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https://www.readbyqxmd.com/read/30116252/dissecting-the-genetic-basis-underlying-combining-ability-of-plant-height-related-traits-in-maize
#1
Zhiqiang Zhou, Chaoshu Zhang, Xiaohuan Lu, Liwei Wang, Zhuanfang Hao, Mingshun Li, Degui Zhang, Hongjun Yong, Hanyong Zhu, Jianfeng Weng, Xinhai Li
Maize plant height related traits including plant height, ear height, and internode number are tightly linked with biomass, planting density, and grain yield in the field. Previous studies have focused on understanding the genetic basis of plant architecture traits per se , but the genetic basis of combining ability remains poorly understood. In this study, 328 recombinant inbred lines were inter-group crossed with two testers to produce 656 hybrids using the North Carolina II mating design. Both of the parental lines and hybrids were evaluated in two summer maize-growing regions of China in 2015 and 2016...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30048667/full-likelihood-inference-from-the-site-frequency-spectrum-based-on-the-optimal-tree-resolution
#2
Raazesh Sainudiin, Amandine Véber
We develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated...
July 23, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/30025026/four-parent-maize-fpm-population-effects-of-mating-designs-on-linkage-disequilibrium-and-mapping-quantitative-traits
#3
Steven L Anderson, Adam L Mahan, Seth C Murray, Patricia E Klein
Multiparent advanced generation inter-cross (MAGIC) populations can provide improved genetic mapping resolution by increasing allelic diversity and effective recombination. The Four Parent Maize (FPM; L.) population implemented five different mating designs used in MAGIC and bi-parental populations to compare empirical effects on genetic resolution and power of quantitative trait locus (QTL) detection; the combined population here comprised of 1149 individuals with 118,509 genetic markers. Measurements were recorded for plant height (PH), ear height (EH), days to anthesis (DTA) and silking (DTS) in seven environments, spanning three years...
July 2018: Plant Genome
https://www.readbyqxmd.com/read/30022985/assessing-european-wheat-sensitivities-to-parastagonospora-nodorum-necrotrophic-effectors-and-fine-mapping-the-snn3-b1-locus-conferring-sensitivity-to-the-effector-sntox3
#4
Rowena C Downie, Laura Bouvet, Eiko Furuki, Nick Gosman, Keith A Gardner, Ian J Mackay, Camila Campos Mantello, Greg Mellers, Huyen T T Phan, Gemma A Rose, Kar-Chun Tan, Richard P Oliver, James Cockram
Parastagonospora nodorum is a necrotrophic fungal pathogen of wheat ( Triticum aestivum L.), one of the world's most important crops. P. nodorum mediates host cell death using proteinaceous necrotrophic effectors, presumably liberating nutrients that allow the infection process to continue. The identification of pathogen effectors has allowed host genetic resistance mechanisms to be separated into their constituent parts. In P. nodorum , three proteinaceous effectors have been cloned: SnToxA , SnTox1 , and SnTox3 ...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30020523/conceptual-and-methodological-considerations-on-mrna-and-proteins-as-intercellular-and-long-distance-signals
#5
Nikola Winter, Friedrich Kragler
High throughput studies identified approximately one fifth of Arabidopsis protein encoding transcripts to be graft transmissible and to move over long distances in phloem. In roots, one fifth of transcription factors were annotated as non-cell-autonomous moving between cells. Is this massive transport a way of inter-organ and cell-to-cell communication or does it serve different purposes? On the tissue level, many miRNAs and all siRNAs act non-cell autonomously. Why are these RNAs and proteins not just expressed in cells where they exert their function? Short and long distance transport of these macromolecules raises the question whether all mobile mRNAs and transcription factors could be defined as signalling molecules...
July 18, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29996514/the-genetics-of-a-behavioral-speciation-phenotype-in-an-island-system
#6
Thomas Blankers, Kevin P Oh, Kerry L Shaw
Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variations in the crickets Laupala eukolea and Laupala cerasina , which occur on different islands (Maui and Hawaii)...
