Abstract Imprinting describes the differential expression of alleles based on their parent origin. Deep sequencing RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set ~12,000 that were expressed contained sequence polymorphisms between B73 Mo17 genotypes. The analysis parent-of-origin patterns resulted in identification 100 putative endosperm, including 54 maternally (MEGs) 46 paternally (PEGs). Three these have been...

Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. In this study, fast neutron (FN) radiation was used to induce deletion mutations the soybean (Glycine max) genome. Approximately 120,000 seeds were exposed FN doses of up 32 Gray units develop over 23,000 independent M2 lines. Here, we demonstrate utility population phenotypic screening associated genomic characterization striking agronomically...

Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural were assessed among four soybean (Glycine max) genotypes using array hybridization targeted resequencing. Many chromosomes exhibited relatively low rates of (SV) genotypes. However, several regions both copy number presence-absence variation, the most prominent found on 3, 6, 7, 16, 18. Interestingly, enriched for SV specifically localized gene-rich that...

AMP activated protein kinase (AMPK) plays an important role in regulating myocardial metabolism and synthesis. Activation of AMPK attenuates hypertrophy cultured cardiac myocytes, but the development response to chronic pressure overload is not known. To test hypothesis that AMPKalpha2 protects heart against systolic overload-induced ventricular dysfunction, we studied gene deficient (knockout [KO]) mice wild-type subjected 3 weeks transverse aortic constriction (TAC). Although KO had no...

Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the rate of polymorphisms, wide range heritable phenotypic variation exists. There even evidence for among individuals within some cultivars. Williams 82, soybean cultivar used to produce reference genome sequence, was derived from backcrossing Phytophthora root rot resistance locus donor parent Kingwa into recurrent Williams. To explore genetic...

Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as cellulosic ethanol feedstock. However, the genomics of alfalfa, non-model species, is still in its infancy. The recent advent RNA-Seq, massively parallel sequencing method transcriptome analysis, provides an opportunity to expand identification alfalfa genes and polymorphisms, conduct in-depth transcript profiling. Cell walls stems genotype 708 have higher cellulose lower lignin...

ABSTRACT Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease characterized by high fever, thrombocytopenia, multiorgan dysfunction, and a fatality rate between 12 30%. It caused SFTS virus (SFTSV), novel Phlebovirus in family Bunyaviridae . Although the viral pathogenesis remains largely unknown, hemopoietic cells appear to be targeted virus. In this study we report that human monocytes were susceptible SFTSV, which replicated efficiently, as shown...

Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley more susceptible to waterlogging than other cereals. To gain better understanding, genome-wide gene expression responses roots of waterlogged barley seedlings Yerong Deder2 were analyzed by RNA-Sequencing. A total 6736, 5482, 4538 differentially expressed genes (DEGs) identified at 72 h 120 h, respectively, compared with non-waterlogged control. Gene Ontology (GO)...

The nutritional and economic value of many crops is effectively a function seed protein oil content. Insight into the genetic molecular control mechanisms involved in deposition these constituents developing needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) soybean (Glycine max (L.) Merrill) has striking effect content.A near-isogenic line (NIL) pair contrasting differing an introgressed genomic segment containing LG QTL was used as resource...

The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent leaf rust. However, biological basis for exceptional durability is unclear. We used Affymetrix GeneChip Wheat Genome Array compare transcriptional changes near-isogenic lines Thatcher in a compatible interaction, an incompatible interaction conferred by Lr1, and race-nonspecific response conditioned 3 7 days postinoculation (dpi) with P. triticina. No differentially expressed genes were...

Transcriptome variation plays an important role in affecting the phenotype of organism. However, understanding underlying mechanisms regulating transcriptome segregating populations is still largely unknown. We sought to assess and map transcript abundance maize shoot apices intermated B73×Mo17 recombinant inbred line population. RNA–based sequencing (RNA–seq) allowed for detection quantification derived from 28,603 genes. For a majority these genes, population mean, coefficient variation,...

Abstract Background Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers several applications including marker-assisted breeding, population diversity studies eco-geographical adaption, genotyping germplasm collections, and others. Accurately detecting SNPs large polyploid genomes such as wheat is crucial challenging. A few variant calling methods have previously developed but they show low...

Many flowering plants attract pollinators by offering a reward of floral nectar. Remarkably, the molecular events involved in development nectaries, organs that produce nectar, as well synthesis and secretion nectar itself, are poorly understood. Indeed, to date, no genes have been shown directly affect de novo production or quality To address this gap knowledge, ATH1 Affymetrix GeneChip array was used systematically investigate Arabidopsis nectary transcriptome identify pathways potentially...

Histone deacetylases (HDACs) and lysine acetyltransferases (KATs) catalyze dynamic histone acetylation at regulatory coding regions of transcribed genes. Highly phosphorylated HDAC2 is recruited within corepressor complexes to regions, while the nonphosphorylated form associated with gene body. In this study, we characterized body explored function HDAC-complex-mediated acetylation. HDAC1 2 were coimmunoprecipitated several splicing factors, including serine/arginine-rich factor 1 (SRSF1)...

In order to determine if triclosan can select for mutants of Acinetobacter baumannii ATCC 17978 that display reduced susceptibilities antibiotics, we isolated a triclosan-resistant mutant, A. AB042, by serial passaging in growth medium supplemented with triclosan. The antimicrobial susceptibility AB042 was analyzed the 2-fold dilution method. Expression five different resistance-nodulation-division (RND) pump-encoding genes (adeB, adeG, adeJ, A1S_2818, and A1S_3217), two outer membrane...

Abstract Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping introgressions in these materials. Here, we compare some existing and emerging methodologies introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide (SNP) genotyping, de novo SNP discovery via RNA-Seq analysis next-generation sequence data. We used...

Microbe-associated molecular pattern-triggered immunity (MTI) is an important component of the plant innate response to invading pathogens. However, most our knowledge MTI comes from studies model systems with relatively little work done crop plants. In this work, we report on variation in both microbe-associated oxidative burst and gene expression across four soybean (Glycine max) genotypes. Variation correlated level pathogen resistance for each genotype. A quantitative trait locus...

The initial interaction between host cell and pathogen sets the stage for ensuing infection ultimately determine course of disease. However, there is limited knowledge transcripts utilized by how they may impact one another during this critical step. purpose study was to create a host-Mycobacterium avium subsp. paratuberculosis (MAP) interactome early in an epithelium-macrophage co-culture system using RNA-seq. Establishment host-MAP revealed novel iron assimilation carboxymycobactin. Iron...

Mycobacterium avium subsp. paratuberculosis (MAP) persistently infects intestines and mesenteric lymph nodes leading to a prolonged subclinical disease. The MAP genome sequence was published in 2005, yet its transcriptional organization natural infection is unknown. While prior research analyzed regulated gene sets utilizing defined, vitro stress related or advanced surgical methods with various animal species, we investigated the intracellular lifestyle of understand pathways that function...