; identification of genes and genetic loci for resistance to rice sheath blight disease; and development and genetic characterization of a mapping population for rice grain quality. The significance of the results was discussed with regional, national, and international rice researchers, and members of the rice industry. PARTICIPANTS: In addition to co-PIs Oard, Sha, Groth, Linscombe, and Wang, the following individuals were involved in the project: Dr. Nelson, (Kansas State University); Drs. McClung (USDA-Stuttgart), Fjellstrom (USDA-Stuttgart), Moldenhauer (Univ. AR,),Boza (Univ. AR,), Jodari (Univ. CA-Davis), Scheffler and Yeater (USDA); Drs. Jia (USDA-Stuttgart), Liu (USDA-Stuttgart), Correa-Victoria (RiceTec), Bryant (USDA-Stuttgart), and Correll (Univ. AR) Drs. Scheffler (USDA) Farmer (NCGR) Woodward (NCGR), May (NCGR); LSU PhD students Silva, Sanabria, DeGuzman, and Galam. TARGET AUDIENCES: Target audiences for the results of this project include U.S. and international rice breeders, geneticists, and pathologists, rice commodity federations, groups, and research boards, individual U.S. rice producers, county agents, and consultants. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The new Jazzman rice variety, developed by the LSU Agcenter Rice Research Station, is an adapted aromatic, long-grain rice with high yield, good milling and grain quality characteristics. Jazzman was the first Louisiana commercial variety to be developed in part through the assistance of DNA-marker technology. Development of four germplasm lines provided critical new genetic stocks that will lead to creation of new elite varieties resistant to sheath blight and blast fungal diseases. The USDA-funded RiceCAP project generated whole genome sequences for 13 lines currently used to develop new elite U.S. varieties. Analysis and filtering of genomic sequences resulted in identification of candidate disease resistance genes that were validated in different breeding stocks and in one mapping population. Researchers from five states contributed to the RiceCAP project that resulted in development of a mapping population for studies of rice grain quality. Genetic loci and chromosomal regions were identified and associated with high grain quality in Louisiana and Arkansas derived cultivars. The mapping population will be extremely valuable to identify and map additional genetic and environmental factors that contribute to improvement in grain quality of U.S. rice.

Publications

  • Sha, X.Y., S. D. Linscombe, F. Jodari, Q. R. Chu, D. E. Groth, S. B. Blanche, D. L. Harrell, L. M. White, J. H. Oard, M. H. Chen, S. J. Theunissen and B. J. Henry. 2011. Registration of Jazzman rice. J. of Plant Registrations 5(3): 304-308.
  • Silva, J., Groth, D.E., Moldenhauer, K.A., Oard, J.H. 2011. GGE biplot exploration of resistance to sheath blight disease in doubled-haploid lines of rice. Crop Science. 51:1028-1035.
  • Nelson JC, McClung AM, Fjellstrom RG, Moldenhauer KA, Boza E, Jodari F, Oard JH, Linscombe S, Scheffler BE, Yeater KM. 2011. Mapping QTL main and interaction influences on milling quality in elite US rice germplasm. Theor Appl Genet 122: 291-309.
  • Jia, Y., G. Liu, F. J. Correa-Victoria, A. M. McClung, J. H. Oard, R. J. Bryant, M.H. Jia, J. C. Correll. 2011. Registration of four rice germplasm lines with improved resistance to sheath blight and blast diseases. J. of Plant Registrations. 6:95-100.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: 1. Use of DNA marker technology for rapid development of new Louisiana rice variety Jazzman 2. This project worked in close cooperation with the LAES Rice Breeders, specially Dr. Xueyan Sha, to rapidly select via DNA markers the specific lines with appropriate cooking quality that led to rapid development and commercial release of this new long-grain, aromatic variety. 2. Development of two procedures for identification of candidate DNA variants and genes from next-generation genomic DNA sequences. This project worked in cooperation with the National Center for Genome Resources in Santa Fe, New Mexico, to develop "common variant" and "principal component - biplot" methods to identify candidate variants from DNA genomic databases. 3. Development, release, and registration of rice mapping population for high grain quality traits. The MY2 mapping population was created to identify markers and genes associated with high whole-grain yield in U.S. rice varieties. 4. Identification of DNA markers associated with high grain quality in U.S. rice. Association mapping techniques were used with 200 inbred lines to identify DNA markers associated with high-whole grain yield in rice. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Target audiences include rice researchers, rice breeders, rice farmers, U.S. rice commodity groups and organizations. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
1. We found that DNA-based SNP markers for cooking quality can be a useful tool for rapid development of commercial rice varieties. We noted that use of the markers hastened release of the Jazzman 2 variety by at least two years, which has important economic impact for the Louisiana rice industry. This is the first instance where DNA marker technology has participated directly in the breeding of a Louisiana rice variety. We anticipate that DNA marker technology will continue to play an important role in Louisiana rice varietal development. 2. Next generation sequencing has recently identified genes associated disease susceptibility in humans. We found that our recently developed informatic procedures can efficiently identify DNA variants from large genomic databases. These methods will be discussed and made available to the plant research community via publications and scientific meetings in 2011. 3. More than 200 candidate genes identified for sheath blight resistance were grouped into 42 categories based on gene family/gene ontology. Several candidate genes belonged to families reported in previous studies, and a few novel candidates were also identified. More than 25 genes to date have been validated by Sanger sequencing and SNP genotyping. Several candidate genes have been detected in Louisiana breeding lines and in one accession of Oryza nivara. Access to the candidate gene database will be made available via publications and scientific meetings. The potential impact includes acceleration of development of sheath blight resistant U.S. rice varieties. 4. The MY2 population will serve as a valuable genetic mapping and genomic resource for the rice community to identify genes and develop marker technology for breeding high grain quality U.S. rice varieties. 5. The selected DNA markers have the potential to assist in efficient breeding of new elite rice varieties with high whole-grain yields that are required for the commercial U.S.rice industry.

