A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.)

Jin, Qingsheng; Waters, Daniel Le; Cordeiro, Giovanni M; Henry, Robert J.; Reinke, Russell

doi:10.1016/s0168-9452(03)00195-x

Cited by 80 publications

(44 citation statements)

References 20 publications

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“…Some progress has been made towards the identification of molecular markers linked to fragrance genes, including the SCU015RM (Cordeiro et al 2002) SNP marker (Jin et al 2003) and a single tube allele specific amplification (ASA) assay (Bradbury et al 2005b). However, these assays cannot work on a broad range of any one rice sample and predictions made from the results are not of high accuracy.…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae)

Sun

Gao

et al. 2008

Genet. Mol. Biol.

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We investigated inheritance and carried out gene fine mapping of aroma in crosses between the aromatic elite hybrid rice Oryza sativa indica variety Chuanxiang-29B (Ch-29B) and the non-aromatic rice O. sativa indica variety R2 and O. sativa japonica Lemont (Le). The F 1 grains and leaves were non-aromatic while the F 2 non-aroma to aroma segregation pattern was 3:1. The F 3 segregation ratio was consistent with the expected 1:2:1 for a single recessive aroma gene in Ch-29B. Linkage analysis between simple sequence repeat (SSR) markers and the aroma locus for the aromatic F 2 plants mapped the Ch-29B aroma gene to a chromosome 8 region flanked by SSR markers RM23120 at 0.52 cM and RM3459 at 1.23 cM, a replicate F 2 population confirming these results. Three bacterial artificial chromosome (BAC) clones cover chromosome 8 markers RM23120 and RM3459. Our molecular mapping data from the two populations indicated that the aroma locus occurs in a 142.85 kb interval on BAC clones AP005301 or AP005537, implying that it might be the same gene reported by Bradbury et al (2005a; Plant Biotec J. 3:363-370). The flanking markers Aro7, RM23120 and RM3459 identified by us could greatly accelerate the efficiency and precision of aromatic rice breeding programs.

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Section: Discussionmentioning

confidence: 99%

Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae)

Sun

Gao

et al. 2008

Genet. Mol. Biol.

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“…Genetic analysis shows that a single recessive gene (fgr) on chromosome 8 is associated with rice fragrance and that the dominant Fgr allele is associated with lack of fragrance (Sood and Siddiq, 1978;Huang et al, 1994;Jin et al, 2003). A number of markers were identified that are closely linked to fgr (Ahn et al, 1992;Causse et al, 1994;Chen et al, 1997;Cho et al, 1998;Jin et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

“…A number of markers were identified that are closely linked to fgr (Ahn et al, 1992;Causse et al, 1994;Chen et al, 1997;Cho et al, 1998;Jin et al, 2003). Two restriction fragment length polymorphism markers, RG1 and RG28, were identified that flank fgr, with the estimates of genetic distances ranging from 10 centimorgan (cM) (Causse et al, 1994) to 12 cM (Lorieux et al, 1996) to 25.5 cM (Cho et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Badh2, Encoding Betaine Aldehyde Dehydrogenase, Inhibits the Biosynthesis of 2-Acetyl-1-Pyrroline, a Major Component in Rice Fragrance

et al. 2008

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In rice (Oryza sativa), the presence of a dominant Badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) inhibits the synthesis of 2-acetyl-1-pyrroline (2AP), a potent flavor component in rice fragrance. By contrast, its two recessive alleles, badh2-E2 and badh2-E7, induce 2AP formation. Badh2 was found to be transcribed in all tissues tested except for roots, and the transcript was detected at higher abundance in young, healthy leaves than in other tissues. Multiple Badh2 transcript lengths were detected, and the complete, full-length Badh2 transcript was much less abundant than partial Badh2 transcripts. 2AP levels were significantly reduced in cauliflower mosaic virus 35S-driven transgenic lines expressing the complete, but not the partial, Badh2 coding sequences. In accordance, the intact, full-length BADH2 protein (503 residues) appeared exclusively in nonfragrant transgenic lines and rice varieties. These results indicate that the full-length BADH2 protein encoded by Badh2 renders rice nonfragrant by inhibiting 2AP biosynthesis. The BADH2 enzyme was predicted to contain three domains: NAD binding, substrate binding, and oligomerization domains. BADH2 was distributed throughout the cytoplasm, where it is predicted to catalyze the oxidization of betaine aldehyde, 4-aminobutyraldehyde (ABald), and 3-aminopropionaldehyde. The presence of null badh2 alleles resulted in AB-ald accumulation and enhanced 2AP biosynthesis. In summary, these data support the hypothesis that BADH2 inhibits 2AP biosynthesis by exhausting AB-ald, a presumed 2AP precursor.

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“…Several independent lines of evidence suggest the genetic cause of rice fragrance is due to the loss of function of the betaine aldehyde dehydrogenase (BAD) homolog. Fragrance is a recessive trait (Lorieux et al 1996;Garland et al 2000;Jin et al 2003) which suggests it is a loss, rather than gain, of gene function that is responsible for fragrance. Several mapping studies have independently identified BAD2 as the candidate gene responsible for fragrance (Bradbury et al 2005a, b;Vanavichit et al 2006;Amarawathi et al 2008;Shi et al 2008) and sequencing of BAD2 in each case found a deletion within the gene which would render the gene non-functional.…”

Section: Introductionmentioning

confidence: 99%

Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice

et al. 2008

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Rice (Oryza sativa) has two betaine aldehyde dehydrogenase homologs, BAD1 and BAD2, encoded on chromosome four and chromosome eight respectively. BAD2 is responsible for the characteristic aroma of fragrant rice. Complementary DNA clones of both BAD1 and BAD2 were isolated and expressed in E. coli. BAD2 had optimum activity at pH 10, little to no affinity towards Nacetyl-c-aminobutyraldehyde (NAGABald) with a Km of approximately 10 mM and moderate affinity towards c-guanidinobutyraldehyde (GGBald) and betaine aldehyde (bet-ald) with Km values of approximately 260 lM and 63 lM respectively. A lower Km of approximately 9 lM was observed with c-aminobutyraldehyde (GABald), suggesting BAD2 has a higher affinity towards this substate in vivo. The enzyme encoded on chromosome four, BAD1, had optimum activity at pH 9.5, showed little to no affinity towards bet-ald with a Km of 3 mM and had moderate affinity towards GGBald, NAGABald and GABald with Km values of approximately 545, 420 and 497 lM respectively. BAD1 had a half life roughly double that of BAD2. We discuss the implications of these findings on the pathway of fragrance generation in Basmati and Jasmine rice and the potential of rice to accumulate the osmoprotectant glycine betaine.

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A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.)

Cited by 80 publications

References 20 publications

Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae)

Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae)

Badh2, Encoding Betaine Aldehyde Dehydrogenase, Inhibits the Biosynthesis of 2-Acetyl-1-Pyrroline, a Major Component in Rice Fragrance

Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice

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