Improvement in Flavonoids and Phenolic Acids Production and Pharmaceutical Quality of Sweet Basil (Ocimum basilicum L.) by Ultraviolet-B Irradiation.

Sweet basil (Ocimum basilicum Linnaeus) is aromatic herb that has been utilized in traditional medicine. To improve the phytochemical constituents and pharmaceutical quality of sweet basil leaves, ultraviolet (UV)-B irradiation at different intensities (2.30, 3.60, and 4.80 W/m²) and durations (4, 6, 8, and 10-h) was applied at the post-harvest stage. Total flavonoid content (TFC) and total phenolic content (TPC) were measured using spectrophotometric method, and individual flavonoids and phenolic acids were identified using ultra-high performance liquid chromatography. As a key enzyme for the metabolism of flavonoids, chalcone synthase (CHS) activity, was measured using a CHS assay. Antioxidant activity and antiproliferative activity of extracts against a breast cancer cell line (MCF-7) were evaluated using 1,1-diphenyl-2-picrylhydrazyl (DPPH) assays and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays, respectively. UV-B irradiation at an intensity of 3.60 W/m² increased TFC approximately 0.85-fold and also increased quercetin (0.41-fold), catechin (0.85-fold), kaempferol (0.65-fold) rutin (0.68-fold) and luteolin (1.00-fold) content. The highest TPC and individual phenolic acid (gallic acid, cinnamic acid and ferulic acid) was observed in the 3.60 W/m² of UV-B treatment. Cinnamic acid and luteolin were not detected in the control plants, production being induced by UV-B irradiation. Production of these secondary metabolites was also significantly influenced by the duration of UV-B irradiation. Irradiation for 8-h led to higher TFC, TPC and individual flavonoids and phenolic acids than for the other durations (4, 8, and 10-h) except for cinnamic acid, which was detected at higher concentration when irradiated for 6-h. Irradiation for 10-h significantly decreased the secondary metabolite production in sweet basil leaves. CHS activity was induced by UV-B irradiation and highest activity was observed at 3.60 W/m² of UV-B irradiation. UV-B treated leaves presented the highest DPPH activity and antiproliferative activity with a half-maximal inhibitory concentration (IC50) value of 56.0 and 40.8 µg/mL, respectively, over that of the control plants (78.0 and 58.2 µg/mL, respectively). These observations suggest that post-harvest irradiation with UV-B can be considered a promising technique to improve the healthy-nutritional and pharmaceutical properties of sweet basil leaves.

Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice.

Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865 mg g(-1) in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2.

Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins.

Alternative pre-mRNA splicing provides a source of vast protein diversity by removing non-coding sequences (introns) and accurately linking different exonic regions in the correct reading frame. The regulation of alternative splicing is essential for various cellular functions in both pathological and physiological conditions. In eukaryotic cells, this process is commonly used to increase proteomic diversity and to control gene expression either co- or post-transcriptionally. Alternative splicing occurs within a megadalton-sized, multi-component machine consisting of RNA and proteins; during the splicing process, this complex undergoes dynamic changes via RNA-RNA, protein-protein and RNA-protein interactions. Co-transcriptional splicing functionally integrates the transcriptional machinery, thereby enabling the two processes to influence one another, whereas post-transcriptional splicing facilitates the coupling of RNA splicing with post-splicing events. This review addresses the structural aspects of spliceosomes and the mechanistic implications of their stepwise assembly on the regulation of pre-mRNA splicing. Moreover, the role of phosphorylation-based, signal-induced changes in the regulation of the splicing process is demonstrated.

Variation in secondary metabolite production as well as antioxidant and antibacterial activities of Zingiber zerumbet (L.) at different stages of growth.