Publications

  • Ordonez, S.A., Silva, J., Oard, J.H. 2010. Association mapping of grain quality and flowering time in elite japonica rice germplasm. J.Cereal Science. 51:337-343.
  • Oard, J.A. Moldenhauer, K., Fjellstrom, B., Nelson, J.C., Scheffler, B., Linscombe, S., Correll, J.,Silva, J., May, G.D. 2010. Registration of the MY2 Cypress/LaGrue Rice Recombinant Inbred Line Mapping Population. Journal of Plant Registrations 4: 1-5.


Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: (1) Elite breeding line RU0802022, considered as a potential varietal release, was identified and advanced by DNA marker-assisted technology in cooperation with Dr. Sha, LSU AgCenter Breeding Program; (2) A total of 25 male sterile, maintainer, and restorer lines for Louisiana hybrids were developed from crosses of Chinese, Philippine, and U.S. sources; (3) Two sheath blight-resistant lines were developed and provided to the LSU AgCenter Breeding Program; (4) Fifteen DNA markers for sheath blight resistance, whole-grain milling yield, plant height, and flowering time were identified; (5) Agronomic and molecular data from 500 elite U.S. breeding lines to be used in marker-trait studies were analyzed for level of diversity and population genetic structure. PARTICIPANTS: Individuals: Drs. Samuel Ordonez, Xueyan Sha, Weike Li, and Steve Linscombe cooperated on hybrid rice project. Drs. Steve Linscombe, Karen Moldenhauer, Clare Nelson, James Correll, Brian Scheffler, and Anna McClung cooperated on RiceCAP Project. Dr. Samuel Ordonez and PhD student James Garcia cooperated on sheath blight project. James Silvia participated in Salvinia research. Partner organizations: USDA (RiceCAP), University of Arkansas, Kansas State University TARGET AUDIENCES: Target Audience: U.S. rice industry, U.S. rice producers, U.S. rice researchers, graduate and undergraduate students. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
(1) The line RU0802022 identified by DNA markers for proper aroma and gelatinization temperature was also the top yielding line among 200 elite U.S. breeding lines in the 2009 multi-state Uniform Rice Regional Nursery. The marker-assisted method accelerated the identification and advance of RU0802022 by two or more years. This approach showed that, in close cooperation with rice breeders, it can have a direct impact on rapid selection and advancement of elite breeding lines; (2) Considerable progress was made in height, maturity, pollen viability, and seed production for 25 inbred lines developed for creation of future Louisiana hybrid rice varieties; (3) The sheath blight resistant germplasm was selected as parents to be used by the LSU AgCenter Breeding Program for development of new disease resistant varieties; (4) Analysis of DNA marker data for disease resistance and three important agronomic traits were identified from replicated field studies in Louisiana, Arkansas, and Texas. Use of these markers will accelerate advance and release of new elite Louisiana rice varieties; (5) Analysis of 500 U.S. rice lines and varieties showed that closely related inbred material exhibited sufficient agronomic and molecular diversity to be suitable for future marker-trait association studies of grain yield, disease resistance, and grain quality.

Publications

  • Ordonez, S., Sha, X., Linscombe, S.D., Blanche, B., and Oard, J.H. 2009.Initiation Of Cooperative Research For Development Of Hybrid Rice Germplasm Adapted To Louisiana. Online PAG conference abstract, http://www.intl-pag.org/17/abstracts/P05b_PAGXVII_240.html.
  • Solomon, W., Oard, J., McClung, A., Wright, M., Zhao, K., Reynolds, A., Bustamante, C., Kanter, D., McCouch, S., and Scheffler, B.E. 2009. Analysis Of The RiceCAP Germplasm Panel For SNP Diversity, Population Structure And Seven Yield-Component Traits Of Rice. Online PAG conference abstract, http://www.intl-pag.org/17/abstracts/P05b_PAGXVII_220.html.
  • Ordonez, S.A., Wang, J., Oard, J.H. 2009. Identification Of Candidate DNA Markers For Complex Traits In Rice Using Non-Linear Support Vector Regression And Random Forest Regression. Online PAG conference abstract, http://www.intl-pag.org/17/abstracts/P05b_PAGXVII_225.html.