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United States Department of Agriculture

Agricultural Research Service

Development of Molecular Markers for Cultivar Improvement - Recent Accomplishments
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Development of DNA Markers Associated with Major Rice Blast Resistance Genes

Rice blast disease causes yield losses world-wide. Development of resistant cultivars is difficult because the pathogen can rapidly evolve to overcome resistance genes. Each gene confers a unique spectrum of resistance to different races (pathotypes) of blast. Some resistance genes mask the presence of other genes due to overlapping resistance spectra.

Genetic markers have been developed with collaborators at Texas A&M University that are closely linked to the rice blast resistance genes Pi-b, Pi-kh and Pi-ta2 located on chromosomes 2, 11, and 12, respectively. The presence of these markers indicate a 98 to nearly 100% probability that the desired disease resistance gene is also present.

Genetic markers for these genes will facilitate stacking of blast resistance genes in unique combinations to give broad spectrum disease resistance.

DNA microsatellite markers (RM138, 208, and 166) demonstrate the first successful transfer of the Pi-b disease resistance gene into the new U.S. cultivar 'Saber' from the Chinese cultivar 'Teqing' . The microsatellite markers show products for both susceptible (Gulfmont, Cypress, and Lemont) and resistant plants and are more useful than scoring for the Pi-b gene itself (scored by the presence or absence of a DNA product), since plants with a failed marker reaction can be confused with those showing no Pi-b gene product.

Our marker research was also used to discover the Pi-kh resistance gene in the cultivars 'Madison', and 'Kaybonnet', which was previously unknown since Pi-kh is masked by presence of the Pi-ta2 resistance gene in these cultivars. The presence of both disease resistance genes in these cultivars indicates they have multiple genetic mechanisms for recognizing and preventing rice blast infection.


Development of a High-Throughput Method for Analyzing Markers Associated with Amylose Content in Grain

Amylose: Principal grain component affecting rice cooking and processing quality.
Waxy gene: Gene for enzyme controlling rice starch synthesis and highly associated with amylose content.
Waxy gene markers: Developed in collaboration with Texas A&M partners, these markers signify high, intermediate, or low amylose content types.

The improved method saves considerable time and labor in sample preparation and uses novel modifications of electrophoretic separation technology to rapidly analyze the marker. This method is now being used to accurately analyze cooking quality for thousands of breeding lines in U.S. variety development programs. 

Different DNA marker bands, referenced by the number of CT repeats in the marker DNA sequence, represent different classes of amylose content. For example, 20 CT repeats are found in long grain rices that typically look dry and not-sticky, whereas 18 CT repeats are found in medium grain rices which cook soft and sticky.

Development of Markers Suitable for Marker-Assisted Selection of Grain Fragrance in U.S  Breeding Lines

Grain fragrance (aroma) is an important feature of premium-value rices (e.g., Jasmine and Basmati). One of the major genes controlling grain fragrance has been mapped on chromosome 8 of rice. However, the markers previously used to tag this gene were not suitable for screening U.S. breeding materials because of the time, labor, and cost needed to assay them.

Using DNA sequence information from a marker near this fragrance gene, we have developed a rapid and technologically easy method using PCR markers for identifying the presence or absence of the fragrance gene. This marker will facilitate the development of cultivars for this high-value market.



Last Modified: 1/31/2005
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