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https://www.readbyqxmd.com/read/28448537/mapping-of-quantitative-trait-loci-associated-with-resistance-to-net-form-net-blotch-pyrenophora-teres-f-teres-in-a-doubled-haploid-norwegian-barley-population
#1
Ronja Wonneberger, Andrea Ficke, Morten Lillemo
Barley net blotch caused by the necrotrophic fungus Pyrenophora teres is a major barley disease in Norway. It can cause grain shriveling and yield losses, and resistance in currently grown cultivars is insufficient. In this study, a set of 589 polymorphic SNP markers was used to map resistance loci in a population of 109 doubled haploid lines from a cross between the closely related Norwegian cultivars Arve (moderately susceptible) and Lavrans (moderately resistant). Resistance to three net form net blotch (P...
2017: PloS One
https://www.readbyqxmd.com/read/28446797/fetiform-teratoma-was-a-parthenogenetic-tumor-arising-from-a-mature-ovum
#2
Kiyonori Miura, Takumi Kurabayashi, Chisei Satoh, Kensaku Sasaki, Tatsuya Ishiguro, Koh-Ichiro Yoshiura, Hideaki Masuzaki
The aim of this study was to investigate the parthenogenetic origin of fetiform teratoma by using molecular genetic studies and methylation status analyses. A fetiform teratoma was removed from a 35-year-old nulligravida woman. Genotyping of microsatellite marker loci, microarray analysis of single-nucleotide polymorphism (SNP) loci and methylation status analysis of the differentially methylated region (DMR) within the human IGF2-H19 locus were performed. Karyotypes of the host and the fetiform teratoma were 46, XX...
April 27, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28439856/the-generation-of-doubled-haploid-lines-for-qtl-mapping
#3
Daniele L Filiault, Danelle K Seymour, Ravi Maruthachalam, Julin N Maloof
Recombinant inbred lines (RILs) are an essential tool for quantitative trait locus (QTL) mapping in Arabidopsis thaliana. Conventionally, the development of these lines is a time-consuming and tedious process requiring six to eight generations of selfing. Here, we describe an alternative approach: the rapid generation of RILs in A. thaliana via the creation of doubled haploids. In this method, F1 plants are crossed to an engineered haploid inducer to produce haploid plants. The chromosomes of these haploids then spontaneously double, generating immortalized homozygous F2 lines called doubled haploid RILs (DH RILs)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28432826/ploidy-has-little-effect-on-timing-early-embryonic-events-in-the-haplo-diploid-wasp-nasonia
#4
Deanna Arsala, Jeremy A Lynch
The nucleocytoplasmic (N/C) ratio plays a prominent role in the maternal-to-zygotic transition (MZT) in many animals. The effect of the N/C ratio on cell-cycle lengthening and zygotic genome activation (ZGA) has been studied extensively in Drosophila, where haploid embryos experience an additional division prior to completing cellularization and triploid embryos cellularize precociously by one division. In this study, we set out to understand how the obligate difference in ploidy in the haplodiploid wasp, Nasonia, affects the MZT and which aspects of the Drosophila MZT are conserved...
April 22, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28429474/the-influence-of-glu-1-and-glu-3-loci-on-dough-rheology-and-bread-making-properties-in-wheat-t-aestivum-l-doubled-haploid-lines
#5
Monika Langner, Karolina Krystkowiak, Bolesław P Salmanowicz, Tadeusz Adamski, Paweł Krajewski, Zygmunt Kaczmarek, Maria Surma
BACKGROUND: The major determinants of wheat quality are Glu-1 and Glu-3 glutenin loci and environmental factors. Additive effects of alleles at Glu-1 and Glu-3 loci, and their interactions were evaluated for dough rheology and baking properties in four groups of wheat doubled haploid lines differing in HMW-GS and LMW-GS composition. RESULTS: Flour quality, Reomixer, dough extension, Farinograph and baking parameters were determined. Groups of lines with the alleles Glu-A3b and Glu-B3d were characterized by higher values of dough and baking parameters than those with the Glu-A3e and Glu-B3a alleles...
