Advertisement

Theoretical and Applied Genetics

, Volume 125, Issue 5, pp 887–896 | Cite as

A PCR-based marker for a locus conferring the aroma in Myanmar rice (Oryza sativa L.)

  • Khin Myo Myint
  • Siwaret Arikit
  • Samart Wanchana
  • Tadashi Yoshihashi
  • Kiattawee Choowongkomon
  • Apichart Vanavichit
Original Paper

Abstract

Aromatic rice is an important commodity for international trade, which has encouraged the interest of rice breeders to identify the genetic control of rice aroma. The recessive Os2AP gene, which is located on chromosome 8, has been reported to be associated with rice aroma. The 8-bp deletion in exon 7 is an aromatic allele that is present in most aromatic accessions, including the most popular aromatic rice varieties, Jasmine and Basmati. However, other mutations associated with aroma have been detected, but the other mutations are less frequent. In this study, we report an aromatic allele, a 3-bp insertion in exon 13 of Os2AP, as a major allele found in aromatic rice varieties from Myanmar. The insertion is in frame and causes an additional tyrosine (Y) in the amino acid sequence. However, the mutation does not affect the expression of the Os2AP gene. A functional marker for detecting this allele was developed and tested in an aroma-segregating F2 population. The aroma phenotypes and genotypes showed perfect co-segregation of this population. The marker was also used for screening a collection of aromatic rice varieties collected from different geographical sites of Myanmar. Twice as many aromatic Myanmar rice varieties containing the 3-bp insertion allele were found as the varieties containing the 8-bp deletion allele, which suggested that the 3-bp insertion allele originated in regions of Myanmar.

Keywords

Reverse Transcription Polymerase Chain Reaction Rice Variety Functional Marker Single Recessive Gene Aromatic Rice 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We gratefully acknowledge the financial support of the Thai-French Trilateral Development Cooperation and Joint Fellowship Program for Doctoral Students under the Royal Golden Jubilee Program (Grant No. PHD/0123/2550), from the Thailand Research Fund (TRF) to K.M. Myint, and the Agricultural Research Development Agency (public organization), Thailand. The authors would also like to thank the Plant Biotechnology Center at the Myanma Agriculture Service (Yangon, Myanmar) and the Department of Agricultural Research at Yezin (Nay Pyi Taw, Myanmar) for kindly providing the rice materials used in this study. All experiments in this study complied with the current Biosafety Guidelines of Thailand.

