Publications (27) View all
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Article: Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.).
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ABSTRACT: Oil palm (Elaeis guineensis Jacq.) is an economically important crop, which is grown for oil production. To better understand the molecular basis of oil palm chloroplasts, we characterized the complete chloroplast (cp) genome sequence obtained from 454 pyrosequencing. The oil palm cp genome is 156,973 bp in length consisting of a large single-copy region of 85,192 bp flanked on each side by inverted repeats of 27,071 bp with a small single-copy region of 17,639 bp joining the repeats. The genome contains 112 unique genes: 79 protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. By aligning the cp genome sequence with oil palm cDNA sequences, we observed 18 non-silent and 10 silent RNA editing events among 19 cp protein-coding genes. Creation of an initiation codon by RNA editing in rpl2 has been reported in several monocots and was also found in the oil palm cp genome. Fifty common chloroplast protein-coding genes from 33 plant taxa were used to construct ML and MP phylogenetic trees. Their topologies are similar and strongly support for the position of E. guineensis as the sister of closely related species Phoenix dactylifera in Arecaceae (palm families) of monocot subtrees.Gene 04/2012; 500(2):172-80. · 2.34 Impact Factor -
Article: The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships.
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ABSTRACT: Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.DNA Research 12/2009; 17(1):11-22. · 5.16 Impact Factor -
Article: Small GTP-Binding Protein Gene Is Associated with QTL for Submergence Tolerance in Rice
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ABSTRACT: Small GTP-binding proteins play critical roles in signal transduction in mammalian and plant systems. In this study, sequence variation of a small GTP-binding protein identified in the subgenomic region was analyzed. The major quantitative trait locus (QTL) controlling submergence tolerance on the 6.5-cM region of chromosome 9 was previously mapped, sequenced, and annotated. One of the most interesting candidate genes located in this QTL was a 5.2-kb sequence, which included a coding sequence consisting of two exons and a promoter. The deduced amino acid sequence corresponded to a 24.8 kD protein consisting of 226 amino acids, with 98% identity to RGP1, a small GTP-binding protein involved in a signal pathway responding to hormones, such as cytokinin and ethylene. According to the amino acid sequence, a putative small G-protein was classified as a small Ras-related GTP-binding protein. DNA gel blot analysis showed that the putative gene encoding the Ras-related GTP-binding protein was present as a single copy in the rice genome. Comparison of genomic sequences from several rice cultivars tolerant to submergence identified single nucleotide polymorphisms located in the TATA box of the Ras promoter region. Linkage analysis showed that the putative gene for GTP-binding protein was tightly linked to the peak of the QTL previously mapped on the long arm of chromosome 9. The single strand conformation polymorphism of the putative GTP-binding protein gene can be used for allele discrimination and marker assisted selection for tolerance to flash flooding.Russian Journal of Plant Physiology 08/2004; 51(5):648-657. · 0.71 Impact Factor -
Article: Thai jasmine rice carrying QTLch9 (SubQTL) is submergence tolerant.
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ABSTRACT: Submergence tolerance is an important agronomic trait for rice grown in South-East Asia, where flash flooding occurs frequently and unpredictably during the monsoons. Although mapping locations of one major and several minor quantitative trait loci (QTL) were known previously, improving submergence tolerance in agronomically desirable types of rice has not been achieved. KDML105 is jasmine rice widely grown in rain-fed lowland regions of Thailand. This cultivar is very intolerant of submergence stress. To improve submergence tolerance in this cultivar, three submergence-tolerant cultivars, FR13A, IR67819F2-CA-61 and IR49830-7-1-2-2, were cross-pollinated with KDML105. Transferring the major QTL for submergence tolerance was facilitated by four back-crossings to the recipient KDML105. Molecular markers tightly linked to the gene(s) involved were developed to facilitate molecular genotyping. We demonstrated that individuals of a BC4F3 line that retained a critical region on chromosome 9 transferred from tolerant lines were also tolerant of complete submergence while retaining all the agronomically desirable traits of KDML105. In addition, effects of secondary QTLch2 were detected statistically in back-cross progenies. Effects of secondary QTLch7 were not statistically significant. The close association between tightly linked markers of the tolerance locus on chromosome 9 and submergence tolerance in the field demonstrates the considerable promise of using these markers in lowland rice breeding programmes for selecting increased submergence tolerance.Annals of Botany 02/2003; 91 Spec No:255-61. · 4.03 Impact Factor -
Article: Molecular genetics of submergence tolerance in rice: QTL analysis of key traits.
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ABSTRACT: Flash flooding of young rice plants is a common problem for rice farmers in south and south-east Asia. It severely reduces grain yield and increases the unpredictability of cropping. The inheritance and expression of traits associated with submergence stress tolerance at the seedling stage are physiologically and genetically complex. We exploited naturally occurring differences between certain rice lines in their tolerance to submergence and used quantitative trait loci (QTL) mapping to improve understanding of the genetic and physiological basis of submergence tolerance. Three rice populations, each derived from a single cross between two cultivars differing in their response to submergence, were used to identify QTL associated with plant survival and various linked traits. These included total shoot elongation under water, the extent of stimulation of shoot elongation caused by submergence, a visual submergence tolerance score, and leaf senescence under different field conditions, locations and years. Several major QTL determining plant survival, plant height, stimulation of shoot elongation, visual tolerance score and leaf senescence each mapped to the same locus on chromosome 9. These QTL were detected consistently in experiments across all years and in the genetic backgrounds of all three mapping populations. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 5, 7, 10 and 11. These QTL were specific to particular traits, environments, or genetic backgrounds. All identified QTL contributed to increased submergence tolerance through their effects on decreased underwater shoot elongation or increased maintenance of chlorophyll levels, or on both. These findings establish the foundations of a marker-assisted scheme for introducing submergence tolerance into agriculturally desirable cultivars of rice.Annals of Botany 02/2003; 91 Spec No:243-53. · 4.03 Impact Factor
