Progress and prospectus in genetics and genomics of root and stem rot resistance in soybean ( L.).

Soybean is one of the largest sources of protein and oil in the world and is also considered a "super crop" due to several industrial advantages. However, enhanced acreage and adoption of monoculture practices rendered the crop vulnerable to several diseases. Phytophthora root and stem rot (PRSR) caused by is one of the most prevalent diseases adversely affecting soybean production globally.

Modulation of GmFAD3 expression alters abiotic stress responses in soybean.

This study focused on enhancing resilience of soybean crops to drought and salinity stresses by overexpression of GmFAD3A gene, which plays an important role in modulating membrane fluidity and ultimately influence plants response to various abiotic stresses. Fatty acid desaturases (FADs) are a class of enzymes that mediate desaturation of fatty acids by introducing double bonds. They play an important role in modulating membrane fluidity in response to various abiotic stresses.

Breeding for higher yield, early maturity, wider adaptability and waterlogging tolerance in soybean (Glycine max L.): A case study.

Breeding for higher yield and wider adaptability are major objectives of soybean crop improvement. In the present study, 68 advanced breeding lines along with seven best checks were evaluated for yield and attributing traits by following group balanced block design. Three blocks were constituted based on the maturity duration of the breeding lines.

Turning Waste into Beneficial Resource: Implication of Ageratum conyzoides L. in Sustainable Agriculture, Environment and Biopharma Sectors.

The annual herb, Ageratum conyzoides L. (Asteraceae), is distributed throughout the world. Although invasive, it can be very useful as a source of essential oils, pharmaceuticals, biopesticides, and bioenergy.

Probabilistically sampled and spectrally clustered plant species using phenotypic characteristics.

Phenotypic characteristics of a plant species refers to its physical properties as cataloged by plant biologists at different research centers around the world. Clustering species based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of phenotypic data.

Apache Spark based kernelized fuzzy clustering framework for single nucleotide polymorphism sequence analysis.

This paper introduces a kernel based fuzzy clustering approach to deal with the non-linear separable problems by applying kernel Radial Basis Functions (RBF) which maps the input data space non-linearly into a high-dimensional feature space. Discovering clusters in the high-dimensional genomics data is extremely challenging for the bioinformatics researchers for genome analysis. To support the investigations in bioinformatics, explicitly on genomic clustering, we proposed high-dimensional kernelized fuzzy clustering algorithms based on Apache Spark framework for clustering of Single Nucleotide Polymorphism (SNP) sequences.

First report of root rot and damping off disease in soybean caused by in India.

Seedling rot symptoms were observed at Research Farm of ICAR-Indian Institute of Soybean Research, Indore, India. The infected seedlings had water-soaked lesions on the cotyledons and hypocotyls that gradually developed into brown lesions and further progressed to soft rot. These seedlings could be easily pulled-off from the soil.

A versatile system to introduce clusters of genomic double-strand breaks in large cell populations.

In vitro assays for clustered DNA lesions will facilitate the analysis of the mechanisms underlying complex genome rearrangements such as chromothripsis, including the recruitment of repair factors to sites of DNA double-strand breaks (DSBs). We present a novel method generating localized DNA DSBs using UV irradiation with photomasks. The size of the damage foci and the spacing between lesions are fully adjustable, making the assay suitable for different cell types and targeted areas.

Vector Quantized Spectral Clustering Applied to Whole Genome Sequences of Plants.

We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of spectral clustering (SC) and vector quantization (VQ) sampling for grouping genome sequences of plants. The inspiration here is to use SC for its accuracy and VQ to make the algorithm computationally cheap (the complexity of SC is cubic in terms of the input size). Although the combination of SC and VQ is not new, the novelty of our work is in developing the crucial similarity matrix in SC as well as use of -medoids in VQ, both adapted for the plant genome data.

Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors.

Chromothripsis and chromoanasynthesis are catastrophic events leading to clustered genomic rearrangements. Whole-genome sequencing revealed frequent complex genomic rearrangements (n = 16/26) in brain tumors developing in mice deficient for factors involved in homologous-recombination-repair or non-homologous-end-joining. Catastrophic events were tightly linked to Myc/Mycn amplification, with increased DNA damage and inefficient apoptotic response already observable at early postnatal stages.

Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis.

Recent developments in sequencing technologies led to the discovery of a novel form of genomic instability, termed chromothripsis. This catastrophic genomic event, involved in tumorigenesis, is characterized by tens to hundreds of simultaneously acquired locally clustered rearrangements on one chromosome. We hypothesized that leukemias developing in individuals with Ataxia Telangiectasia, who are born with two mutated copies of the ATM gene, an essential guardian of genome stability, would show a higher prevalence of chromothripsis due to the associated defect in DNA double-strand break repair.

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding.

Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported.

MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species.

Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once.

Comparative and evolutionary analysis of major peanut allergen gene families.

Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens.

Plant miRNAome and antiviral resistance: a retrospective view and prospective challenges.

MicroRNAs (miRNAs) are small regulatory RNAs that play a defining role in post-transcriptional gene silencing of eukaryotes by either mRNA cleavage or translational inhibition. Plant miRNAs have been implicated in innumerable growth and developmental processes that extend beyond their ability to respond to biotic and abiotic stresses. Active in an organism's immune defence response, host miRNAs display a propensity to target viral genomes.

The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome.

Background And Aims: Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes.

Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine.

We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare.

Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence.

Cultivated peanut is an allotetraploid with an AB-genome. In order to learn more of the genomic structure of peanut, we characterized and studied the evolution of a retrotransposon originally isolated from a resistance gene analog (RGA)-containing bacterial artificial chromosome (BAC) clone. It is a moderate copy number Ty1-copia retrotransposon from the Bianca lineage and we named it Matita.

Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny.

• Plant genomes contain numerous disease resistance genes (R genes) that play roles in defense against pathogens. Scarcity of genetic polymorphism makes peanut (Arachis hypogaea) especially vulnerable to a wide variety of pathogens. • Here, we isolated and characterized peanut bacterial artificial chromosomes (BACs) containing a high density of R genes.

Replication of nonautonomous retroelements in soybean appears to be both recent and common.

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max).

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago.

Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library.

Resistance to grapevine powdery mildew is controlled by Run1, a single dominant gene present in the wild grapevine species, Muscadinia rotundifolia, but absent from the cultivated species, Vitis vinifera. Run1 has been introgressed into V. vinifera using a pseudo-backcross strategy, and genetic markers have previously been identified that are linked to the resistance locus.

Inheritance of inter-simple-sequence-repeat polymorphisms and linkage with a fusarium wilt resistance gene in chickpea.

The inheritance of an inter-simple-sequence-repeat (ISSR) polymorphism was studied in a cross of cultivated chickpea (Cicer arietinum L.) and a closely related wild species (C. reticulatum Lad.