Molecular Breeding

, Volume 26, Issue 3, pp 419–424 | Cite as

The genetic origin of fragrance in NERICA1

  • Maxwell Darko Asante
  • Michael J. Kovach
  • Lingxia Huang
  • Sandra Harrington
  • Paul Kofi Dartey
  • Richard Akromah
  • Mande Semon
  • Susan McCouch


In this study, we investigated the cause and origin of fragrance in NERICA1, a fragrant rice inbred line developed from an interspecific cross between two non-fragrant parents. The genetic cause of fragrance in NERICA1 was found to be due to a previously reported mutation in the BADH2 gene, the same allele responsible for the majority of modern fragrant rice varieties. Haplotype analysis around the BADH2 gene in NERICA1, its parents, and 95 other varieties carrying the badh2.1 allele identified the source of the badh2.1 allele in NERICA1 was a fragrant tropical japonica variety, WAB638-1, which had been growing in the vicinity of the NERICA1 nursery during varietal development. The allele-specific marker for the badh2.1 allele consistently predicted fragrance in the diverse African germplasm tested, making it very useful for marker-assisted breeding of fragrant rice varieties in Africa.


Rice Fragrance NERICA1 BADH2 



We are grateful to the Generation Challenge Program for providing a 6-month fellowship to MDA that allowed this research to be conducted in the lab of SRM and the Plant Genome Program of the National Science Foundation (Award Number #0606461).

Supplementary material

11032_2009_9382_MOESM1_ESM.pdf (410 kb)
Supplementary material 1 (PDF 410 kb)
11032_2009_9382_MOESM2_ESM.pdf (56 kb)
Supplementary material 2 (PDF 56 kb)
11032_2009_9382_MOESM3_ESM.pdf (351 kb)
Supplementary material 3 (PDF 351 kb)


