Integrating molecular markers and phenotypic analysis to assess cold tolerance in rice germplasm.

Unlabelled: Rice ( L.) is a crucial staple food for most of the world's population. However, it is highly vulnerable to low temperatures, which can induce growth retardation and yield loss.

Analysis of quantitative trait loci and candidate gene exploration associated with cold tolerance in rice ( L.) during the seedling stage.

Cold stress during the seedling stage significantly threatens rice ( L.) production, specifically in temperate climates. This study aimed to identify quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage.

Application of Transcriptome-Based Gene Set Featurization for Machine Learning Model to Predict the Origin of Metastatic Cancer.

Identifying the primary site of origin of metastatic cancer is vital for guiding treatment decisions, especially for patients with cancer of unknown primary (CUP). Despite advanced diagnostic techniques, CUP remains difficult to pinpoint and is responsible for a considerable number of cancer-related fatalities. Understanding its origin is crucial for effective management and potentially improving patient outcomes.

Rice ( L.) Grain Size, Shape, and Weight-Related QTLs Identified Using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers.

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]-High-Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs).

Dry-milled flour rice 'Seolgaeng' harbors a mutated fructose-6-phosphate 2-kinase/fructose-2,6-bisphosphatase2.

'Seolgaeng', an opaque-endosperm rice () mutant, is used to prepare high-quality dry-milled rice flour. The mutation causing its opaque-endosperm phenotype was unknown. Map-based cloning identified a missense mutation in the gene () in Seolgaeng.

Comparative Proteome-wide Characterization of Three Different Tissues of High-Protein Mutant and Wild Type Unravels Protein Accumulation Mechanisms in Rice Seeds.

Improving the proteins and amino acid contents of rice seeds is one of the prime objectives of plant breeders. We recently developed an EMS mutant/high-protein mutant (HPM) of rice that exhibits 14.8% of the total protein content as compared to its parent Dharial (wild-type), which shows only 9.

Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects.

Although mounting evidence suggests that the microbiome has a tremendous influence on intractable disease, the relationship between circulating microbial extracellular vesicles (EVs) and respiratory disease remains unexplored. Here, we developed predictive diagnostic models for COPD, asthma, and lung cancer by applying machine learning to microbial EV metagenomes isolated from patient serum and coded by their accumulated taxonomic hierarchy. All models demonstrated high predictive strength with mean AUC values ranging from 0.

Multiple Facets of Nitrogen: From Atmospheric Gas to Indispensable Agricultural Input.

Nitrogen (N) is a gas and the fifth most abundant element naturally found in the atmosphere. N's role in agriculture and plant metabolism has been widely investigated for decades, and extensive information regarding this subject is available. However, the advent of sequencing technology and the advances in plant biotechnology, coupled with the growing interest in functional genomics-related studies and the various environmental challenges, have paved novel paths to rediscovering the fundamentals of N and its dynamics in physiological and biological processes, as well as biochemical reactions under both normal and stress conditions.

Interaction of and alleles increases amylose content and alters physico-chemical properties in rice ( L.).

Four near-isogenic lines (NILs) with different allele combinations of the () and () were developed by crossing the rice cultivars "Dodamssal" and "Hwayeong." The associations between sequence variations in and , and starch-related traits were investigated. These sequence variations led to changes in seed morphology, starch structure, starch crystallinity, amylopectin chain length distribution, digestibility, apparent amylose content (AAC), and resistant starch content (RS).

Novel QTL Associated with Aerenchyma-Mediated Radial Oxygen Loss (ROL) in Rice ( L.) under Iron (II) Sulfide.

In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH) due to the abundance in application of nitrogen (N)-rich fertilizers. In this study, we evaluated the root growth behavior and ROL rate of a doubled haploid (DH) population ( = 117) and parental lines 93-11 (P1, ) and Milyang352 (P2, ) in response to iron (II) sulfide (FeS). In addition, we performed a linkage mapping and quantitative trait locus (QTL) analysis on the same population for the target traits.

