150,653 results match your criteria mapping gene


Genome-wide Target Mapping Shows Histone Deacetylase Complex1 Regulates Cell Proliferation in Cucumber Fruit1[OPEN].

Plant Physiol 2020 Jan;182(1):167-184

College of Horticulture, Northwest A&F University, Yangling 712100, China.

Histone deacetylase (HDAC) proteins participate in diverse and tissue-specific developmental processes by forming various corepressor complexes with different regulatory subunits. An important HDAC machinery hub, the Histone Deacetylase Complex1 (HDC1) protein, participates in multiple protein-protein interactions and regulates organ size in plants. However, the mechanistic basis for this regulation remains unclear. Read More

View Article and Full-Text PDF
January 2020

The Photoperiodic Flowering Time Regulator FKF1 Negatively Regulates Cellulose Biosynthesis.

Plant Physiol 2019 Jul;180(4):2240-2253

Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409.

Cellulose synthesis is precisely regulated by internal and external cues, and emerging evidence suggests that light regulates cellulose biosynthesis through specific light receptors. Recently, the blue light receptor CRYPTOCHROME 1 (CRY1) was shown to positively regulate secondary cell wall biosynthesis in Arabidopsis (Arabidopsis thaliana). Here, we characterize the role of FLAVIN-BINDING KELCH REPEAT, F-BOX 1 (FKF1), another blue light receptor and well-known photoperiodic flowering time regulator, in cellulose biosynthesis. Read More

View Article and Full-Text PDF

Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology.

Genes Genomics 2021 Apr 21. Epub 2021 Apr 21.

Institute For Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, Republic of Korea.

Background: Currently, Tigers (the top predator of an ecosystem) are on the list of endangered species. Thus the need is to understand the tiger's population genomics to design their conservation strategies.

Objective: We analyzed the molecular evolution of tiger diversity using NADH dehydrogenase subunit 4 (ND4), a significant electron transport chain component. Read More

View Article and Full-Text PDF

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium.

Genome Med 2021 Apr 21;13(1):66. Epub 2021 Apr 21.

Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.

Background: The large airway epithelial barrier provides one of the first lines of defense against respiratory viruses, including SARS-CoV-2 that causes COVID-19. Substantial inter-individual variability in individual disease courses is hypothesized to be partially mediated by the differential regulation of the genes that interact with the SARS-CoV-2 virus or are involved in the subsequent host response. Here, we comprehensively investigated non-genetic and genetic factors influencing COVID-19-relevant bronchial epithelial gene expression. Read More

View Article and Full-Text PDF

Beyond association: successes and challenges in linking non-coding genetic variation to functional consequences that modulate Alzheimer's disease risk.

Mol Neurodegener 2021 Apr 21;16(1):27. Epub 2021 Apr 21.

Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Alzheimer's disease (AD) is the most common type of dementia, affecting millions of people worldwide; however, no disease-modifying treatments are currently available. Genome-wide association studies (GWASs) have identified more than 40 loci associated with AD risk. However, most of the disease-associated variants reside in non-coding regions of the genome, making it difficult to elucidate how they affect disease susceptibility. Read More

View Article and Full-Text PDF

Brain proteomic changes by histone deacetylase inhibition after traumatic brain injury.

Trauma Surg Acute Care Open 2021 24;6(1):e000682. Epub 2021 Mar 24.

Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA.

Background: Traumatic brain injury (TBI) is a leading cause of morbidity and mortality. There are currently no cytoprotective treatments for TBI. There is growing evidence that the histone deacetylase inhibitor valproic acid (VPA) may be beneficial in the treatment of TBI associated with hemorrhagic shock and in isolation. Read More

View Article and Full-Text PDF

The ecological, genetic and genomic architecture of local adaptation and population differentiation in .

Proc Biol Sci 2021 Apr 21;288(1949):20202472. Epub 2021 Apr 21.

Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan.

Differential local adaptation restricts gene flow between populations inhabiting distinct environments, resulting in isolation by adaptation. In addition to the statistical inferences of genotype-environment associations, an integrative approach is needed to investigate the effect of local adaptation on population divergence at the ecological, genetic and genomic scale. Here, we combine reciprocal transplant, genome-environment association and QTL mapping to investigate local adaptation in (Drummond's rockcress). Read More

View Article and Full-Text PDF

Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella.

G3 (Bethesda) 2019 Jul;9(7):2349-2361

Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045.

Specific characteristics of the male Achroia grisella acoustic mating signal determine a male's attractiveness toward females. These features are genetically variable in populations, and mapping experiments have been used to identify loci contributing to song variation, and understand the evolutionary forces acting on this important sexual trait. Here we built on this foundation and carried out QTL (Quantitative Trait Locus) mapping using >1,000 recombinant individuals, genotyping this large cohort at thousands of sequence-based markers covering the entire collection of 30 A. Read More

View Article and Full-Text PDF

Mapping the functional and strain diversity of the main microbiota involved in cocoa fermentation from Cote d'Ivoire.

