Abstract
Allele specific amplification (ASA) is a low-cost, robust technique that can be utilised to discriminate between alleles that differ by SNP's, insertions or deletions, within a single PCR tube. Fragrance in rice, a recessive trait, has been shown to be due to an eight bp deletion and three SNP's in a gene on chromosome 8 which encodes a putative betaine aldehyde dehydrogenase 2 (BAD2). Here we report a single tube ASA assay which allows discrimination between fragrant and non-fragrant rice varieties and identifies homozygous fragrant, homozygous non-fragrant and heterozygous non-fragrant individuals in a population segregating for fragrance. External primers generate a fragment of approximately 580 bp as a positive control for each sample. Internal and corresponding external primers produce a 355 bp fragment from a non-fragrant allele and a 257 bp fragment from a fragrant allele, allowing simple analysis on agarose gels.
Similar content being viewed by others
Abbreviations
- 2AP:
-
2-Acetyl-1-pyrroline
- ASA:
-
Allele specific amplification
- BAD2:
-
Betaine aldehyde dehydrogenase 2
- SNP:
-
Single nucleotide polymorphism
References
C.J. Bergman J.T. Delgado A.M. McClung R.G. Fjellstrom (2001) ArticleTitleAn improved method for using a microsatellite in the rice waxy gene to determine amylose class Cereal Chem. 78 257–260 Occurrence Handle1:CAS:528:DC%2BD3MXktlWitrk%3D
D.K. Berner B.J. Hoff (1986) ArticleTitleInheritance of scent in American long grain rice Crop Sci. 26 876–878 Occurrence Handle10.2135/cropsci1986.0011183X002600050008x
L.M.T. Bradbury T.L. Fitzgerald R.J. Henry Q. Jin D.L.E. Waters (2005) ArticleTitleThe gene for fragrance in rice Plant Biotech. J. 3 363–370 Occurrence Handle10.1111/j.1467-7652.2005.00131.x Occurrence Handle1:CAS:528:DC%2BD2MXltV2ktbo%3D
R.G. Buttery L.C. Ling B.O. Juliano J.G. Turnbaugh (1983) ArticleTitleCooked Rice aroma and 2-acetyl-1-pyrroline J. Agric. Food Chem. 31 823–826 Occurrence Handle1:CAS:528:DyaL3sXktlOhu7Y%3D
G.M. Cordeiro M.J. Christopher R.J. Henry R.F. Reinke (2002) ArticleTitleIdentification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence Mol. Breed. 9 245–250 Occurrence Handle10.1023/A:1020350725667 Occurrence Handle1:CAS:528:DC%2BD38Xnt1ahtLw%3D
M. Lorieux M. Petrov N. Huang E. Guiderdoni A. Ghesquiere (1996) ArticleTitleAroma in rice: Genetic analysis of a quantitative trait Theor. Appl. Genet. 93 1145–1151 Occurrence Handle1:CAS:528:DyaK2sXpvFOiuw%3D%3D
R.F. Reinke L.A. Welsh J.E. Reece L.G. Lewin A.B. Blakeney (1991) ArticleTitleProcedures for quality selection of aromatic rice varieties Int. Rice Res. Newslett. 16 10–11
B.C. Sood E.A. Sidiq (1978) ArticleTitleA rapid technique for scent determination in rice Indian J. Genetic Plant Breed. 38 268–271
R. Widjaja J.D. Craske M. Wootton (1996) ArticleTitleComparative studies on volatile components of non-fragrant and fragrant rices J. Sci. Food Agric. 70 151–161 Occurrence Handle10.1002/(SICI)1097-0010(199602)70:2<151::AID-JSFA478>3.0.CO;2-U Occurrence Handle1:CAS:528:DyaK28XhtFaqurk%3D
T. Yoshihashi (2002) ArticleTitleQuantitative analysis on 2-acetyl-1-pyrroline of an aromatic rice by stable isotope dilution method and model studies on its formation during cooking J. Food Sci. 67 619–622 Occurrence Handle1:CAS:528:DC%2BD38XivVeisr4%3D
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bradbury, L.M.T., Henry, R.J., Jin, Q. et al. A Perfect Marker for Fragrance Genotyping in Rice. Mol Breeding 16, 279–283 (2005). https://doi.org/10.1007/s11032-005-0776-y
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s11032-005-0776-y