BACKGROUND: Zingiber zerumbet (L.) is a traditional Malaysian folk remedy that contains several interesting bioactive compounds of pharmaceutical quality. METHODS: Total flavonoids and total phenolics content from the leaf, stem, and rhizome of Z. zerumbet at 3 different growth stages (3, 6, and 9 months) were determined using spectrophotometric methods and individual flavonoid and phenolic compounds were identified using ultra-high performance liquid chromatography method. Chalcone Synthase (CHS) activity was measured using a CHS assay. Antioxidant activities were evaluated by ferric reducing antioxidant potential (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) assays. The antibacterial activity was determined against Gram-positive and Gram-negative bacteria using the disc diffusion method. RESULTS: Highest content of total flavonoid [29.7 mg quercetin equivalents (QE)/g dry material (DM)] and total phenolic (44.8 mg gallic acid equivalents (GAE)/g DM) were detected in the rhizome extracts of 9-month-old plants. As the plant matured from 3 to 9 months, the total flavonoid content (TFC) and total phenolic content (TPC) decreased in the leaf, but increased significantly in the rhizomes. Among the secondary metabolites identified, the most abundant, based on the concentrations, were as follows: flavonoids, catechin > quercetin > rutin > luteolin > myricetin > kaempferol; phenolic acids, gallic acid > ferulic acid > caffeic acid > cinnamic acid. Rhizome extracts from 9-month-old plants demonstrated the highest CHS activity (7.48 nkat/mg protein), followed by the 6-month-old rhizomes (5.79 nkat/mg protein) and 3-month-old leaf (4.76 nkat/mg protein). Nine-month-old rhizomes exhibited the highest DPPH activity (76.42 %), followed by the 6-month-old rhizomes (59.41 %) and 3-month-old leaves (57.82 %), with half maximal inhibitory concentration (IC50) of 55.8, 86.4, and 98.5 µg/mL, respectively, compared to that of α- tocopherol (84.19 %; 44.8 µg/mL) and butylated hydroxytoluene (BHT) (70.25 %; 58.6 µg/mL). The highest FRAP activity was observed in 9-month-old rhizomes, with IC50 of 62.4 µg/mL. Minimal Inhibitory Concentration (MIC) of Z. zerumbet extracts against Gram-positive and Gram-negative bacteria ranged from 30 to >100 µg/mL. Among the bacterial strains examined, Staphylococcus aureus was sensitive to the leaf extract of Z. zerumbet, with MIC of 30.0 µg/mL and other strains were sensitive to the rhizome extracts. CONCLUSIONS: Three- and 9-month-old plants are recommended when harvesting the leaf and rhizome of Z. zerumbet, respectively, in order to obtain effective pharmaceutical quality of the desired compounds.

Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop.

Rice is a staple and most important security food crop consumed by almost half of the world's population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control.

Secondary metabolites constituents and antioxidant, anticancer and antibacterial activities of Etlingera elatior (Jack) R.M.Sm grown in different locations of Malaysia.

BACKGROUND: Etlingera elatior is a well-known herb in Malaysia with various pharmaceutical properties. METHODS: E. elatior flowers grown in three different locations of Malaysia (Kelantan, Pahang and Johor), were investigated for differences in their content of secondary metabolites (total phenolics [TPC], total flavonoids [TFC], and total tannin content [TTC]) as well as for their antioxidant, anticancer, and antibacterial properties. Phenolic acids and flavonoids were isolated and identified using ultra-high performance liquid chromatography (UHPLC). Ferric reducing antioxidant potential (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) assays were used to evaluate the antioxidant activities. The anticancer activity of extracts was evaluated using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. RESULTS: When extracted with various solvents (aqueous and ethanolic), samples from the different locations yielded significantly different results for TPC, TFC, and TTC as well as antioxidant activity. Aqueous extracts of E. elatior flowers collected from Kelantan exhibited the highest values: TPC (618.9 mg/100 g DM), TFC (354.2 mg/100 g DM), TTC (129.5 mg/100 g DM), DPPH (76.4 %), and FRAP (6.88 mM of Fe (II)/g) activity with a half-maximal inhibitory concentration (IC50) of 34.5 µg/mL compared with extracts of flowers collected from the other two locations. The most important phenolic compounds isolated in this study, based on concentration, were: gallic acid > caffeic acid > tannic acid > chlorogenic acid; and the most important flavonoids were: quercetin > apigenin > kaempferol > luteolin > myricetin. Extracts of flowers from Kelantan exhibited potent anticancer activity with a IC50of 173.1 and 196.2 µg/mL against the tumor cell lines MCF-7 and MDA-MB-231 respectively, compared with extracts from Pahang (IC50 = 204.5 and 246.2 µg/mL) and Johor samples (IC50 = 277.1 and 296.7 µg/mL). Extracts of E. elatior flowers also showed antibacterial activities against Staphylococcus aureus, Bacillus subtilis, Listeria monocytogenes, Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa with minimal inhibitory concentrations (MIC) ranging from 30 to >100 µg/mL. CONCLUSIONS: In general, therefore, based on the potent antioxidant and anticancer activity of flower extracts, it appears that E. elatior grown in the North-east of Malaysia (Kelantan) is a potential source of therapeutic compounds with anti-cancer activity.