July 10, 2018: Genes
https://www.readbyqxmd.com/read/29987918/inter-%C3%AE-inhibitor-deficiency-in-the-mouse-is-associated-with-alterations-in-anxiety-like-behavior-exploration-and-social-approach
#7
David R Goulding, Viktoriya D Nikolova, Lopa Mishra, Lisheng Zhuo, Koji Kimata, Sandra J McBride, Sheryl S Moy, G Jean Harry, Stavros Garantziotis
In recent years, several genome-wide association studies have identified candidate regions for genetic susceptibility in major mood disorders. Most notable are regions in a locus in chromosome 3p21, encompassing the genes NEK4-ITIH1-ITIH3-ITIH4. Three of these genes represent heavy chains of the composite protein inter-α-inhibitor (IαI). In order to further establish associations of these genes with mood disorders, we evaluated behavioral phenotypes in mice deficient in either Ambp/bikunin, which is necessary for functional ITIH1 and ITIH3 complexes, or in Itih4, the gene encoding the heavy chain Itih4...
July 10, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29973912/a-comparative-study-of-two-blast-induced-traumatic-brain-injury-models-changes-in-monoamine-and-galanin-systems-following-single-and-repeated-exposure
#8
Lizan Kawa, Alaa Kamnaksh, Joseph B Long, Ulf P Arborelius, Tomas Hökfelt, Denes V Agoston, Mårten Risling
Repeated mild blast-induced traumatic brain injury (rmbTBI), caused by recurrent exposure to low levels of explosive blast, is a significant concern for military health systems. However, the pathobiology of rmbTBI is currently poorly understood. Animal models are important tools to identify the molecular changes of rmbTBI, but comparisons across different models can present their own challenges. In this study, we compared two well-established rodent models of mbTBI, the "KI model" and the "USU/WRAIR model...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/29953920/evidence-for-positive-selection-on-recent-human-transposable-element-insertions
#9
Lavanya Rishishwar, Lu Wang, Jianrong Wang, Soojin V Yi, Joseph Lachance, I King Jordan
Insertional activity of transposable elements (TEs) has had a major impact on the human genome; approximately one-half to two-thirds of the genome sequence is likely to be derived from TE insertions. Several families of human TEs - primarily Alu, L1 and SVA - continue to actively transpose, thereby generating insertional polymorphisms among individual genomes. The impact that TE insertions have on their human hosts' fitness, and accordingly the role that natural selection plays in shaping patterns of TE polymorphisms among populations, have yet to be systematically evaluated using whole genome sequence data...
June 25, 2018: Gene
https://www.readbyqxmd.com/read/29945120/inter-laboratory-validation-study-of-the-forenseq%C3%A2-dna-signature-prep-kit
#10
Steffi Köcher, Petra Müller, Burkhard Berger, Martin Bodner, Walther Parson, Lutz Roewer, Sascha Willuweit
The implementation of massively parallel sequencing (MPS) in forensic science revealed the advantages of the new method compared to the forensic benchmark in DNA-STR analysis, the capillary-electrophoresis (CE): Sequence information and the possibility to multiplex hundreds of markers in one multiplex PCR increase the discrimination power of a forensic (STR-) profile. The EU funded project DNASeqEx (DNA-STR Massive Sequencing & International Information Exchange) aims to evaluate MPS-based materials in their respective developmental stages using the two established platforms MiSeq FGx (Illumina) and Ion S5™ (Thermo Fisher Scientific)...
May 17, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29938135/unusually-low-genetic-divergence-at-coi-barcode-locus-between-two-species-of-intertidal-thalassaphorura-collembola-onychiuridae
#11
Xin Sun, Anne Bedos, Louis Deharveng
Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species...
2018: PeerJ
https://www.readbyqxmd.com/read/29916064/investigating-the-genetic-diversity-of-echinococcus-granulosus-sensu-stricto-with-new-microsatellites
#12
Gérald Umhang, Frédéric Grenouillet, Vanessa Bastid, Selim M'Rad, Benoît Valot, Myriam Oudni-M'Rad, Hamouda Babba, Franck Boué
Cystic echinococcosis is a zoonotic disease with worldwide distribution caused by the larval stage of the Cestode parasite Echinococcus granulosus sensu lato. Due to the predominance or even the exclusive presence of E. granulosus sensu stricto (s.s.) among E. granulosus species in many areas, the genetic diversity needs to be further investigated at the species level to better understand the inter- and intra-focus epidemiological features. Short sequences of mitochondrial or nuclear genes generally lack or have limited discriminatory power, hindering the detection of polymorphisms to reflect geographically based peculiarities and/or any history of infection...
