Biochemical and Enzymatic Study of Rice BADH Wild-Type and Mutants: An Insight into Fragrance in Rice

Wongpanya, Ratree; Boonyalai, Nonlawat; Thammachuchourat, Napaporn; Horata, Natharinee; Arikit, Siwaret; Myint, Khin Myo; Vanavichit, Apichart; Choowongkomon, Kiattawee

doi:10.1007/s10930-011-9358-5

Cited by 15 publications

(12 citation statements)

References 28 publications

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“…But the 3 bp insertion was present at a much higher frequency in our sample. It was recently demonstrated that this insertion did not modify the gene expression but the addition of a tyrosine to the peptide interfered with cofactor NAD + binding, lowered enzyme activity and led to accumulation of acetyl-pyrroline, although at a lower level than in accessions carrying the 8 bp deletion ( [Vanavichit and Yoshihashi 2010], [Wongpanya et al 2011], [Myint et al 2012]). We found one additional deletion of 43 bp at the very end of the gene in 22 accessions that was specific to Myanmar accessions.…”

Section: Discussionmentioning

confidence: 99%

Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Myint

Courtois

Risterucci

et al. 2012

Rice

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BackgroundAfter observing peculiar rice varieties in Myanmar, in terms of classification in varietal groups and of grain quality, we focused on Myanmar varieties and analyzed variations at 19 microsatellite loci as well as sequences of the aroma gene BADH2.ResultsMicrosatellites were able to retrieve the well-established classification into Indica (isozyme group 1), Japonica (group 6, comprising temperate and tropical forms) and specific groups from the Himalayan foothills including some Aus varieties (group 2) and some aromatic varieties (group 5). They revealed a new cluster of accessions close to, but distinct from, non-Myanmar varieties in group 5. With reference to earlier terminology, we propose to distinguish a group “5A” including group 5 varieties from the Indian subcontinent (South and West Asia) and a group “5B” including most group 5 varieties from Myanmar. In Myanmar varieties, aroma was distributed in group 1 (Indica) and in group 5B. New BADH2 variants were found. Some accessions carried a 43 bp deletion in the 3’ UTR that was not completely associated with aroma. Other accessions, all of group 5B, displayed a particular BADH2 allele with a 3 bp insertion and 100% association with aroma.ConclusionWith the new group and the new alleles found in Myanmar varieties, our study shows that the Himalayan foothills contain series of non-Indica and non-Japonica varietal types with novel variations for useful traits.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-20) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Myint

Courtois

Risterucci

et al. 2012

Rice

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“…The crystallization of the 503-amino acid Os2AP protein from the non-aromatic isogenic line was reported (Kuaprasert et al 2011 ). The structure was predicted to contain three binding domains: an NAD+ binding, an oligomerization, and a substrate binding domain where an aldehyde dehydrogenase cysteine subdomain was located (Chen et al 2008 ; Wongpanya et al 2011 ). In the aromatic isogenic lines and KDML105, the specific 8-bp deletion was identified within exon 7 of the AMADH of KDML105, causing a premature stop codon, non-sense-mediated decay, and non-functioning of Os2AP , respectively (Vanavichit et al 2005 ).…”

Section: Cooking Quality Fragrance and Interaction With Environmentmentioning

confidence: 99%

Thai Hom Mali Rice: Origin and Breeding for Subsistence Rainfed Lowland Rice System

Vanavichit

Kamolsukyeunyong

Siangliw

et al. 2018

Rice

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The world-renowned Thai Hom Mali Rice has been the most important aromatic rice originating in Thailand. The aromatic variety was collected from Chachoengsao, a central province, and after pure-line selection, it was officially named as Khao Dawk Mali 105, (KDML105). Because of its superb fragrance and cooking quality, KDML105 has been a model variety for studying genes controlling grain quality and aroma. The aromatic gene was cloned in KDML105, as an amino aldehyde dehydrogenase (AMADH) or better known as BADH2 located on chromosome 8. Later on, all other aromatic rice genes were discovered as allelic to the AMADH. As a selection of local landrace variety found in rainfed areas, the Thai Jasmine rice showed adaptive advantages over improved irrigated rice in less fertile lowland rainfed conditions. Because KDML105 was susceptible to most diseases and insect pests, marker-assisted backcross selection (MABC) was used for the genetic improvement since 2000. After nearly 17 years of MABC for integrating new traits into KDML105, a new generation of KDML105, designated HM84, was developed which maintains the cooking quality and fragrance, and has gained advantages during flash flooding, disease, and insect outbreak.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0212-7) contains supplementary material, which is available to authorized users.

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“…In aromatic coconut, a base substitution was identified, which resulted in an amino acid change from alanine to proline at position 442 near the C-terminal of the protein. This might result in the fragrant phenotype in coconut, because this amino acid change was located within the substrate binding domain of the enzyme Wongpanya et al, 2011). Proline contains a side chain with a ring structure that may affect the overall structure of this domain of the enzyme (Figure 3), resulting in instability and a non-functional enzyme.…”

Section: Discussionmentioning

confidence: 99%

“…However, in rice, biosynthesis of this aromatic compound results from the metabolism of 4-aminobutyraldehyde (AB-ald) to 1-pyrroline, which is then converted to 2AP due to the lack of the functional enzyme, betaine aldehyde dehydrogenase homologue 2 (BADH2) (Yoshihashi et al, 2002;Vanavichit et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Single base substitution causing the fragrant phenotype and development of a type-specific marker in aromatic coconut (Cocos nucifera)

et al. 2016

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ABSTRACT. The fragrance gene, betaine aldehyde dehydrogenase 2 (Badh2), has been well studied in many plant species. The objectives of this study were to clone Badh2 and compare the sequences between aromatic and non-aromatic coconuts. The complete coding region was cloned from cDNA of both aromatic and non-aromatic coconuts. The nucleotide sequences were highly homologous to Badh2 genes of other plants. Badh2 consisted of a 1512-bp open reading frame encoding 503 amino acids. A single nucleotide difference between aromatic and non-aromatic coconuts resulted in the conversion of alanine (non-aromatic) to proline (aromatic) at position 442, which was the substrate binding site of BADH2. The ring side chain of proline could destabilize the structure leading to a non-functional enzyme. Badh2 genomic DNA was cloned from exon 1 to 4, and from exon 5 to 15 from the two coconut types, except for intron 4 that was very long. The intron sequences of the two coconut groups were highly homologous. No differences in Badh2 expression were found among the tissues of aromatic coconut or between aromatic and non-aromatic coconuts. The amino acid sequences of BADH2 from coconut and other plants were compared and the genetic relationship was analyzed using MEGA 7.0. The phylogenetic tree reconstructed by the Bayesian information criterion consisted of two distinct groups of monocots and dicots. Among the monocots, coconut (Cocos nucifera) and oil palm (Elaeis guineensis) were the most closely related species. A marker for coconut differentiation was developed from one-base substitution site and could be successfully used.

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Biochemical and Enzymatic Study of Rice BADH Wild-Type and Mutants: An Insight into Fragrance in Rice

Cited by 15 publications

References 28 publications

Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Thai Hom Mali Rice: Origin and Breeding for Subsistence Rainfed Lowland Rice System

Single base substitution causing the fragrant phenotype and development of a type-specific marker in aromatic coconut (Cocos nucifera)

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