Food Microbiol 2021 Sep 24;98:103767. Epub 2021 Feb 24.

Laboratoire d'Agriculture, Biotechnologie et Valorisation des Ressources Naturelles UFR Biosciences, University Felix Houphouet-Boigny, Abidjan, Cote D'Ivoire.

The variable quality of cocoa produced by farmers is still a problem in the value chain, strongly depending on microbial activities. We analyzed the variability of cocoa microbiota from all twelve producing regions in Cote d'Ivoire, and described the geographical distribution of isolated microbiota, using a mapping. Microbial species were identified by ribosomal genes sequencing, strains were typed by RFLP and their techno-functional capacities were further investigated. Read More

View Article and Full-Text PDF
September 2021

Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.

BMC Genomics 2021 Apr 20;22(1):285. Epub 2021 Apr 20.

Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada.

Background: Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Read More

View Article and Full-Text PDF

Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa.

BMC Genomics 2021 Apr 19;22(1):284. Epub 2021 Apr 19.

Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.

Background: Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Read More

View Article and Full-Text PDF

Molecular markers in plant ecology.

Authors:
Konrad Bachmann

New Phytol 1994 Mar;126(3):403-418

Hugo de Vries Laboratory, University of Amsterdam, Kruislaan 318, NL-1098 SM Amsterdam, The Netherlands.

Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations arc briefly discussed. Read More

View Article and Full-Text PDF

An arsenate tolerance gene on chromosome 6 of rice.

New Phytol 2004 Jul;163(1):45-49

Department of Plant and Soil Science, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK.

•  The genetics of arsenic tolerance in plants has not been extensively studied and no arsenic tolerance gene has been genetically mapped. •  Screening 20 diverse genotypes of rice for reduced root growth in 13.3 m arsenate identified marked differences in tolerance. Read More

View Article and Full-Text PDF

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence.

New Phytol 2004 Oct;164(1):95-105

Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37830-6422, USA.

•  In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa, we have mapped two resistance loci, MXC3 and MER, and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations. •  We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun-sequence data in the region containing markers linked to MXC3. •  The two loci were mapped to different linkage groups. Read More

View Article and Full-Text PDF
October 2004

What has QTL mapping taught us about plant domestication?

New Phytol 2002 Jun;154(3):591-608

Center for Applied Genetic Technologies; and Departments of Crop and Soil Science; Botany; and Genetics; University of Georgia, Athens GA, USA.

The aim of this paper is to survey the general area of quantitative trait locus (QTL) mapping, and its specific impact on current understanding of plant domestication. Plant domestication is not only of historical interest, but is also of ongoing importance as changing human needs and availability of nonrenewable resources impel continuing (and perhaps even accelerated) investigation of prospective new crops. New genomic tools applied in conjunction with now-established approaches such as QTL mapping are opening new doors into searches for the 'footprints' of domestication, and promise to accelerate and streamline the identification of specific genes integral to domestication(s), building on early successes. Read More

View Article and Full-Text PDF

Chlamydomonas reinhardtii as a eukaryotic photosynthetic model for studies of heavy metal homeostasis and tolerance.

Authors:
M Hanikenne

New Phytol 2003 Aug;159(2):331-340

Genetics of Microorganisms, Department of Life Sciences, B22, University of Liège, B4000 Liège, Belgium.

The green alga Chlamydomonas reinhardtii is a useful model of a photosynthetic cell. This unicellular eukaryote has been intensively used for studies of a number of physiological processes such as photosynthesis, respiration, nitrogen assimilation, flagella motility and basal body function. Its easy-to-manipulate and short life cycle make this organism a powerful tool for genetic analysis. Read More

View Article and Full-Text PDF

Genetic architecture of Al toxicity tolerance in rice F populations determined through QTL mapping.

Ecotoxicology 2021 Apr 19. Epub 2021 Apr 19.

School of Biological Sciences, University of the Punjab, Lahore, Pakistan.

Aluminum (Al) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al toxicity ranging from 0 to 20 mM at pH 4 ± 0. Read More

View Article and Full-Text PDF

QTL mapping of the genetic basis of stem diameter in soybean.

Planta 2021 Apr 19;253(5):109. Epub 2021 Apr 19.

Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.

Main Conclusion: QTL mapping of stem diameter was carried out in three RIL populations using a high-density genetic map, and candidate genes related to stem diameter were predicted. Stem diameter is an important agronomic trait affecting soybean lodging and productivity. However, this trait is underexploited, and the underlying genetic mechanism in soybean remains unclear. Read More

View Article and Full-Text PDF

Genomic basis of striking fin shapes and colours in the fighting fish.

Mol Biol Evol 2021 Apr 19. Epub 2021 Apr 19.

Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.

Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Read More

View Article and Full-Text PDF

The mitochondrial genomes of the human pathogens Coccidioides immitis and C. posadasii.

