Eccoilopus formosanus (Taiwan Oil Millet, TOM) is an orphan cereal endemic to Taiwan that was domesticated by the aboriginal population. TOM is a perennial C4 species, remarkable in that it secretes large quantities of oil and/or liquid wax on the panicle and copious amounts of solid wax on the leaf sheaths of a substantial vegetative biomass. TOM seeds possess an exceptionally large embryo, rich in triacylglycerol and protein. TOM constitutes an oil-rich cereal crop possessing an energy-rich biomass. The panicle exudate contains fatty acids, with high % of C28 chain lengths together with diverse alkanes. The leaf sheath epiderm secretes a uniform cuticular wax and a solid wax in the form of hairs from arrays of pores. The wax hairs comprise fatty acids chain length up to C26 and abundant alkanes up to C34. The seed contains 13.3% protein and 11% triacylglycerol, exceptionally high for cereals, enriched in linoleic acids. The species is unique in the combination of physiological attributes and may constitute a multifunctional crop of value as an energy-rich biomass and/or a source of plant waxes for industrial uses as well as a protein-calorie rich seed. We are currently work on the omics analysis of this crop, we also are developing it into ideal staple crop and forage crop.

DNA barcodes are standardized DNA sequences that usually range between 400 to 800 bp, vary at different taxonomic levels and make it possible to quickly identify new individuals of species that have been previously sequenced and classified taxonomically. Several barcodes have been identified and evaluated for different groups in the tree of life, however, there are many groups that still lack a good DNA marker, and even more so, accurate strategies that enable the verification of their taxonomic affiliation. For plants there are several DNA barcodes that have been postulated, nonetheless, their classification potential has not been evaluated systematically, and as a result, it would appear as not one excels above the others. One of the tools that has recently gained traction in this field is the use of Naïve Bayesian Classifiers. This type of classifier is based on the autonomy of attributes and the allocation of categories on a given context, having been mainly used in the classification of genes such as the bacterial 16S. In the present study we evaluate the classification power of several plant biomarkers that may work as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH and psbK) using a Naïve Bayesian Classifier, in order to determine markers what work best at different taxonomic levels.

Classification performance of the proposed biomarkers is differential, having all of them enough resolution to classify at family level, and two of them (trnL and matK) had the best performance at genus level. None of the markers had enough resolution for species level. Increasing K-mer size has an effect on taxonomic classification, however this benefit is marginal with respect to the computational cost. Confusion matrix indicates that genera with lots of species tend to misclassify more often than genera with less species. Finally, we provide Greengenes-like databases derived from NCBI data for researchers who want to use these resources in their own research.

After big genotypic dataset such as the 3000-rice genome (3K-RG) are becoming open through various platforms, one-stand solutions which could offer user-friendly web services for users with overwhelming phenotyping data based on the sequenced genomes are sincerely desired. Here we introduce a new version of the Rice Functional Genomic and Breeding (RFGBv2.0). It includes five major modules, which are: Phenotype, Haplotype, SNP & InDel, Restore Sequence, and Germplasm. Their functions are described with the embedded 3K-RG data as example. Four tips of iceberg for user cases of RFGB v2.0 with corresponding technical routes were presented including: 1) exploring favorable donors for higher zinc concentration in milled grains, 2) shortlisting candidate genes for grain length with near isogenic lines, 3) mining favorable haplotypes for seedling vigor traits under paddy direct seeding system, and 4) variations and restore sequence seeking for a leaf rolling QTL region. RFGB v2.0 has offered a unique view on bridging the huge gaps between two big datasets of genome and phenome from 3K-RG, which will spark more ideas on deeper mining of complex traits in rice.

Cytosine-to-Uridine (C-to-U) and adenine-to-inosine (A-to-I) RNA editing involves the deamination phenomenon, which is common in animals and plants; however, the amination of U-to-C is confined to the plants. In this study, the high-throughput RNA sequencing (RNA-seq) of 12-days-old Arabidopsis seedlings was performed, which enables transcriptome-wide identification of RNA editing sites to analyse differentially expressed genes (DEGs) and nucleotide base conversions. The results showed that DEGs were expressed to higher levels in 12-days-old seedlings than in 20-days-old seedlings. This was confirmed by higher higher Fragment Per Kilobase of transcript per Million mapped reads (FPKM) values, read counts, and more up-regulated genes, in 12-days-old seedlings. Additionally, pentatricopeptide repeat (PPR) genes were also expressed at higher levels as indicated by the log₂FC values. The U-to-C RNA editing are predominantly found in the untranslated region (UTR) region of the mature mRNA and affect its secondary structure. Our results suggest that U-to-C RNA editing in mature transcripts impacts plant physiology. Furthermore, we investigated the physiological role of U-to-C RNA editing in Arabidopsis by using the transcription inhibitor, Actinomycin D (ActD). Addition of ActD to the cell suspension culture of transgenic Arabidopsis generated by Agrobacterium-mediated transformation revealed that single nucleotide conversion adversely affects the secondary structure and mRNA half-life of PPR protein.