RNA-Seq and Electrical Penetration Graph Revealed the Role of -Mediated Activation of Defense Mechanisms towards Green Rice Leafhopper ( Uhler) Resistance in Rice ( L.).

The green rice leafhopper (GRH, Uhler) is one of the most important insect pests causing serious damage to rice production and yield loss in East Asia. Prior to performing RNA-Seq analysis, we conducted an electrical penetration graph (EPG) test to investigate the feeding behavior of GRH on Ilpum (recurrent parent, GRH-susceptible cultivar), a near-isogenic line (NIL carrying ) compared to the donor parent (Shingwang). Then, we conducted a transcriptome-wide analysis of GRH-responsive genes in Ilpum and NIL, which was followed by the validation of RNA-Seq data by qPCR.

Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice ( L.) under Low Nitrogen Cultivation.

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential.

Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster.

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster.

Corrigendum: A Coordinated Suite of Wild-Introgression Lines in and Elite Backgrounds.

[This corrects the article DOI: 10.3389/fpls.2020.

Mapping of a Major QTL, , for Bakanae Disease Resistance in Rice.

Bakanae disease is a fungal disease of rice ( L.) caused by the pathogen (also known as ). This study was carried out to identify novel quantitative trait loci (QTLs) from an variety Zenith.

A Coordinated Suite of Wild-Introgression Lines in and Elite Backgrounds.

Rice, L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, and , which result from a combination of natural and human selection.

Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice.

Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BCF lines derived from an interspecific cross between the Korean cultivar "Hwaseong" and . In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F population (154 plants) along with parental lines, Hwaseong and , were evaluated for LTG and coleoptile length under low-temperature conditions (13 °C).

A RING-Type E3 Ubiquitin Ligase, Controls Chlorophyll Content and Dark-Induced Senescence in Rice.

Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice ( L.).

A Variant of SLC1A5 Is a Mitochondrial Glutamine Transporter for Metabolic Reprogramming in Cancer Cells.

Glutamine is an essential nutrient that regulates energy production, redox homeostasis, and signaling in cancer cells. Despite the importance of glutamine in mitochondrial metabolism, the mitochondrial glutamine transporter has long been unknown. Here, we show that the SLC1A5 variant plays a critical role in cancer metabolic reprogramming by transporting glutamine into mitochondria.

Accelerated development of rice stripe virus-resistant, near-isogenic rice lines through marker-assisted backcrossing.

The development of new improved varieties is one of the major goals of plant breeding. Concomitantly, the demand for stable, eco-friendly, and high-quality rice production is constantly increasing. However, most farmers prefer to cultivate familiar rice varieties developed more than 10 years ago to minimize economic risk.

OsTGA2 confers disease resistance to rice against leaf blight by regulating expression levels of disease related genes via interaction with NH1.

How plants defend themselves from microbial infection is one of the most critical issues for sustainable crop production. Some TGA transcription factors belonging to bZIP superfamily can regulate disease resistance through NPR1-mediated immunity mechanisms in Arabidopsis. Here, we examined biological roles of OsTGA2 (grouped into the same subclade as Arabidopsis TGAs) in bacterial leaf blight resistance.

Generation of trichogenic adipose-derived stem cells by expression of three factors.

Background: Previous studies demonstrated that adipose-derived stem cells (ASCs) can promote hair growth, but unmet needs exist for enhancing ASC hair inductivity.

Objective: Therefore, we introduced three trichogenic factors platelet-derived growth factor-A, SOX2, and β-catenin to ASCs (tfASCs) and evaluated whether tfASCs have similar characteristics as dermal papilla (DP) cells.

Method: Global gene expression was examined using NGS analysis.

Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice.

A quantitative trait locus (QTL) gw8.1 was detected in the population derived from a cross between the elite japonica cultivar, 'Hwaseong' and Oryza rufipogon (IRGC 105491). Near isogenic lines (NILs) harboring the O.