Identification of novel inhibitors against VP40 protein of Marburg virus by integrating molecular modeling and dynamics approaches.

Marburg virus (MV) is a highly etiological agent of haemorrhagic fever in humans and has spread across the world. Its outbreaks caused a 23-90% human death rate. However, there are currently no authorized preventive or curative measures yet.

Contribution of Duplicated Nucleotide-Binding Leucine-Rich Repeat (NLR) Genes to Wheat Disease Resistance.

Wheat has a large and diverse repertoire of NLRs involved in disease resistance, with over 1500 NLRs detected in some studies. These NLR genes occur as singletons or clusters containing copies of NLRs from different phylogenetic clades. The number of NLRs and cluster size can differ drastically among ecotypes and cultivars.

Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice.

Background: Heat stress threatens rice yield and quality at flowering stage. In this study, average relative seed setting rate under heat stress (RHSR) and genotypes of 284 varieties were used for a genome-wide association study.

Results: We identified eight and six QTLs distributed on chromosomes 1, 3, 4, 5, 7 and 12 in the full population and indica, respectively.

Microsatellite markers-aided dissection of iron, zinc and cadmium accumulation potential in .

Background: Wheat is a staple cereal food around the globe. It provides a significant source of proteins, carbohydrates, and other micronutrients to humans. When grown on cadmium (Cd) contaminated soils, the uptake of trace elements .

Genomic diversity of aquaporins across genus Oryza provides a rich genetic resource for development of climate resilient rice cultivars.

Background: Plant aquaporins are critical genetic players performing multiple biological functions, especially climate resilience and water-use efficiency. Their genomic diversity across genus Oryza is yet to be explored.

Results: This study identified 369 aquaporin-encoding genes from 11 cultivated and wild rice species and further categorized these into four major subfamilies, among which small basic intrinsic proteins are speculated to be ancestral to all land plant aquaporins.

Computational analysis and expression profiling of potassium transport-related gene families in mango () indicate their role in stress response and fruit development.

Mango () fruit is known for its taste, health benefits, and drought tolerance. Potassium (K) is one of the most abundant ions in a plant cell. It is important for various biological functions related to plant growth, development, and flowering/fruiting.

Combined transcriptome and metabolome analysis reveals the effects of light quality on maize hybrids.

Background: Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis.

Exploration of the genomic atlas of Dof transcription factor family across genus provides novel insights on rice breeding in changing climate.

DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach.

Interaction estimation of pathogenicity determinant protein βC1 encoded by Cotton leaf curl Multan Betasatellite with Nuclear Transport Factor 2.

Background: Begomovirus is one of the most devastating pathogens that can cause more than 90% yield loss in various crop plants. The pathogenicity determinant βC1, located on the betasatellite associated with monopartite begomoviruses, alters the host signaling mechanism to enhance the viral disease phenotype by undermining the host immunity. The understanding of its interacting proteins in host plants to develop disease symptoms such as curly leaves, enations, vein swelling, and chlorosis is crucial to enhance the disease resistance in crop plants.

Genome wide association study on development and evolution of glutinous rice.

Background: Glutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers' preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous.

Natural Variation in Contributes to Grain Size and Chalkiness in Rice.

Rice ( L.) is an important staple food crop for more than half of the world's population. Enhancing the grain quality and yield of rice to meet growing demand remains a major challenge.

Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization.

Background: The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes.

Genome-wide investigation and expression analysis of APETALA-2 transcription factor subfamily reveals its evolution, expansion and regulatory role in abiotic stress responses in Indica Rice (Oryza sativa L. ssp. indica).

Rice is an important cereal crop that serves as staple food for more than half of the world population. Abiotic stresses resulting from changing climatic conditions are continuously threating its yield and production. Genes in APETALA-2 (AP2) family encode transcriptional regulators implicated during regulation of developmental processes and abiotic stress responses but their identification and characterization in indica rice was still missing.

Insights on Calcium-Dependent Protein Kinases (CPKs) Signaling for Abiotic Stress Tolerance in Plants.

Abiotic stresses are the major limiting factors influencing the growth and productivity of plants species. To combat these stresses, plants can modify numerous physiological, biochemical, and molecular processes through cellular and subcellular signaling pathways. Calcium-dependent protein kinases (CDPKs or CPKs) are the unique and key calcium-binding proteins, which act as a sensor for the increase and decrease in the calcium (Ca) concentrations.

Collection and Evaluation of Genetic Diversity and Population Structure of Potato Landraces and Varieties in China.

China is the world's leading country for potato production but potato is not native to China. To gain insights into the genetic diversity of potato germplasm various studies have been performed but no study has been reported for potato landraces in China. To improve the available genepool for future potato breeding programs, a diverse population containing 292 genotypes (including foreign elite lines, local landraces and cultivars) was developed and genotyped using 30 SSR markers covering the entire potato genome.

Genetic analysis of roots and shoots in rice seedling by association mapping.

The vigorous shoots and roots help to improve drought resistance and post-transplanting recovery in rice seedlings (Oryza sativa L.). Hundreds of loci related to root system have been identified recently, but little research has been done on shoot traits, and the relationship between roots and shoots development is also still unclear.

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions.

A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development.

Alternative splicing of OsLG3b controls grain length and yield in japonica rice.

Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS-box transcription factor 1 (OsMADS1).