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. 2008 Aug;117(3):353-68.
doi: 10.1007/s00122-008-0780-9. Epub 2008 May 20.

Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice

F Bourgis  1 , R Guyot, H Gherbi, E Tailliez, I Amabile, J Salse, M Lorieux, M Delseny, A Ghesquière
Affiliations

Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice

F Bourgis et al. Theor Appl Genet. 2008 Aug.

Abstract

In Asian cultivated rice (Oryza sativa L.), aroma is one of the most valuable traits in grain quality and 2-ACP is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. Although the major locus for grain fragrance (frg gene) has been described recently in Basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different varieties is still limited. Here we report on characterisation of the frg gene in the Azucena variety, one of the few aromatic japonica cultivars. We used a RIL population from a cross between Azucena and IR64, a non-aromatic indica, the reference genomic sequence of Nipponbare (japonica) and 93-11 (indica) as well as an Azucena BAC library, to identify the major fragance gene in Azucena. We thus identified a betaine aldehyde dehydrogenase gene, badh2, as the candidate locus responsible for aroma, which presented exactly the same mutation as that identified in Basmati and Jasmine-like rices. Comparative genomic analyses showed very high sequence conservation between Azucena and Nipponbare BADH2, and a MITE was identified in the promotor region of the BADH2 allele in 93-11. The badh2 mutation and MITE were surveyed in a representative rice collection, including traditional aromatic and non-aromatic rice varieties, and strongly suggested a monophylogenetic origin of this badh2 mutation in Asian cultivated rices. Altogether these new data are discussed here in the light of current hypotheses on the origin of rice genetic diversity.

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Figures

Fig. 1
Fig. 1
Genotyping confirmation by Ecotilling and the presence of a deletion in the Azucena badh2 gene. Ecotilling was performed on genomic DNA of the nine individual RILs (16C, 19A, 35B, 122A, 159B, 166A, 186A, 259B and 274A) and the two parents Azucena and IR64. PCR amplification controls were performed on Nipponbare, Azucena and IR64. Control for heteroduplex formation and digestion was performed with Azucena and IR64 fragments
Fig. 2
Fig. 2
a Dot-plot alignments of aroma orthologous regions from Nipponbare (Nipponbare badh2; 43 kbp, horizontal) and Azucena (Azucena badh2; 38.6 kbp, vertical) O. sativa ssp. japonica varieties. Nucleotide conservation between orthologs is indicated by diagonal lines. Horizontal annotations correspond to the aligned segments of Nipponbare and vertical annotations to Azucena. Black boxes represent predicted genes and coloured boxes represent the different types of TEs. Blue arrows indicate the location of the mutation in the Azucena badh2 allele in both the annotations and aligned sequences. Vertical bars represent SNPs. b Orthologous regions from Azucena. Comparisons of the SNP content in Azucena and Nipponbare and, Azucena and 93-11. Vertical bars represent SNPs
Fig. 3
Fig. 3
Identification of the Azucena aroma allele badh2 and sequence alignment of BADH2 alleles in different rice varieties harbouring aroma haplotypes. The 12 bp sequence variation identified in the badh2 Azucena aroma allele is identical to that identified in Basmati and Jasmine rice aroma gene candidates. Nipponbare and 93-11 displayed no sequence variation, showing that they only contain the no-aromatic allele badh2. Four varieties not classified as aromatic (Arias, JC120, Khao Kap Xang, JC157) show the 12 bp mutation in BAD (Table 5)
Fig. 4
Fig. 4
Dot-plot alignments of badh2 orthologous alleles, from Nipponbare (Nipponbare BADH2, horizontal) and Azucena (Azucena badh2, vertical) O. sativa ssp. japonica varieties (a), from O. sativa ssp. indica 93-11 (93-11 BADH2, horizontal) and Azucena (Azucena badh2, vertical) (b). Nucleotide conservation between orthologous regions is indicated by diagonal lines. A break in the alignment between O. sativa 93-11 and Azucena shows the insertion of a TE in the promoter region of the 93-11 sequence (yellow arrow). Black boxes represent exons of badh2 alleles and coloured boxes represent different types of TEs. Blue arrows indicate the location of the mutation in the Azucena aroma badh2 allele in both the annotations and aligned sequences
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References

    1. Ahn SN, Bollisch CN, Tanksley SD. RFLP tagging of a gene for aroma in rice. Theor Appl Genet. 1992;84:825–828. doi: 10.1007/BF00227391. - DOI - PubMed
    1. Albar L, Bangratz-Reyser M, Hebrard E, Ndjiondjop MN, Jones M, Ghesquière A. Mutations in the eIF(iso) 4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus. Plant J. 2006;47:417–426. doi: 10.1111/j.1365-313X.2006.02792.x. - DOI - PubMed
    1. Amarawathi Y, Singh R, Sing AK, Singh VP, Mohapatra T, Sharma TR, Singh NK (2007) Mapping ofd quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol Breed. doi:10.1007/s11032-007-9108-8
    1. Bautista NS, Solis R, Kamijima O, Ishii T. RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice. Genes Genet Syst. 2001;76:71–79. doi: 10.1266/ggs.76.71. - DOI - PubMed
    1. Bradbury LM, Fitgerald TL, Henry RJ, Jin Q, Waters DLE. The gene for fragrance in rice. Plant Biotech J. 2005;3:363–370. doi: 10.1111/j.1467-7652.2005.00131.x. - DOI - PubMed

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