Molecular-Marker Assisted
Rice Improvement - 2007



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Project Leader and Principal  Investigators

Thomas H. Tai, research geneticist, USDA-ARS, Dept. of Plant Sciences, UC Davis


This ongoing project combines molecular genetics with conventional plant breeding methods to develop improved rice varieties adapted for California. Work continues with molecular markers to identify traits of interest, such as stem rot resistance and cold tolerance. Work on the development of molecular markers for blast resistance and grain quality is shifting to the Rice Experiment Station.

Stem Rot

In 2007, approximately 150 recombinant lines derived from a long-grain cross were advanced. Seeds collected from these lines will be used in disease tests in 2008. Because plants grown from individual lines are essentially identical, they should produce consistent disease scoring when exposed to the stem rot fungus. This will facilitate more accurate disease scoring.

A second genetic mapping population derived from a cross between stem rot-tolerant 87-Y-550 and stem rot-susceptible S-102 was advanced in 2007. Third generation seeds were harvested from approximately 330 individual plants from this cross. These lines will be advanced.

Work also continued on stem rot isolates to better understand differences in virulence. Previously, these isolates were selected for analysis of traits such as growth on complex media, sclerotia production, fungicide sensitivity, and other factors that might be involved in this disease’s prevalence in nature. Several DNA markers were identified that may be used to distinguish different stem rot isolates. These markers should also be useful in developing a genetic map of the fungus for gene mapping and isolation studies.

Paper disc inoculation of rice seedlings (S-102) with stem rot isolates (dics removed prior to photographing). Discs covered with stem rot mycelia are placed on stem about 2-4 cm above roots. Uninoculated control (top left), cc23 isolate (upper right), cc3 (lower left), cc21 (lower right)

In addition to DNA characterization, a new laboratory inoculation method was used to examine the ability of some of these isolates to cause disease on young rice plants. With this new technique, the site of infection and progression of the fungus was more defined than in standard field tests. Initial testing indicates that this method produces consistent results and may be used to distinguish the virulence of different stem rot isolates. This information will provide a foundation for identifying the stem rot genes involved in the disease and may be targets for control strategies. Tests to determine whether this inoculation method can be used to distinguish the response of tolerant and susceptible rice cultivars are planned.

Cold Tolerance

Two sets of 96 entries each were identified from the USDA’s core collection for seedling cold tolerance analysis. Some of these varieties appear to be more tolerant than M-202 and may provide a source of seedling cold tolerance. These lines will be retested in 2008 and will be examined further with DNA markers. Germplasm development also continued with the advancement of backcross lines that will be tested in the field and in controlled environments in coming years.

A set of 483 recombinant inbred lines derived from a cross between M-202 and IR50 was planted for assessment of heading date. These lines have been used in previous cold tolerance research and have been extensively characterized. Information collected from this work will help provide a better understanding of cold tolerance effects on fertility at the booting (reproductive) stage.


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