Molecular Market-Assisted
Rice Improvement - 2005



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Project Leader and Principal UC Investigators

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




This ongoing project integrates advanced techniques in molecular biology with conventional plant breeding methods to develop improved rice germplasm adapted for California. Molecular markers are the primary tool used in this genetic fingerprinting work. Progress on disease resistance, cold tolerance and grain quality is reported below.

Disease Resistance

The primary objective of stem rot-related genetics research is to identify DNA markers linked to disease resistance that exists in the wild species Oryza rufipogon and to transfer these traits into California varieties with marker-assisted selection. Field and greenhouse experiments to identify genes conferring disease resistance from a long-grain breeding line, 87-Y-550, were repeated in 2005. As in 2004, progeny were tested for their reaction to inoculation with stem rot. The total number of lines in this work expanded from 94 to 116. A large amount of data was generated from this research and is under analysis.

A genetic mapping population from a cross made between M-206 and O. rufipogon is also being developed. Tissue collected from these lines will be used to prepare DNA for marker analysis and trait assessment. DNA marker analysis has been performed on parental lines 87-Y-550 (resistant) and 96-Y-480 (susceptible). Approximately 237 microsatellite markers were assessed using DNA from these parents in 2005. Of the total 500 markers now examined, 90 appear to be useful for genetic mapping and 80 of these have been used to examine DNA from 123 lines. Mapping data were obtained from 41 of these markers. Data from another 110 markers are needed to facilitate preliminary mapping of this population and to determine the number and location of genes involved in stem rot resistance in 87-Y-550.

Cold Tolerance

The second major area of marker-assisted genetics research is cold tolerance. Fine genetic mapping of a region on the chromosome that confers tolerance to cold-induced wilting in seedlings resulted in the identification of four candidate genes. One of these genes has previously been reported to have a role in enhancing cold tolerance in rice. Several DNA markers have been developed as a result of this work and will be tested in 2006 to determine their usefulness for California breeding materials.

A population of 1,954 recombinant inbred lines derived from a cross between M-202 and the indica variety IR50 is being used to identify other genes involved in seedling cold tolerance.

Grain Quality

Grain quality work continues with the use of a waxy marker to assess breeding lines and progeny of crosses. This marker is of interest because of the waxy gene’s role in starch development. In 2005 training and assistance were provided to Rice Experiment Station staff in analyzing advanced short- and long-grain lines with the waxy grain quality marker.


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