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INVESTIGATOR: Utomo, H. S.

PERFORMING INSTITUTION:
RICE RESEARCH STATION
LOUISIANA STATE UNIVERSITY
BATON ROUGE, LOUISIANA 70893

APPLICATION OF MARKER-ASSISTED BREEDING FOR GENETIC IMPROVEMENT OF SOUTHERN U.S. RICE

OBJECTIVES: The objectives are (1) to evaluate currently available markers for their suitability for use in Louisiana breeding materials and develop mapping populations to identify molecular markers for important traits, such as disease resistance (sheath blight), insect tolerance (water weevil tolerance), grain quality, protein content, grain elongation, and yield components, (2) to develop improved breeding lines by introgression or gene pyramiding through marker-assisted recurrent selection or marker-assisted backcross, and (3) to develop a database of DNA fingerprintings for varietal identification, purity verification, determination of mixtures/off-types, and examination of genetic shift as varieties are propagated in different environments.

APPROACH: Parental lines and hundreds of advanced lines will be screened using currently available markers such as blast, amylose content, aroma, and elongation markers. Any discrepancy between markers and actual phenotypic data will be used as a basis for developing new markers for Louisiana breeding lines. Mapping populations for new marker identification will consist of recombinant inbred lines (RILs) or doubled-haploid lines and will be evaluated in replicated field plots with potential compounding variables closely controlled. Traditional genetics, molecular genetics, and sequencing data, together with field, greenhouse, and laboratory analysis, will be used to locate and map important genes. Linkage maps will be constructed using Kosambi function. Molecular mapping will be focused on traits of importance to the Louisiana breeding program such as disease resistance (sheath blight resistance), insect tolerance (water weevil tolerance), grain quality, protein content, grain elongation, and yield related traits. The search for a molecular marker will be based on random primer screening of bulked segregant DNA. Hundreds of SSR primers will be used. Primers that produce polymorphic DNA fragments will be subjected to segregation analysis. Consistent polymorphic fragments will be isolated, cloned, sequenced, and analyzed. Some of the SSR markers will be converted into dominant markers. Primers will be designed by incorporating several critical parameters, such as primer size, melting temperature, GC content, and the size of PCR products. Since several primers (multiplex) will be put in a single PCR run, primers for all markers will be designed in a way that allows the same PCR conditions and gel separations. Mathematical and statistical tools will be used to estimate QTL effects, to detect and study interactions of QTLs with each other and with environments, to study relationships among traits, and to map markers and QTLs. Currently available markers will be used in developing improved breeding lines. Newly developed markers will also be used as they become available. Marker-assisted breeding will include the use of blast markers to improve Clearfield rice lines for blast resistance. Marker-aided pyramiding will be used to introgress multiple desirable traits from different origins into elite genetic backgrounds. Individuals with the best combination of favorable alleles will be selected. If the desirable level of allele combinations has not been met, a pyramiding strategy will be conducted. To accelerate development of homozygous breeding lines from MAS, anther culture will be used. Marker analysis will be used to deal with impurity problems that have been observed on some of the semidwarf varieties. The database of DNA fingerprinting for varietal identification will be developed. All varieties released by the Rice Research Station, LSU Ag. Center, together with several promising advanced lines will be genotyped using well distributed anchor DNA markers, including STSs, RAPDs, microsatellites, and AFLPs. Graphic genotyping will be constructed to visualize the conserved regions found among the entries.

NON-TECHNICAL SUMMARY: Molecular marker technology can increase breeding efficiency. The purpose of this project is to utilize marker technology to develop improved breeding lines.

PROJECT CONTACT:

Name: Utomo, H. S.
Phone: 337-788-7531
Fax: 337-788-7553
Email: hutomo@agcenter.lsu.edu