Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Rice

Volumn 5, Issue 1, 2012, Pages

  Myint, Khin Myo ^a,d   Courtois, Brigitte ^b   Risterucci, Ange Marie ^b   Frouin, Julien ^b   Soe, Khin ^c   Thet, Khin Maung ^a   Vanavichit, Apichart ^d   Glaszmann, Jean Christophe ^b  

^a Plant Biotechnology Center   (Myanmar)

^b UMR AGAP   (France)

^c Department of Agricultural research ^*  (Myanmar)

^d KASETSART UNIVERSITY   (Thailand)

Author keywords

aroma; BADH2; genetic diversity; Oryza sativa; SSR

Indexed keywords

EID: 84865129026     PISSN: 19398425     EISSN: 19398433     Source Type: Journal    
DOI: 10.1186/1939-8433-5-20     Document Type: Article

References (43)

1. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecic phylogenies. Mol Biol Evol 16:37-48.
2. Bourgis F, Guyot R, Gherbi H, Tailliez AI, Salse J, Lorieux M, Delseny GA (2008) Characterization of the major fragrance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice. Theor Appl Genet 117:353-368.
3. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005) The gene for fragrance in rice. Plant Biotechnol J 3:363-370.
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 68:439-449.
5. Breiman L, Friedman JH, Olshen R, Stone CJ (1984) Classification and regression trees. Wadsworth and Brooks, Pacific Grove, California.
6. Buttery RG, Ling LC, Juliano BO (1982) 2-Acetyl-1-pyrroline: an important aroma component of cooked rice. Chem Ind (London) 23:958-959.
7. Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, Cheng Z, Liu X, Xu M (2008) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20:1850-1861.
8. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611-2620.
9. Excoffier L, Laval G, Schneider S (2006) Arlequin v3.1. An integrated software for population genetic data analysis., http://cmpg.unibe.ch/software/arlequin3.
10. Fitzgerald MA, Sackville Hamilton NR, Calingacion MN, Verhoeven HA, Butardo VM (2008) Is there a second fragrance gene in rice? Plant Biotechnol J 6:416-423.
11. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity of O. sativa. Genetics 169:1631-1638.
12. Gay F, Maraval I, Roques S, Gunata Z, Boulanger R, Audebert A, Mestres C (2010) Effect of salinity on yield and 2-acetyl-1-pyrroline content in the grains of three fragrant rice cultivars in Camargue. Field Crop Res 117:154-160.
13. Glaszmann J-C (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21-30.
14. Glaszmann J-C (1988) Geographic pattern of variation among Asian native rice cultivars based on fifteen isozyme loci. Genome 30:782-792.
15. Glaszmann J-C, Arraudeau M (1986) Rice plant type variation: Japonica-Javanica relationships. Rice Genet Newsl 3:41-43.
16. Glaszmann J-C, Mew T, Hibino H, Kim CK, Mew TI, Vera Cruz CH, Notteghem J-L, Bonman JM (1995) Molecular variation as a diverse source of disease resistance in cultivated rice. In: Rice Genetics III. IRRI, Los Baños, Philippines, pp 460-466.
17. Juliano BO (2007) Rice chemistry and quality. Philrice, Philippines, p 402.
18. Kato S, Kosaha H, Hara S (1928) On the affinity of rice varieties as shown by the fertility of rice plants. Bull Sci Central Agric Kyushu Imperial Univ 2:241-276.
19. Khush GS, Brar D, Virk PS, Tang SX, Malik SS, Busto GA, Lee YT, McNally R, Trinh LN, Jiang Y, Shat MAM (2003) Classifying rice germplasm by isozyme polymorphism and origin of cultivated rice. In: IRRI Discussion Paper 46.p 279.
20. Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR (2009) The origin and evolution of fragrance in rice. PNAS 106(34):14444-14449.
21. Liu K, Muse SV (2005) PowerMarker: Integrated analysis environment for genetic marker data. Bioinformatics 31(9):2128-2129.
22. Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquière A (1996) Aroma in rice: genetic analysis of quantitative trait. Theor Appl Genet 93:1145-1151.
23. Matsuo T (1952) Genecological studies on cultivated rice. Bull Natl Inst Agric Sci Jpn 3:1-111.
24. Myint KM, Arikit S, Wanchana S, Yoshihashi T, Choowongkomon K, Vanavichit A (2012) A PCR-based marker for a locus conferring the aroma in Myanmar rice (Oryza sativa L.). Theor Appl Genet: DOI 10.1007/s00122-012-1880-0.
25. 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 down-regulation of OsBADH2 results in aroma (2-acetyl- 1-pyrroline) production in rice (Oryza sativa L.). BMC Plant Biol 8:100.
26. Oka HI (1958) Varietal variation and classification of cultivated rice. Ind J Genet Plant Breed 18:78-79.
27. Perrier X, Jacquemoud-Collet JP (2006) DARwin software.: http://darwin.cirad.fr/.
28. Petrov M, Danzart M, Giampaoli P, Fayre J, Richard H (1996) Rice aroma analysis. Discrimination between a scented and non-scented rice. Sci Aliment 16:347-360.
29. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959.
30. Risterucci AM, Grivet L, N'Goran JAK, Pieretti I, Flament MH, Lanaud C (2000) A high density linkage map of Theobroma cacao L. Theor Appl Genet 101:948-955.
31. Roy R, Steffens DL, Gratside B, Jang GY, Brumbaugh JA (1996) Producing STR locus patterns from bloodstains and other forensic samples using an infrared fluorescent automated DNA sequencer. J Forensic Sci 41:418-424.
32. Sakthivel K, Sundaram RM, Rani NS, Balachandran SM, Neereja CN (2009) Genetic and molecular basis of fragrance in rice. Biotechnol Adv 27:468-473.
33. 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 22:185-192.
34. Singh RK, Singh US, Khush GS (2000) Aromatic rices. Oxford and IBH Publishing Co, New Delhi, India, p 292.
35. Singh A, Singh PK, Singh R, Pandit A, Mahato AK, Gupta DK, Tyagi K, Singh AK, Singh NK, Sharma TR (2010) SNP haplotypes of the BADH1 gene and their association with aroma in rice (O. sativa L.). Mol Breed 26:325-338.
36. Sood BG, Siddiq EA (1978) A rapid technique for scent determination in rice. Indian J Genet Plant Breed 38:268-271.
37. Tun YT (2006) Characterization of Myanmar rice landraces based on analyses of genetic diversity of various traits. PhD thesis. Tokyo University of Agriculture, Japan, p 248.
38. Unnevher LJ, Duff B, Juliano BO (1992) Consumer demand for rice grain quality. IRRI, Manila Philippines and IDRC, Ottawa, Canada, p 248.
39. Vanavichit A, Yoshihashi T (2010) Molecular aspects of fragrance and aroma in rice. Adv Bot Res 56:49-73.
40. 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 7(319):181.
41. 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 30:529-538.
42. Wright S (1978) Evolution and the genetics of populations. Variability within and among natural population. University of Chicago Press, Chicago, p 590.
43. Yamanaka S, Jatoi SA, Yi SS, Kothari SL, Htut T, Watanabe KN (2011) Genetic diversity of Myanmar rice and their implementation on management methods. Afr J Biotechnol 10(8):1290-1298.