Climate change is becoming a world problem because of its harmful effects on crop productivity. In this regard, it is crucial to carry out studies to determine the crop's response molecular mechanism to heatwave stress. Response molecular mechanisms during the development and ripening of mango fruit (Mangifera indica L. cv. Chaunsa White) under extreme heatwaves were studied. Mango flowers were tagged and fruits with 18, 34, 62, 79, 92 days after flowering (DAF) as well as fruits with 10 and 15 days of postharvest shelf life were studied through RNA-seq and metabolome of the fruit mesocarp. The environmental temperature was recorded during experiment. Roughly, 2,000,000 clean reads were generated and assembled into 12,876 redundant transcripts and 2,674 non-redundant transcripts. The expression of genes playing a role in oxidative stress, circadian rhythm, senescence, glycolysis, secondary metabolite biosynthesis, flavonoid biosynthesis and monoterpenoid biosynthesis was quantified as well as changes in reactive oxygen species. Higher expressions of six abiotic stress genes and a senescent associated gene was found at 79 DAF (recorded temperature 44 oC). Higher expressions of nucleoredoxin and glutathione S-transferase 1 family protein were also recorded. Activation of the GABA-shunt pathway was detected by the glutamate decarboxylase transcript expression at 79 DAF. Larger energy demands at the beginning of fruit ripening were indicated by an increase in fructose-bisphosphate aldolase gene expression. Finally, the radical-scavenging effect of mango fruit inflorescence and fruit pulp extracts showed decline upon heatwave exposure. We recorded a broad genetic response of mango fruit suggesting the activation of several metabolic pathways which indicated the occurrence of genetic and metabolic crosstalks in response to intense heatwaves. Collectively, this study presents experimental evidences to help in the elucidation of the molecular mechanism of crops response to heat stress which in turn will help in the designing of protocols to increase crop productivity in the face of World’s climate change.

The genetic architecture of drought tolerance is expected to involve multiple loci that are unlikely to all segregate for alternative alleles in a single bi-parental population. Therefore, the identification of quantitative trait loci (QTL) that are expressed in diverse genetic backgrounds of multiple bi-parental populations provides evidence about both background-specific and common genetic variants. The purpose of this study was to map QTL related to drought tolerance using three connected mapping populations of different genetic backgrounds, to gain insight into the genomic landscape of this important trait in elite Ethiopian germplasm. The three bi-parental populations, each with 207 F_2:3 lines were evaluated using an alpha lattice design with two replications under two moisture stress environments. Drought tolerance related traits were analyzed separately for each population using composite interval mapping, finding a total of 105 QTLs. All the QTLs identified from individual populations were projected on a combined consensus map, comprising a total of 25 meta QTLs for seven traits. The consensus map allowed us to deduce locations of a larger number of markers than possible in any individual map, providing a reference for genetic studies in different genetic backgrounds. The mQTL identified in this study could be used for marker- assisted breeding programs in sorghum after validation. Only one trait, reduced leaf senescence, showed a striking bias of allele distribution, indicating substantial standing variation among present varieties that might employed in improving drought tolerance of Ethiopian and other sorghums.

Moringa is one of the 13 diverse species present in the genus of tropical plant family Moringaceae. It has been a wonder crop with many beneficial compounds present in it. The leaves of Moringa are a very rich source of iron and the pods are said to be rich in fiber. A total of 48 polymorphic expressed sequence tag based microsatellite markers (EST-SSRs) were mined from transcriptome data of different parts of Moringa plant. A set of 32 genotypes selected from the germplasm have been assessed using the EST-SSRs thus designed. Of the different types of SSRs, we have 38% mononucleotide repeat motifs followed by 21% di-nucleotide repeats. The trinucleotide repeat like [(ATC/TGA/TCT/GAA)] were also found along with multinucleotide compound repeats. The mean expected heterozygosity (HE) ranged from 0.605 to 0.958 and observed heterozygosity (HO) ranged from 0.938 to 1.00 and PIC value ranged from 0.511 to 0.94. The diversity analysis using the EST-SSR data clustered the Moringa accessions into three clusters. These developed EST-SSRs can be useful in future population genetics analysis and breeding programs in Moringa species.

Statement of the problem: The Coronavirus (COVID-19) epidemic has impacted people’s health and health-related importance of life. In addition to non-   pharmaceutical interventions, nutrition, and other lifestyle measures influence immune strength and susceptibility to infectious disease. Since the outbreak, there has been no vaccine or specific antiviral medication or clinically approved drug so based on the contribution of past traditional medicine (ethnomedicine) and immune-based therapy as a treatment in critical pathogen outbreaks, we aim the potential use of medicinal and aromatic plants in enhancing immunity as a preventive solution.  Methodology & Theoretical Orientation: This paper focuses on the antiviral potential of medicinal plants against coronavirus disease as they are enhanced with diverse phytochemicals through highly active secondary metabolites that can interrupt the replication of several highly pathogenic viruses. The main focus of researchers around the world is designing and identifying inhibitors against all possible viral key protein targets with one of the drug target guanine-N7 methyltransferase which plays a key role in capping the 5Í´-ends of viral genomic RNA and sub-genomic RNAs to escape host innate immunity. The various computational approach used are homology modeling, protein and ligand preparation, Substrate docking, Molecular docking, High throughput virtual screening, and Molecular dynamics simulation. Findings: A combination of all these computational approaches provides the screened compounds that readily interact with the G3A binding site of the homology modeled N7-MTase domain and will have strong potency towards inhibiting the substrate binding and efficiently hinder the capping mechanism thus making the final compounds COVID-19 therapeutics. Conclusion & Significance: The anti-viral phytochemicals target N7-MTase inhibiting SARS-CoV-2 with the ability of RNA capping mechanism and the failure of which leads to viral RNA degradation, eventually hindering the replication cycle thereby