June 18, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29890955/a-genome-wide-linkage-study-of-autism-spectrum-disorder-and-the-broad-autism-phenotype-in-extended-pedigrees
#13
Marc Woodbury-Smith, Andrew D Paterson, Irene O'Connor, Mehdi Zarrei, Ryan K C Yuen, Jennifer L Howe, Ann Thompson, Morgan Parlier, Bridget Fernandez, Joseph Piven, Stephen W Scherer, Veronica Vieland, Peter Szatmari
BACKGROUND: Although several genetic variants for autism spectrum disorder (ASD) have now been identified, these largely occur sporadically or are de novo. Much less progress has been made in identifying inherited variants, even though the disorder itself is familial in the majority of cases. The objective of this study was to identify chromosomal regions that harbor inherited variants increasing the risk for ASD using an approach that examined both ASD and the broad autism phenotype (BAP) among a unique sample of extended pedigrees...
June 11, 2018: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/29807156/phylogenetic-analysis-of-the-tree-kangaroos-dendrolagus-reveals-multiple-divergent-lineages-within-new-guinea
#14
Mark D B Eldridge, Sally Potter, Kristofer M Helgen, Martua H Sinaga, Ken P Aplin, Tim F Flannery, Rebecca N Johnson
Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus, has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue samples from 36 individual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci...
October 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29778183/high-genetic-diversity-of-extended-spectrum-%C3%AE-lactamases-producing-escherichia-coli-in-feces-of-horses
#15
Syndia Sadikalay, Yann Reynaud, Stéphanie Guyomard-Rabenirina, Mélanie Falord, Célia Ducat, Laetitia Fabre, Simon Le Hello, Antoine Talarmin, Séverine Ferdinand
Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29695967/influence-of-apoa5-locus-on-the-treatment-efficacy-of-three-statins-evidence-from-a-randomized-pilot-study-in-chinese-subjects
#16
Sha Hua, Chuanxiang Ma, Jun Zhang, Jing Li, Weiwei Wu, Ning Xu, Guanghua Luo, Jianrong Zhao
Pharmacogenetics or pharmacogenomics approaches are important for addressing the individual variabilities of drug efficacy especially in the era of precision medicine. One particular interesting gene to investigate is APOA5 , which has been repeatedly linked with the inter-individual variations of serum triglycerides. Here, we explored APOA5 -statin interactions in 195 Chinese subjects randomized to rosuvastatin (5-10 mg/day), atorvastatin (10-20 mg/day), or simvastatin (40 mg/day) for 12 weeks by performing a targeted genotyping analysis of the APOA5 promoter SNP rs662799 (-1131T > C)...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29674435/phylogenetic-and-phylogenomic-definition-of-rhizopus-species
#17
Andrii P Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M Anishchenko, Kerstin Voigt, G Sybren de Hoog, Matthew E Smith, Joseph Heitman, Rytas Vilgalys, Jason E Stajich
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R...
May 31, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29673315/inter-genome-comparison-of-the-quorn-fungus-fusarium-venenatum-and-the-closely-related-plant-infecting-pathogen-fusarium-graminearum
#18
Robert King, Neil Andrew Brown, Martin Urban, Kim E Hammond-Kosack
BACKGROUND: The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. RESULTS: Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29666338/identification-of-ssr-and-retrotransposon-based-molecular-markers-linked-to-morphological-characters-in-oily-sunfl-ower-helianthus-annuus-l-under-natural-and-water-limited-states
#19
Soleimani Gezeljeh Ali, Reza Darvishzadeh, Asa Ebrahimi, Mohammad Reza Bihamta
Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29615250/mycobacterium-aviumsubsp-paratuberculosis-isolated-from-wild-red-deer-cervus-elaphus-in-northern-italy
#20
Alessia Galiero, Simone Leo, Chiara Garbarino, Norma Arrigoni, Simone Russo, Stefano Giacomelli, Alessandro Bianchi, Karin Trevisiol, Ilda Idrizi, Gezim Daka, Filippo Fratini, Barbara Turchi, Domenico Cerri, Matteo Ricchi
Paratuberculosis (or Johne's disease) is an infectious disease which affects mainly ruminants and it is caused by Mycobacterium avium subsp. paratuberculosis (MAP). During a culling program (years 2011-2015) aimed at controlling the red deer (Cervus elaphus) population in Stelvio National Park (Italian Alps), where paratuberculosis was already described in this species, 382 tissue samples from the Lombardy Region and 102 fecal specimens from the Autonomous Province of Bolzano were analyzed by PCR. Of these, 77 samples (20...
April 2018: Veterinary Microbiology
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