ARS | Publication request: Analysis of an SFP marker in the rice fgr/BAD2 gene and fragrance in US rice germplasm

Submitted to: American Society of Agronomy Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: August 1, 2007
Publication Date: November 1, 2007
Citation: Fjellstrom, R.G., McClung, A.M., Chen, M.H., Bockelman, H.E., Yan, W. 2007. Analysis of an SFP marker in the rice fgr/BAD2 gene and fragrance in US rice germplasm. [abstract] American Society of Agronomy Abstracts. p. 259-3.

Technical Abstract: The fgr gene on rice chromosome 8 has been identified to control the presence of grain fragrance/aroma in rice. An eight base in the fgr gene was found by Bradbury et. al (2005) in aromatic rice accessions, with this recessive mutation causing a loss in function of the betaine aldehyde dehydrogenase (BAD2) enzyme it encodes, reslting in the accumulation of the fragrant compound 2-acetyl-1-pyrroline (2AP). We developed an easily assayed single functional polymorphism (SFP) marker to test for the presence of this deletion in rice germplasm and its association with grain fragrance. The SFP marker was assayed on all rice accessions in the USDA-ARS-GRIN collection listed as being aromoatic, as well as on all Basmati rice accessions, the entire USDA-ARS rice core collection, and elite US rice breeding materials being tested in the Uniform Regional Rice Nursery. The SFP marker, using one labeled forward and an unlabeled reverse primer spanning the deleted region, was amplified via PCR and scored by both capillary and agarose electrophoresis. A single DNA amplification product was produced by these primers, with an eight base pair reduction in size detected in aromatic control samples when compared to non-aromatic controls. Our results demonstrated that some accessions listed in GRIN as aromatic neither possessed the marker-detected deletion nor were fragrant, while other accessions were heterogeneous for the presence of the fgr gene deletion. The presence of the fgr deletion was highly correlated with the presence of 2AP in the grain samples of all the rice germplasm analyzed. The SFP marker we developed is useful for detecting the presence of the fgr gene deletion and is an effective tool for marker aided selection of this valuable trait in rice.