Effects of Tinospora tuberculata leaf methanol extract on seedling growth of rice and associated weed species in hydroponic culture

The study was conducted to evaluate the responses of rice and rice weed seedlings (barnyardgrass and weedy rice) at the three-leaf stage to Tinospora tuberculata leaf methanol extract (3.12, 6.25 and 12.5 g L−1) under hydroponic culture. It shows that the leaf methanol extract had various degrees effects depending on target plant species and each tested index (biomass, root length, shoot length, transpiration volume, chlorophyll a, chlorophyll b and carotenoid contents). The effective concentration of the leaf extract capable of reducing 50% of rice growth was higher than those of target weed species. Moreover, the root length was more tolerant to leaf methanol extract in comparison to the other plant parameters measured. A greater reduction was observed in chlorophyll a content compared to chlorophyll b and carotenoid. The results revealed that the reduction of transpiration volume closely coincided with the magnitude of growth inhibition of tested plants. Ultra-fast liquid chromatography analysis revealed 11 of 32 peaks in chemical profile, including benzoic acid, caffeic acid, chlorogenic acid, isoorientin, isovitexin, orientin, p-anisic acid, syringic acid, trans-cinnamic acid, trans-ferulic acid, and vitexin have the same retention time with those peaks of the extract. The amount of compounds was present in the range of between 4 817 and 115.5 mg kg−1 dry weight (DW). The concentration-response bioassay of all 11 individual compounds and their equimolar mixture against the seeds of barnyardgrass revealed their contribution in the allelopahic activity of T. tuberculata leaf extract. The examined compounds and their combination exhibited various degrees of growth inhibitory effects on the early growth of barnyardgrass. Therefore, the specific number, concentration, combination and inhibitory activity of bioactive compounds leads to allelopathy activity of T. tuberculata leaves which could be employable directly as a natural herbicide and its growth inhibitor compounds can be used as a template for producing new herbicides

Blast disease intimidation towards rice cultivation: a review of pathogen and strategies to control

Rice blast is the most destructive disease to rice production globally. The objective of this review is to know the fundamentals of rice blast disease and to know the different methods for controlling blast disease. Rice blast disease has been recognised in more than 85 rice-producing countries worldwide. Currently, more than 100 R genes for blast resistance have been identified in rice. These resistance genes can be introgressed into a susceptible variety through marker-assisted backcrossing. Infested residues and seeds are the primary inoculum sources to spread the disease. Considering the importance of this disease, various management approaches have been practiced to control blast disease. The use of resistant varieties is an important measure to manage the disease. This review will provide use fulfacts about the pathogen and its epidemiology, assessment of resistance genes and effective control measure of rice blast disease through breeding and management. This update information will be helpful and guide to the research students and rice breeders to develop durable blast resistant rice varieties. So farmers will able to manage the blast disease in future

Allelopathic effect of methanol extracts from Tinospora tuberculata on selected crops and rice weeds

Herbicidal potential of aerial parts of Tinospora tuberculata on germination and seedling growth of seven test plant species, namely rice (Oryza sativa L.); two rice weeds, barnyardgrass (Echinochloa crus-galli L.) and weedy rice (O. sativa f. spontanea); and four vegetable crops, lettuce (Lactuca sativa L.), tomato (Solanum lycopersicum L.), carrot (Daucus carota L.), and cucumber (Cucumis sativus L.) were evaluated. Six concentrations of methanol extract (3.12, 6.25, 12.5, 25, 50, and 100 g L−1) were compared with the control (distilled water). The rate of seed germination and the radicle and hypocotyl length of 7-day-old test plant seedlings were reduced as the concentration of extracts increased compared to the control. Generally, the degree of toxicity of extracts derived from the leaves was more than the extracts derived from the stem. Cluster analysis and the concentrations required for 50% inhibition (defined as EC50) of all parameters showed that radicle growth was more suppressed than germination and hypocotyl growth. Lettuce and carrot were observed as the most sensitive plants while rice showed the highest tolerance to both extracts. Moreover, the dicot target plants were affected more severely than the monocots when treated with leaf extract. The chemical composition of the T. tuberculata methanolic extracts was analyzed by a GC–MS system. A total of 92 and 22 constituents (not previously identified) were found in the leaves and stem, respectively. The results showed that 17 of the 92 components in the leaves, as compared to 4 of 22 compounds in the stem, are known as toxic compounds. These results suggest that T. tuberculata contains a significant source of plant growth inhibitors with potential for the development of future natural herbicide