References

  1. Bourgis F, Guyot R, Gherbi H, Amabile I, Tailliez, Salse J, Lorieux M, Ghesquière A, Delseny (2008) Characterization of the major fragrance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice. Theor Appl Genet 117:353–368PubMedCrossRefGoogle Scholar
  2. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005a) The gene for fragrance in rice. Plant Biotech J 3:363–370CrossRefGoogle Scholar
  3. Bradbury LMT, Henry RJ, Jin QS, Reinke RF, Waters DLE (2005b) A perfect marker for fragrance genotyping in rice. Mol Breed 16:279–283CrossRefGoogle Scholar
  4. Bradbury LMT, Gillies SA, Brushett DJ, Waters DLE, Henry RJ (2008) Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Mol Biol 68:439–449PubMedCrossRefGoogle Scholar
  5. Buttery RG, Ling LC, Juliano BO (1982) 2-Acetyl-1-pyrroline: an important aroma component of cooked rice. Chem Ind (Lond) 12:958–959Google Scholar
  6. Chen SH, Wu J, Yang Y, Shi WW, Xu ML (2006) The fgr gene responsible for rice fragrance was restricted within 69 kb. Plant Sci 171:505–514CrossRefGoogle Scholar
  7. Dhulappanavar CV (1976) Inheritance of scent in rice. Euphytica 25:659–662CrossRefGoogle Scholar
  8. Fitzgerald MA, Sackville Hamilton NR, Calingacion MN, Verhoeven HA, Butardo VM (2008) Is there a second fragrance gene in rice? Plant Biotech J 6:416–423CrossRefGoogle Scholar
  9. Ghose RLM, Butany WT (1952) Studies on the inheritance of some characters in rice (Oryza sativa L.). Indian J Genet Plant Breed 12:26–30Google Scholar
  10. Hien NL, Yoshihashi T, Sarhadi WA, Hirata Y (2006) Sensory test for aroma and quantitative analysis of 2-acetyl-1-pyrroline in Asian aromatic rice varieties. Plant Prod Sci 9:294–297CrossRefGoogle Scholar
  11. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877PubMedCrossRefGoogle Scholar
  12. Khush GS, Brar DS, Virk PS, Tang SX, Malik SS, Busto GA, Lee YT, McNally R, Trinh LN, Jiang Y, Shata MAM (2003) Classifying rice germplasm by isozyme polymorphism and origin of cultivated rice. IRRI Discussion Paper Series No.46. International Rice Research Institute, Los Banos, p 279Google Scholar
  13. Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci USA 106(34):14444–14449PubMedCrossRefGoogle Scholar
  14. Lorieux M, Petrov M, Hunag N, guiderdoni E, Ghesquière A (1996) Aroma in rice: genetic analysis of quantitative trait. Theor Appl Genet 93:1145–1151CrossRefGoogle Scholar
  15. Mahatheeranont S, Keawsa-Ard S, Dumri K (2001) Quantification of the rice aroma compound, 2-acetyl-1-pyrroline, in uncooked Khao Dawk Mali 105 brown rice. J Agric Food Chem 49:773–779PubMedCrossRefGoogle Scholar
  16. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497CrossRefGoogle Scholar
  17. Nakagahra M (1978) The differentiation, classification and center of genetic diversity of cultivated rice by isozyme analyses. Trop Agr Res Ser 11:77–82Google Scholar
  18. Niu X, Tang W, Huang W, Ren G, Wang Q, Luo D, Xiao Y, Yang S, Wang F, Lu BR, Gao F, Lu T, Liu Y (2008) RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.) B. BMC Plant Biol 8:100PubMedCrossRefGoogle Scholar
  19. Petrov M, Danzart M, Giampaoli P, Fayre J, Richard H (1996) Rice aroma analysis: discrimination between a scented and non-scented rice. Sci Aliments 16:347–360Google Scholar
  20. Shi W, Yang Y, Chen S, Xu M (2008) Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol Breed 22:185–192CrossRefGoogle Scholar
  21. Sood BC, Siddiq EA (1978) A rapid technique for scent determination in rice. Indian J Genet Plant Breed 38:268–271Google Scholar
  22. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  23. Vanavichit A, Tragoonrung S, Toojinda T, Wanchana S, Kamolsukyunyong W (2008) Transgenic rice plants with reduced expression of Os2AP and elevated levels of 2-acetyl-1-pyrroline. US patent No. 7,319,181Google Scholar
  24. Wanchana S, Kamolsukyunyong W, Ruengphayak S, Toojinda T, Tragoonrung S, Vanavichit A (2005) A rapid construction of a physical contig across a 4.5 cM region for rice grain aroma facilitates marker enrichment for positional cloning. Sci Asia 31:299–306CrossRefGoogle Scholar
  25. Wongpanya R, Boonyalai N, Thammachuchourat N, Horata N, Arikit S, Myint KM, Vanavichit A, Choowongkomon K (2011) Biochemical and enzymatic study of rice BADH wild-type and mutants: an insight into fragrance in rice. Protein J 30:529–538PubMedCrossRefGoogle Scholar
  26. Wongpornchai S, Dumri K, Jongkaewwattana S, Siri B (2004) Effects of drying methods and storage time on the aroma and milling quality of rice (Oryza sativa L.) cv. Khao Dawk Mali 105. Food Chem 87:407–414CrossRefGoogle Scholar
  27. Yoshihashi T (2002) Quantitative 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 67:619–622CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Khin Myo Myint
    • 1
    • 2
  • Siwaret Arikit
    • 2
  • Samart Wanchana
    • 3
  • Tadashi Yoshihashi
    • 4
  • Kiattawee Choowongkomon
    • 5
  • Apichart Vanavichit
    • 2
    • 6
  1. 1.Tropical Agriculture ProgramKasetsart UniversityNakhon PathomThailand
  2. 2.Rice Science Center and Rice Gene DiscoveryKasetsart UniversityNakhon PathomThailand
  3. 3.International Rice Research InstituteLos BañosPhilippines
  4. 4.Postharvest Science and Technology DivisionJapan International Research Center for Agricultural SciencesTsukubaJapan
  5. 5.Department of Biochemistry, Faculty of ScienceKasetsart UniversityBangkokThailand
  6. 6.Department of AgronomyKasetsart UniversityNakhon PathomThailand

Personalised recommendations