April 21, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28429058/effects-of-genome-duplication-on-phenotypes-and-industrial-applications-of-saccharomyces-cerevisiae-strains
#6
Ke Zhang, Ya-Hong Fang, Ke-Hui Gao, Yang Sui, Dao-Qiong Zheng, Xue-Chang Wu
Polyploidy is common in Saccharomyces cerevisiae strains, but the physiological and phenotypic effects of ploidy changes have not been fully clarified. Here, isogenic diploid, triploid, and tetraploid S. cerevisiae strains were constructed from a haploid strain, CEN.PK2-1C. Stress tolerance and ethanol fermentation performance of the four euploid strains were compared. Each euploid strain had strengths and weaknesses in tolerance to certain stressors, and no single strain was tolerant of all stressors. The diploid had higher ethanol production than the other strains in normal fermentation medium, while the triploid strain showed the fastest fermentation rate in the presence of inhibitors found in lignocellulosic hydrolysate...
April 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28428821/genome-wide-search-for-candidate-genes-for-yeast-robustness-improvement-against-formic-acid-reveals-novel-susceptibility-trk1-and-positive-regulators-and-resistance-haa1-regulon-determinants
#7
Sílvia F Henriques, Nuno P Mira, Isabel Sá-Correia
BACKGROUND: Formic acid is an inhibitory compound present in lignocellulosic hydrolysates. Understanding the complex molecular mechanisms underlying Saccharomyces cerevisiae tolerance to this weak acid at the system level is instrumental to guide synthetic pathway engineering for robustness improvement of industrial strains envisaging their use in lignocellulosic biorefineries. RESULTS: This study was performed to identify, at a genome-wide scale, genes whose expression confers protection or susceptibility to formic acid, based on the screening of a haploid deletion mutant collection to search for these phenotypes in the presence of 60, 70 and 80 mM of this acid, at pH 4...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28421861/the-plant-dependent-life-cycle-of-thecaphora-thlaspeos-a-smut-fungus-adapted-to-brassicaceae
#8
Lamprinos Frantzeskakis, Kaitlyn J Courville, Lesley Plücker, Ronny Kellner, Julia Kruse, Andreas Brachmann, Michael Feldbrügge, Vera Göhre
Smut fungi are globally distributed plant pathogens that infect agriculturally important crop plants such as maize or potato. To date, molecular studies on plant responses to smut fungi are challenging due to the genetic complexity of their host plants. Therefore, we set out to investigate the known smut fungus of Brassicaceae hosts, Thecaphora thlaspeos. T. thlaspeos infects different Brassicaceae plant species throughout Europe, including the perennial model plant Arabis alpina. In contrast to characterized smut fungi, mature and dry T...
April 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28417960/normally-lethal-amino-acid-substitutions-suppress-an-ultramutator-dna-polymerase-%C3%AE-variant
#9
Daniel G Dennis, Jill McKay-Fleisch, Kaila Eitzen, Ian Dowsett, Scott R Kennedy, Alan J Herr
In yeast, the pol3-01,L612M double mutant allele, which causes defects in DNA polymerase delta (Pol δ) proofreading (pol3-01) and nucleotide selectivity (pol3-L612M), confers an "ultramutator" phenotype that rapidly drives extinction of haploid and diploid MMR-proficient cells. Here, we investigate antimutator mutations that encode amino acid substitutions in Pol δ that suppress this lethal phenotype. We find that most of the antimutator mutations individually suppress the pol3-01 and pol3-L612M mutator phenotypes...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28413956/structure-roles-and-inhibitors-of-a-mitotic-protein-kinase-haspin
#10
Katrin Kestav, Asko Uri, Darja Lavogina
Background Haspin (haploid germ cell-specific nuclear protein kinase) is an atypical serine/threonine-protein kinase that was for a long time considered an inactive pseudokinase due to low degree of structural homology of Haspin with the 'classical' protein kinases. However, the discovery of Haspin-catalyzed phosphorylation of histone H3 at Thr3 residue unveiled importance of Haspin in mitosis and provided yet another link between mitotic phosphorylation pathways and chromatin modifications. Results In this review of 111 publications, we have (1) briefly summarized catalytic properties and physiological roles of Haspin, (2) focussed on the architecture of Haspin and mechanisms behind its substrate recognition, (3) provided detailed insight into the advances in the development and characterization of Haspin-selective inhibitors, and (4) given overview of inhibitor scaffolds that despite targeting other protein kinases feature Haspin as a common off-target...