Biochemical, genetic and molecular advances of fragrance characteristics in rice

One of the most valuable traits in high-quality rice is aroma or fragrance, which is important for consumer preference and global trade. Aromatic rice is unique and recognized as a badge of honor and an asset in many countries. Among more than 100 volatile components, 2-acetyl-1-pyrroline (2AP) is believed to be the main aromatic compound in rice. The principal gene contributing to 2AP is badh2, which was mapped on chromosome 8 by map-based cloning. A deletion in this gene truncates and makes non-functional the BADH2 protein. Thus, the mutant badh2 transcript leads to 2AP accumulation in aromatic rice. The discovery of the gene has led to the clarification of the biochemistry, molecular genetics and evolution of fragrant rice. The breeding of fragrant rice is now faster because of marker assisted selection (MAS), which is based on recognized genes. For a more extensive elucidation of all effective and fundamental factors contributing to rice fragrance, it is essential to further explore target quantitative trait loci (QTLs) and their inheritance and locations

Phytotoxic interference of volatile organic compounds and water extracts of Tinospora tuberculata Beumee on growth of weeds in rice fields

Tinospora tuberculata Beumee is an aromatic shrub with pharmacological properties and belongs to the Menispermaceae family. We assessed T. tuberculata for its ability to suppress growth of weeds in rice fields. In seedling bioassays, the rate of seed germination and the radicle and hypocotyl lengths of barnyardgrass, rice and weedy rice seedlings were reduced as the concentration of aqueous water extracts and volatile organic compounds increased compared to the control. In a glasshouse experiment, T. tuberculata leaf powder also exhibited effective reduction in the emergence and growth of weeds in rice fields. Applications at rates of 4 t ha− 1 completely suppressed emergence of barnyardgrass, sprangletop and smallflower umbrella. The chemical compositions of extracts and volatiles were analyzed by GC–MS and HS-SPME-GC–MS. The results showed that 7 of 43 components in the leaf aqueous extract, as compared to 5 of 15 compounds in the stem aqueous extract, are known to be toxic compounds. Moreover, eight main volatile organic compounds were identified, which accounted for 97 and 95% of the whole fresh and dry leaf volatiles, respectively. We observed qualitative and quantitative differences in the compounds present in the dry and fresh leaf. Confocal laser scanning microscope images showed that the volatile emissions and aqueous extracts also inhibited the main root diameter, and the number and elongation of root hairs of tested weeds in rice fields. These results suggest that T. tuberculata contains a significant source of plant growth inhibitors. Hence, it can be used as a mulch to suppress weeds in rice fields and for developing new herbicide based on phytotoxic compounds release by this plant

The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with ‘MR84’, a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223–SCU015RM (1.63 cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars

Comparative mapping and discovery of segregation distortion and linkage disequilibrium across the known fragrance chromosomal regions in a rice F2 population

Segregation distortion analysis in plant breeding is highly important because deviation factors are occasionally serious barriers for introgression of genes of interest into cultivated species. Also, the identification of major QTLs by high linkage disequilibrium is highly useful for breeders in order for crop improvement programs and the further fine mapping of particular genes. Consequently, simultaneous consideration of segregation distortion and linkage disequilibrium leads to developing fertile hybrids and normal inheritance of agronomically favorable genes. Hence, the goal of this study was to investigate genomic regions known to contain fragrance quantitative trait loci (QTLs) in terms of segregation distortion and linkage disequilibrium pattern, and to seek for a possible relationship between them using codominant markers on chromosomes 3, 4, and 8 in a set containing 189 F2 progenies. For the first time, we discovered the presence and extent of segregation distortion and linkage disequilibrium across the fragrance chromosomal areas of rice. The high frequency of skewed allelic segregations in the chromosomes 3 and 4 supports reports of possible gametic selection (ga) and hybrid sterility (S) genes. Finally, the highest linkage disequilibrium values, the lowest recombination frequency, and the shortest distances were observed in the chromosomal regions without segregation distortion. High linkage disequilibrium correlations between markers at short distances may show that such markers can maintain high linkage disequilibrium with linked QTLs and are influential for both MAS and QTL mapping analysis. Moreover, an indirect relationship between segregation distortion and linkage disequilibrium was detected, and thus linkage disequilibrium maps were introduced as useful diagnostic tools for segregation distortion