  1. Ahn SN, Bollich CN, Tanksley SD (1992) RFLP tagging of a gene for aroma in rice. Theor Appl Genet 84:825–828CrossRefGoogle Scholar
  2. Bhattacharjee P, Singhal RS, Kulkarni PR (2002) Basmati rice: a review. Int J Food Sci Technol 37:1–12CrossRefGoogle Scholar
  3. Bradbury L, Henry R, Jin Q, Reinke RF, Waters DLE (2005a) A perfect marker for fragrance genotyping in rice. Mol Breed 16:279–283CrossRefGoogle Scholar
  4. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005b) The gene for fragrance in rice. Plant Biotechnol J 3:363–370CrossRefPubMedGoogle Scholar
  5. Buttery RG, Ling LC, Juliano BO (1982) 2-acetyl-1-pyrroline: an important aroma component of cooked rice. Chem Ind (London) 12:958–959Google Scholar
  6. Chen S, Wu J, Yang Y, Shi W, Xu M (2006) The fgr gene responsible for rice fragrance was restricted within 69 kb. Plant Sci 171:505–514CrossRefGoogle Scholar
  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 20:1850–1861CrossRefPubMedGoogle Scholar
  8. Dekkers JCM (2004) Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J Anim Sci 82:E313–E328PubMedGoogle Scholar
  9. Dellaporta S, Wood T, Hicks T (1983) A plant DNA mini preparation: version II. Plant Mol Biol Rep 1:19–21CrossRefGoogle Scholar
  10. Dong Y, Tsuzuki E, Terao H (2001) Trisomic genetic analysis of aroma in three Japanese native rice varieties (Oryza sativa L.). Euphytica 117:191–196CrossRefGoogle Scholar
  11. Dorward A, Spencer D, Abalu G, Philip D, Ogungbile D (2008) Evaluation of adoption of NERICA and other improved upland rice varieties following varietal promotion activities in Nigeria: a study for the Gatsby and Rockefeller Foundations. Final report. School of Oriental and African Studies, University of LondonGoogle Scholar
  12. Fitzgerald MA, Sackville Hamilton NR, Calingacion MN, Verhoeven HA, Butardo VM (2008) Is there a second fragrance gene in rice? Plant Biotechnol J 6:416–423CrossRefPubMedGoogle Scholar
  13. Garland S, Lewin L, Blakeney A, Reinke R, Henry R (2000) PCR-based molecular markers for the fragrance gene in rice (Oryza sativa L.). Theor Appl Genet 101:364–371CrossRefGoogle Scholar
  14. Garris A, Tai T, Coburn J, Kresovich S, McCouch SR (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638CrossRefPubMedGoogle Scholar
  15. Ikeda R, Sokei Y, Akintayo I (2007) Reliable multiplication of seed for NERICA varieties of rice, Oryza sativa L. Genet Resour Crop Evol 54:1637–1644CrossRefGoogle Scholar
  16. Itani T (1993) History, cultivation, and breeding of aromatic rice cultivars. Bull Hiroshima Pref Univ 5:267–281Google Scholar
  17. Iyer-Pascuzzi A, McCouch S (2007) Functional markers for xa5 -mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296CrossRefGoogle Scholar
  18. Jia Y, Wang Z, Singh P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42:2145–2149CrossRefGoogle Scholar
  19. Jodon NE (1944) The inheritance of flower fragrance and other characters in rice. J Am Soc Agron 36:844–848Google Scholar
  20. Jones M, Dingkuhn M, Aluko/snm G, Semon M (1997) Interspecific Oryza Sativa L. X O. Glaberrima Steud. progenies in upland rice improvement. Euphytica 94:237–246CrossRefGoogle Scholar
  21. Kadam BS, Patankar VK (1938) Inheritance of aroma in rice. Chronica Botanica 4:32Google Scholar
  22. Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Nat Acad Sci 106(34):14444–14449CrossRefPubMedGoogle Scholar
  23. Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquière A (1996) Aroma in rice: genetic analysis of a quantitative trait. Theor Appl Genet 93:1145–1151CrossRefGoogle Scholar
  24. Qiu ZJ, Zhang YS (2003) Why fragrant rice produced in Thailand can be sold worldwide? World Agric (China) 2:33–36Google Scholar
  25. Semagn K, Ndjiondjop MN, Lorieux M, Cissoko M, Jones M, McCouch SR (2007) Molecular profiling of an interspecific rice population derived from a cross between WAB56–104 (Oryza sativa) and CG14 (Oryza glaberrima). Afr J Biotechnol 6:2014–2022Google Scholar
  26. 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
  27. Sood BC, Siddiq EA (1978) A rapid technique for scent determination in rice. Indian J Genet Plant Breed 38:268–271Google Scholar
  28. Sweeney M, McCouch S (2007) The complex history of the domestication of rice. Ann Bot 100(5):951–957CrossRefPubMedGoogle Scholar
  29. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3:e133CrossRefPubMedGoogle Scholar
  30. Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamate C, Yoshimura A, Doi K, McCouch SR (2009) Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182(4):1323–1334CrossRefPubMedGoogle Scholar
  31. Vaughan DA, Miyazaki S, Miyashita K (2004) The rice gene pool and human migrations. In: Werner D (ed) Biological Resources and Migration, Springer, Berlin, pp 1–13Google Scholar
  32. WARDA (2008) NERICA Adoption and Impact: summary of findings from four countries. Research and Development Brief August 2008Google Scholar
  33. Yamanaka S, Nakamura I, Watanabe K, Sato Y-I (2004) Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet 108:1200–1204CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Maxwell Darko Asante
    • 1
  • Michael J. Kovach
    • 2
  • Lingxia Huang
    • 2
  • Sandra Harrington
    • 2
  • Paul Kofi Dartey
    • 1
  • Richard Akromah
    • 3
  • Mande Semon
    • 4
  • Susan McCouch
    • 2
  1. 1.CSIR-Crops Research InstituteKumasiGhana
  2. 2.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  3. 3.Faculty of Agriculture, Department of Crop & Soil SciencesKwame Nkrumah University of Science and TechnologyKumasiGhana
  4. 4.African Rice Centre (WARDA), 01CotonouBenin

Personalised recommendations