April 14, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28407147/haplomerger2-rebuilding-both-haploid-sub-assemblies-from-high-heterozygosity-diploid-genome-assembly
#11
Shengfeng Huang, Mingjing Kang, Anlong Xu
Summary: De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers...
April 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28406973/tre5-a-retrotransposition-profiling-reveals-putative-rna-polymerase-iii-transcription-complex-binding-sites-on-the-dictyostelium-extrachromosomal-rdna-element
#12
Thomas Spaller, Marco Groth, Gernot Glöckner, Thomas Winckler
The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotransposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions ~47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only ~24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes...
2017: PloS One
https://www.readbyqxmd.com/read/28404855/genome-wide-screening-uncovers-the-significance-of-n-sulfation-of-heparan-sulfate-as-a-host-cell-factor-for-chikungunya-virus-infection
#13
Atsushi Tanaka, Uranan Tumkosit, Shota Nakamura, Daisuke Motooka, Natsuko Kishishita, Thongkoon Priengprom, Areerat Sa-Ngasang, Taroh Kinoshita, Naokazu Takeda, Yusuke Maeda
The molecular mechanisms underlying chikungunya virus (CHIKV) infection are poorly characterized. In this study, we analyzed the host factors involved in CHIKV infection using genome-wide screening. Human haploid HAP1 cells, into which an exon-trapping vector was introduced, were challenged with a vesicular stomatitis virus pseudotype bearing the CHIKV E3-E1 envelope proteins. Analysis of genes enriched in the cells resistant to the pseudotyped virus infection unveiled a critical role of N-sulfation of heparan sulfate (HS) for the infectivity of a clinically isolated CHIKV Thai #16856 strain to HAP1 cells...
April 12, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28403819/qtl-mapping-for-fruit-quality-in-citrus-using-dartseq-markers
#14
Maiara Curtolo, Mariângela Cristofani-Yaly, Rodrigo Gazaffi, Marco Aurélio Takita, Antonio Figueira, Marcos Antonio Machado
BACKGROUND: Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits...
April 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28403145/the-phosphatidylinositol-3-phosphate-5-kinase-inhibitor-apilimod-blocks-filoviral-entry-and-infection
#15
Elizabeth A Nelson, Julie Dyall, Thomas Hoenen, Alyson B Barnes, Huanying Zhou, Janie Y Liang, Julia Michelotti, William H Dewey, Lisa Evans DeWald, Richard S Bennett, Patrick J Morris, Rajarshi Guha, Carleen Klumpp-Thomas, Crystal McKnight, Yu-Chi Chen, Xin Xu, Amy Wang, Emma Hughes, Scott Martin, Craig Thomas, Peter B Jahrling, Lisa E Hensley, Gene G Olinger, Judith M White
Phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) is a lipid kinase involved in endosome maturation that emerged from a haploid genetic screen as being required for Ebola virus (EBOV) infection. Here we analyzed the effects of apilimod, a PIKfyve inhibitor that was reported to be well tolerated in humans in phase 2 clinical trials, for its effects on entry and infection of EBOV and Marburg virus (MARV). We first found that apilimod blocks infections by EBOV and MARV in Huh 7, Vero E6 and primary human macrophage cells, with notable potency in the macrophages (IC50, 10 nM)...
April 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28398878/development-and-validation-of-a-taqman-real-time-pcr-assay-for-the-specific-detection-and-quantification-of-fusarium-fujikuroi-in-rice-plants-and-seeds
#16
Greice Amaral Carneiro, Slavica Matic, Giuseppe Ortu, Angelo Garibaldi, Davide Spadaro, Maria Lodovica Gullino
Bakanae disease, which is caused by the seed-borne pathogen Fusarium fujikuroi, is found throughout the world on rice. A TaqMan real time PCR has been developed on the TEF 1-α gene to detect F. fujikuroi in different rice tissues. Three primer/probe sets were tested. The selected set produced an amplicon of 84 bp, and was specific for F. fujikuroi with respect for eight Fusarium species of rice and six other rice common pathogens. The assay was validated for specificity, selectivity, sensitivity, repeatability, and reproducibility...