Variation in the phytotoxic activity of Tinospora tuberculata extracts as influenced by solvent type and chemical profile

A study was conducted to evaluate the role of secondary metabolites on the allelopathic activity of methanol and water extracts obtained from aerial parts of Tinospora tuberculata on seed germination and the radicle and hypocotyl lengths of barnyard grass. The higher suppressive effects were observed on germination and seedling growth of barnyard grass, when the methanol extracts of Tinospora tuberculata stem or leaf were applied in comparison to the water extracts. Ultra-fast liquid chromatography analysis confirmed that methanol extracts and leaf extracts contained higher number and amount of chemical compounds than did those of the water extracts and stem extracts respectively. Moreover, the concentrations of 11 identified compounds of the extracts and an equimolar mixture of the chemicals required for 50% growth inhibition on barnyard grass germination, radicle and hypocotyle were determined. Trans-cinnamic acid and benzoic acid had the highest allelopathic activity, while chlorogenic acid and orientin had the lowest on the basis of the rank values. Benzoic acid was found in the highest concentration in the methanol leaf extract, while this compound was not identified in the water leaf extract. On the other hand, the predominant compound was orientin for stem extracts. These results suggest that these compounds may be involved in the allelopathy activity of Tinospora tuberculata depending on their number, concentration, combination and inhibitory activity. Tinospora tuberculata could be a potential source of natural inhibitor compounds employable for eco-friendly agriculture

Intelligent mining of large-scale bio-data: bioinformatics applications

Today, there is a collection of a tremendous amount of bio-data because of the computerized applications worldwide. Therefore, scholars have been encouraged to develop effective methods to extract the hidden knowledge in these data. Consequently, a challenging and valuable area for research in artificial intelligence has been created. Bioinformatics creates heuristic approaches and complex algorithms using artificial intelligence and information technology in order to solve biological problems. Intelligent implication of the data can accelerate biological knowledge discovery. Data mining, as biology intelligence, attempts to find reliable, new, useful and meaningful patterns in huge amounts of data. Hence, there is a high potential to raise the interaction between artificial intelligence and bio-data mining. The present paper argues how artificial intelligence can assist bio-data analysis and gives an up-to-date review of different applications of bio-data mining. It also highlights some future perspectives of data mining in bioinformatics that can inspire further developments of data mining instruments. Important and new techniques are critically discussed for intelligent knowledge discovery of different types of row datasets with applicable examples in human, plant and animal sciences. Finally, a broad perception of this hot topic in data science is given

“A Genome Mining Toolbox for CRISPR-associated Cas9 orthologues”

CRISPR-associated protein system can facilitate accurate and targeted editing of genomes. RNA-guided Cas9 can be employed as an efficient genome editing tool in human, plants, and animals. The Cas9 nuclease can be programmed by guide RNA (gRNA) in order to cut DNA at targeted regions. Therefore, concise mutations are introduced by homologous recombination or non-homologous end-joining repairing. Although the CRISPR/Cas9 is a powerful system, alternative strategies have been developed to decrease the risk of off-target activities such as using Cas9 orthologs. Additionally, only one activity can be mediated by the Cas9 protein from Streptococcus pyogenes (Sp) at different target regions. In other words, it is unable to simultaneously mediate a different activity at other targets. Besides SpCas9, some orthologous CRISPR–Cas9 systems from different species have been discovered and utilized for genome editing. Therefore, in order for wider application of CRISPR-Cas, new and applicable Cas proteins, with different requirements for PAM sequence, gRNA length, and tracrRNA and crRNA sequences, have emerged from several species as a new tool for effective genome editing. Consequently, discovery of various potential Cas9 proteins becomes a major concern for CRISPR/Cas-mediated genome editing technology to develop straightforward bioinformatics tools with high efficiency and versatility to facilitate the artificial design of possible gRNAs. Hence, we aimed to create an application tool to perform high-throughput detection of target sites based on the specific sequence and length of PAM followed by a constant length of target site for not only common Streptococcus pyogenes (SpCas9) but also for other CRISPR-Cas systems. To this end, different search modes for gRNA detection were applied including i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching. Also, a complete list of all possible gRNAs along with their useful information can be provided for various potential Cas9 orthologs. Such progress expands the toolbox of genome editing and the possibilities for the site-specific genome engineering