Molecular Marker-Assisted
Rice Improvement - 2008



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Project Leader and Principal  Investigators

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


This project combines molecular genetics with conventional plant breeding methods to develop tools and resources for the improvement of rice varieties adapted for California. Work continues with molecular markers to identify traits of interest, such as stem rot resistance, cold tolerance, and grain quality characteristics. The use of molecular markers is intended to accelerate the selection process and to streamline the breeding of improved varieties.

Cold tolerance

Significant advances have been made in the genetic analysis of cold tolerance. Work is concentrated on identifying genes associated with seedling cold tolerance; characterization of rice varieties obtained from the U.S. Department of Agriculture (USDA); and development of new methods to measure cold tolerance in rice plants.

Characterization of genes that may confer cold tolerance – and the proteins they encode - continues. Multiple differences in two cold-tolerance genes have been identified between M-202 (cold tolerant variety) and IR50 (cold sensitive variety) through DNA sequencing.  Quantitative analysis of the expression of two genes in M-202 and IR50 before and during cold stress showed significant differences. Additional gene expression studies are under way.

Work continued on two sets of 96 entries from USDA’s core rice collection for seedling cold tolerance analysis. Each set consists of 48 varieties rated the most tolerant or sensitive, with M-202 and IR50 as the tolerant and sensitive checks. In 2008, the 10 most tolerant and 10 most sensitive varieties were examined. Reaction of these varieties to cold temperature was consistent with the previous year’s observations.

In addition to molecular analysis of the tolerant and sensitive rice germplasm, these materials were also used to study alternative methods for measuring cold tolerance. These included measurement of relative growth rate, assessment of photosynthetic capacity (photodamage), and assessment of cell membrane damage by measuring electrolyte leakage.

Cold stress is known to affect the photosynthetic capacity of plants, especially under high light conditions. Photosynthetic capacity is reduced under cold stress because of accumulated photodamage. Photodamage was measured with a fluorometer. Refinements of this technique are planned for 2009.

Measuring leakage from plant tissue is another technique. Cell membranes are affected by environmental stresses, growth, and development. Damaged membranes will slowly “leak” into the surrounding medium, which can be detected by an electrical conductivity meter. This technique showed the most promise for screening large numbers of rice plants and for correlating quantitative and qualitative methods for assessing cold tolerance.

In preparation for future studies, germplasm development also continued with the advancement of backcrossed lines that will be tested for seedling cold tolerance in the field and in controlled environments in coming years. An assessment of panicles from 480 recombinant inbred lines (derived from M-202 × IR50) grown in 2007 was also conducted in preparation for future cold blanking studies.

Stem rot

In 2008, work on stem rot resistance concentrated in three principal areas – assessment of rice lines, development of new mapping populations, and characterization of stem rot isolates.

Assessment of two breeding lines (87-Y-550 – stem rot tolerant, 96-Y-480 – stem rot susceptible) was performed using a paper filter inoculation method, slightly modified from the previous year. Three different stem rot isolates were used. No significant differences were observed between the two breeding lines in response to any of the isolates tested.

A genetic mapping population derived from a cross between stem rot-tolerant 87-Y-550 and stem rot-susceptible S-102 was advanced in 2008. Further generational advances will be evaluated for stem rot resistance. However, the ability to accurately score subtle differences in lines derived from crossing these parents remains challenging.

Work also continued on stem rot isolates to better understand why some strains are more virulent than others. Two isolates identified in 2007 were tested for disease response on 87-Y-550 and 96-Y-480. Preliminary assessment was consistent with 2007 observations, with one isolate appearing more virulent than the other. Further studies are needed to determine the basis of this difference.

Additional research activities

Generation advance

During the 2008 growing season, approximately 5,000 lines were grown in the greenhouse for advancement or seed amplification and purification. In addition, 7,200 rows (including 809 marker rows) were also planted in the UC Davis rice field facility nursery.

Mutant population

The varieties S-102 and Terso that were previously subjected to radiation and/or chemically induced mutagenesis were grown in the greenhouse and in field plots. These mutant populations are being screened for useful traits such as early heading.

Mapping population

Three recombinant inbred line-mapping populations were also advanced in the field. These populations should be useful for examining milling yield and other agronomic traits.


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