G3 (Bethesda) 2021 Apr 19. Epub 2021 Apr 19.

Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011 USA.

Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. Read More

View Article and Full-Text PDF

Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. [Moench]) germplasm.

G3 (Bethesda) 2021 Apr 19. Epub 2021 Apr 19.

College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia.

Ethiopia, the probable center of origin and diversity for sorghum (Sorghum bicolor L. [Moench]) and with unique eco-geographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. Read More

View Article and Full-Text PDF

NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data.

iScience 2021 Apr 26;24(4):102361. Epub 2021 Mar 26.

Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. Read More

View Article and Full-Text PDF

RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, .

Comput Struct Biotechnol J 2021 22;19:1641-1653. Epub 2021 Mar 22.

Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China.

Fruiting body development (FBD) of mushroom-forming fungi has attracted tremendous interest. However, the genetic and molecular basis of FBD is poorly known. Here, using (shiitake) as a model, we deciphered the genetic architecture underlying fruiting body-related traits (FBRTs) by combined genomic, genetic and phenotypic data. Read More

View Article and Full-Text PDF

GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases.

Comput Struct Biotechnol J 2021 22;19:1603-1611. Epub 2021 Mar 22.

National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.

Genotype-phenotype correlations are the basis of precision medicine of human genetic diseases. However, it remains a challenge for clinicians and researchers to conveniently access detailed individual-level clinical phenotypic features of patients with various genetic variants. To address this urgent need, we manually searched for genetic studies in PubMed and catalogued 8,309 genetic variants in 1,288 genes from 17,738 patients with detailed clinical phenotypic features from 1,855 publications. Read More

View Article and Full-Text PDF

Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in (Koidz).

Front Genet 2021 31;12:596749. Epub 2021 Mar 31.

Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.

The study on the fast-growing traits of trees, mainly valued by tree height (TH) and diameter at breast height (DBH), is of great significance to promote the development of the forest industry. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for fast-growing traits. In our study, a high-density genetic map for the F population was constructed. Read More

View Article and Full-Text PDF

Construction of ddRADseq-Based High-Density Genetic Map and Identification of Quantitative Trait Loci for Trans-resveratrol Content in Peanut Seeds.

Front Plant Sci 2021 18;12:644402. Epub 2021 Mar 18.

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

Resveratrol (trans-3,4',5-trihydroxystilbene) is a natural stilbene phytoalexin which is also found to be good for human health. Cultivated peanut ( L.), a worldwide important legume crop, is one of the few sources of human's dietary intake of resveratrol. Read More

View Article and Full-Text PDF

GmST1, which encodes a sulfotransferase, confers resistance to soybean mosaic virus strains G2 and G3.

Plant Cell Environ 2021 Apr 18. Epub 2021 Apr 18.

Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China.

Soybean mosaic virus (SMV) is one of the most widespread and devastating viral diseases worldwide. The genetic architecture of qualitative resistance to SMV in soybean remains unclear. Here, the Rsvg2 locus was identified as underlying soybean resistance to SMV by genome-wide association and linkage analyses. Read More

View Article and Full-Text PDF

Mitochondrial DNA abnormalities provide mechanistic insight and predict reactive oxygen species-stimulating drug efficacy.

BMC Cancer 2021 Apr 17;21(1):427. Epub 2021 Apr 17.

School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK.

Background: Associations between mitochondrial genetic abnormalities (variations and copy number, i.e. mtDNAcn, change) and elevated ROS have been reported in cancer compared to normal cells. Read More

View Article and Full-Text PDF

Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch.

Sci Total Environ 2021 Apr 7;783:146960. Epub 2021 Apr 7.

National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India. Electronic address:

The rivers in the megacities face a constant inflow of extremely polluted wastewaters from various sources, and their influence on the connected peri-urban river is still poorly understood. The riverine system in Pune consists of Rivers Mula, Ramnadi, Pawana, Mutha, and Mula-Mutha, traversing through the urban settlements of Pune before joining River Bhima in the peri-urban region. We used MinION-based metagenomic sequencing to generate a comprehensive understanding of the microbial diversity differences between the urban and peri-urban zones, which has not been explored at the meta scale until date. Read More

View Article and Full-Text PDF

Assessment of the genetic contribution to brain MRI lesion load and atrophy measures in multiple sclerosis patients.

Eur J Neurol 2021 Apr 17. Epub 2021 Apr 17.

Unit of Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy.

Background: Multiple Sclerosis (MS) susceptibility is influenced by genetics, however little is known about genetic determinants of disease expression. We aimed at assessing genetic factors influencing quantitative neuroimaging measures in two cohorts of Progressive (PMS) and Relapsing-Remitting (RRMS) patients.

Methods: Ninety-nine PMS and 214 RRMS patients underwent a 3T brain MRI scan, with the measurement of five MRI metrics including T2 lesion volumes and measures of white matter, grey matter, deep grey matter and hippocampal volumes. Read More

View Article and Full-Text PDF