April 11, 2017: Phytopathology
https://www.readbyqxmd.com/read/28396677/gametocidal-factor-transferred-from-aegilops-geniculata-roth-can-be-adapted-for-large-scale-chromosome-manipulations-in-cereals
#17
Michał T Kwiatek, Halina Wiśniewska, Aurelia Ślusarkiewicz-Jarzina, Joanna Majka, Maciej Majka, Jolanta Belter, Hanna Pudelska
Segregation distorters are curious, evolutionarily selfish genetic elements, which distort Mendelian segregation in their favor at the expense of others. Those agents include gametocidal factors (Gc), which ensure their preferential transmission by triggering damages in cells lacking them via chromosome break induction. Hence, we hypothesized that the gametocidal system can be adapted for chromosome manipulations between Triticum and Secale chromosomes in hexaploid triticale (×Triticosecale Wittmack). In this work we studied the little-known gametocidal action of a Gc factor located on Aegilops geniculata Roth chromosome 4M(g)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28396521/evaluation-of-grch38-and-de-novo-haploid-genome-assemblies-demonstrates-the-enduring-quality-of-the-reference-assembly
#18
Valerie A Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A Kitts, Terence D Murphy, Kim D Pruitt, Françoise Thibaud-Nissen, Derek Albracht, Robert S Fulton, Milinn Kremitzki, Vincent Magrini, Chris Markovic, Sean McGrath, Karyn Meltz Steinberg, Kate Auger, William Chow, Joanna Collins, Glenn Harden, Timothy Hubbard, Sarah Pelan, Jared T Simpson, Glen Threadgold, James Torrance, Jonathan M Wood, Laura Clarke, Sergey Koren, Matthew Boitano, Paul Peluso, Heng Li, Chen-Shan Chin, Adam M Phillippy, Richard Durbin, Richard K Wilson, Paul Flicek, Evan E Eichler, Deanna M Church
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28392793/rapid-introgression-of-the-fusarium-wilt-resistance-gene-into-an-elite-cabbage-line-through-the-combined-application-of-a-microspore-culture-genome-background-analysis-and-disease-resistance-specific-marker-assisted-foreground-selection
#19
Xing Liu, Fengqing Han, Congcong Kong, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Mu Zhuang, Yumei Liu, Zhansheng Li, Honghao Lv
Cabbage is an economically important vegetable worldwide. Cabbage Fusarium Wilt (CFW) is a destructive disease that results in considerable yield and quality losses in cole crops. The use of CFW-resistant varieties is the most effective strategy to mitigate the effects of CFW. 01-20 is an elite cabbage line with desirable traits and a high combining ability, but it is highly susceptible to CFW. To rapidly transfer a CFW resistance gene into 01-20 plants, we used microspore cultures to develop 230 doubled haploid (DH) lines from a cross between 01-20 (highly susceptible) and 96-100 (highly resistant)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28389771/qtl-mapping-for-haploid-male-fertility-by-a-segregation-distortion-method-and-fine-mapping-of-a-key-qtl-qhmf4-in-maize
#20
Jiaojiao Ren, Penghao Wu, Xiaolong Tian, Thomas Lübberstedt, Shaojiang Chen
Four QTL related to haploid male fertility were detected by a segregation distortion method and the key QTL qhmf4 was fine mapped to an interval of ~800 kb. Doubled haploid (DH) technology enables rapid development of homozygous lines in maize breeding programs. However, haploid genome doubling is a bottleneck for the commercialization of DH technology and is limited by haploid male fertility (HMF). This is the first study reporting the quantitative trait locus (QTL) analysis of HMF in maize. Four QTL, qhmf1, qhmf2, qhmf3, and qhmf4, controlling HMF have been identified by segregation distortion (SD) loci detection in the selected haploid population derived from 'Yu87-1/Zheng58'...
April 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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