Molecular Marker-Assisted
Rice Improvement-04



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Project Leader and Principal UC Investigators

Thomas H. Tai, research geneticist, USDA/ARS, Dept. of Agronomy and Range Science, UC Davis


The purpose of this ongoing project is to integrate advanced techniques in molecular biology with conventional plant breeding methods in the pursuit of improved rice varieties for California.  Researchers report progress on the application of molecular markers to identify plants with desirable disease resistance, cold tolerance and grain quality traits.

Greenhouse and field tests were conducted in 2004 to assess stem rot and aggregate sheath spot resistance derived from crosses with a long grain experimental (87-Y-550).  The 94 entries in these tests exhibited a range of responses and are currently being assessed with DNA markers. 

Development of a genetic mapping population from a cross between M-206 and a stem rot resistant species, Oryza rufipogon (accession number 100912), was another area of emphasis.  A genetic mapping population consists of a group of related individuals (i.e. plants) that are the result of a cross between two different plants, referred to as parents. These parents differ in characters or traits that are of interest so that some members of the population will be like one parent while others resemble the second parent.

For example, M-206 is susceptible to stem rot and O. rufipogon 100912 is resistant. In addition to differences in physical traits, parents also differ at the DNA or molecular level (i.e. DNA markers). Genetic mapping populations enable researchers to identify DNA markers that are very closely associated with traits of interest. Molecular analysis of resistant and susceptible lines also was performed to identify markers that can point to resistance genes.

In disease resistance work on blast, two short grain crosses utilizing the Pi-z marker were analyzed with DNA markers.  Progeny from other crosses produced seed for use in the RES disease nursery.  DNA markers linked to blast resistance genes were also used to assess 192 entries from the medium grain program and 96 entries from the long grain program.

Efforts to identify genes conferring cold tolerance at the seedling stage are continuing as additional molecular markers become available.  Identifying DNA markers that are very closely associated with seedling cold tolerance traits (referred to as fine genetic mapping) helped narrow down the chromosomal region containing genes potentially conferring cold tolerance.  Additional crosses were advanced to supplement 186 recombinant lines to increase the population of potential cold tolerance sources. 

Genetic populations for field assessment of booting stage cold tolerance are also being developed. Of 546 lines sent to the Hawaii winter nursery, 528 were selected and planted at UC Davis in 2004.  Seeds of these progeny will be grown out in 2005 and used for booting stage cold tolerance evaluation.

The “waxy” gene marker has been applied to a set of long grain breeding materials to assess grain quality.  A laboratory for extracting DNA from plant materials was established at the Rice Experiment Station as a first step toward transferring DNA marker technology to RES breeding programs.


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