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives.

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

Multiplex SSR-PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice.

In the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5'-end with either 6-FAM or HEX using the G5 dye set and incorporated into a multiplex SSR-PCR for the detection of fragments using an automated system. For rice F3 families obtained from crosses between Pongsu Seribu 2 (Malaysian blast resistant cultivar) and Mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex SSR panels were determined. The genotyping assays were performed using a capillary-based ABIPRISM 3100 genetic analyser. The sizes of the SSRs alleles observed in the range from 79 to 324 bp. The observed marker segregation data were analysed using the Chi(2) test. A genetic linkage map covering ten chromosomes and comprising 63 polymorphic SSR markers was constructed, and the distorted loci were localised to linkage groups. The results indicated that distorted loci are presented on eight chromosomes.

Marker-assisted backcrossing: a useful method for rice improvement.

The world's population is increasing very rapidly, reducing the cultivable land of rice, decreasing table water, emerging new diseases and pests, and the climate changes are major issues that must be addressed to researchers to develop sustainable crop varieties with resistance to biotic and abiotic stresses. However, recent scientific discoveries and advances particularly in genetics, genomics and crop physiology have opened up new opportunities to reduce the impact of these stresses which would have been difficult if not impossible as recently as the turn of the century. Marker assisted backcrossing (MABC) is one of the most promising approaches is the use of molecular markers to identify and select genes controlling resistance to those factors. Regarding this, MABC can contribute to develop resistant or high-yielding or quality rice varieties by incorporating a gene of interest into an elite variety which is already well adapted by the farmers. MABC is newly developed efficient tool by which using large population sizes (400 or more plants) for the backcross F1 generations, it is possible to recover the recurrent parent genotype using only two or three backcrosses. So far, many high yielding, biotic and abiotic stresses tolerance, quality and fragrance rice varieties have been developed in rice growing countries through MABC within the shortest timeframe. Nowadays, MABC is being used widely in plant breeding programmes to develop new variety/lines especially in rice. This paper reviews recent literature on some examples of variety/ line development using MABC strategy.

Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.).

Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection.

Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia.

Changes in nutritional metabolites of young ginger (Zingiber officinale Roscoe) in response to elevated carbon dioxide.

The increase of atmospheric CO2 due to global climate change or horticultural practices has direct and indirect effects on food crop quality. One question that needs to be asked, is whether CO2 enrichment affects the nutritional quality of Malaysian young ginger plants. Responses of total carbohydrate, fructose, glucose, sucrose, protein, soluble amino acids and antinutrients to either ambient (400 µmol/mol) and elevated (800 µmol/mol) CO2 treatments were determined in the leaf and rhizome of two ginger varieties namely Halia Bentong and Halia Bara. Increasing of CO2 level from ambient to elevated resulted in increased content of total carbohydrate, sucrose, glucose, and fructose in the leaf and rhizome of ginger varieties. Sucrose was the major sugar followed by glucose and fructose in the leaf and rhizome extract of both varieties. Elevated CO2 resulted in a reduction of total protein content in the leaf (H. Bentong: 38.0%; H. Bara: 35.4%) and rhizome (H. Bentong: 29.0%; H. Bara: 46.2%). In addition, under CO2 enrichment, the concentration of amino acids increased by approximately 14.5% and 98.9% in H. Bentong and 12.0% and 110.3% in H. Bara leaf and rhizome, respectively. The antinutrient contents (cyanide and tannin) except phytic acid were influenced significantly (P ≤ 0.05) by CO2 concentration. Leaf extract of H. Bara exposed to elevated CO2 exhibited highest content of cyanide (336.1 mg HCN/kg DW), while, highest content of tannin (27.5 g/kg DW) and phytic acid (54.1 g/kg DW) were recorded from H.Bara rhizome grown under elevated CO2. These results demonstrate that the CO2 enrichment technique could improve content of some amino acids and antinutrients of ginger as a food crop by enhancing its nutritional and health-promoting properties.

Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus.

Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D(2) statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F2 population of cross, BR11×Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model.