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


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.

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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.

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Correspondence to Apichart Vanavichit.

Additional information

Communicated by E. Guiderdoni.

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Myint, K.M., Arikit, S., Wanchana, S. et al. A PCR-based marker for a locus conferring the aroma in Myanmar rice (Oryza sativa L.). Theor Appl Genet 125, 887–896 (2012).

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  • Reverse Transcription Polymerase Chain Reaction
  • Rice Variety
  • Functional Marker
  • Single Recessive Gene
  • Aromatic Rice