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https://www.readbyqxmd.com/read/27908994/complete-genome-sequence-of-the-barley-pathogen-xanthomonas-translucens-pv-translucens-dsm-18974t-atcc-19319t
#1
Sebastian Jaenicke, Boyke Bunk, Daniel Wibberg, Cathrin Spröer, Lena Hersemann, Jochen Blom, Anika Winkler, Sarah Schatschneider, Stefan P Albaum, Roland Kölliker, Alexander Goesmann, Alfred Pühler, Jörg Overmann, Frank-Jörg Vorhölter
We report here the complete 4.7-Mb genome sequence of Xanthomonas translucens pv. translucens DSM 18974(T), which causes black chaff disease on barley (Hordeum vulgare). Genome data of this X. translucens type strain will improve our understanding of this bacterial species.
December 1, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27908384/dna-replication-after-mutagenic-treatment-in-hordeum-vulgare
#2
Jolanta Kwasniewska, Arita Kus, Monika Swoboda, Agnieszka Braszewska-Zalewska
The temporal and spatial properties of DNA replication in plants related to DNA damage and mutagenesis is poorly understood. Experiments were carried out to explore the relationships between DNA replication, chromatin structure and DNA damage in nuclei from barley root tips. We quantitavely analysed the topological organisation of replication foci using pulse EdU labelling during the S phase and its relationship with the DNA damage induced by mutagenic treatment with maleic hydrazide (MH), nitroso-N-methyl-urea (MNU) and gamma ray...
December 2016: Mutation Research
https://www.readbyqxmd.com/read/27900587/phylogenetic-analysis-of-wheat-dwarf-virus-isolates-from-iran
#3
Mohamad Hamed Ghodoum Parizipour, Jörg Schubert, Seyed Ali Akbar Behjatnia, Alireza Afsharifar, Antje Habekuß, Beilei Wu
Wheat dwarf virus (WDV) adversely affects cereal production in Asia, Europe, and North Africa. In this study, sequences of several WDV isolates from Iran which is located in the Fertile Crescent were analyzed. Analysis revealed a new geographic cluster for WDV-Wheat from Iran. Recombination analysis demonstrated the existence of several breakpoints in different regions of the viral genome. Data analysis demonstrated that WDV-Barley has an older history and lower diversity than WDV-Wheat. Sequence analysis identified a rare occasion of a co-infection of wheat with WDV-Wheat and WDV-Barley...
November 30, 2016: Virus Genes
https://www.readbyqxmd.com/read/27899919/fermentation-of-ammonia-fiber-expansion-treated-and-untreated-barley-straw-in-a-rumen-simulation-technique-using-rumen-inoculum-from-cattle-with-slow-versus-fast-rate-of-fiber-disappearance
#4
Candace L Griffith, Gabriel O Ribeiro, Masahito Oba, Tim A McAllister, Karen A Beauchemin
The purpose of this study was to determine the effect of rumen inoculum from heifers with fast vs. slow rate of in situ fiber digestion on the fermentation of complex versus easily digested fiber sources in the forms of untreated and Ammonia Fiber Expansion (AFEX) treated barley straw, respectively, using an artificial rumen simulation technique (Rusitec). In situ fiber digestion was measured in a previous study by incubating untreated barley straw in the rumen of 16 heifers fed a diet consisting of 700 g/kg barley straw and 300 g/kg concentrate...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27898895/effects-of-subacute-ruminal-acidosis-and-low-feed-intake-on-short-chain-fatty-acid-transporters-and-flux-pathways-in-holstein-steers
#5
A H Laarman, R-L A Pederzolli, K M Wood, G B Penner, B W McBride
The objective of this study was to investigate the role of protein-mediated transport pathways for short-chain fatty acid flux across the ruminal epithelium, using subacute ruminal acidosis (SARA) and feed restriction as models. Twenty-one Holstein steers (216.8 ± 31.4 kg BW) were individually housed and fed a total mixed ration (TMR) with a 50:50 forage:concentrate ad libitum for 5 d. After the 5 d diet adjustment period, calves were assigned 1 of 3 treatments: control (CTRL) calves were fed the TMR ad libitum on d 1, subacute ruminal acidosis calves were given 25% of their ad libitum DMI on d 1 and then given a barley grain challenge at 30% of ad libitum DMI on d2 (ACID) calves were given 25% of their ad libitum DMI on d 1 and then given a barley grain challenge at 30% of ad libitum DMI on d 2, and feed restriction (FR) calves were given 25% of their ad libitum DMI for 5 d...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898871/effect-of-disodium-calcium-malate-or-supplementation-on-growth-performance-carcass-quality-ruminal-fermentation-products-and-blood-metabolites-of-heifers
#6
C Carrasco, P Medel, A Fuentetaja, M J Ranilla, M D Carro
The aim of this study was to assess the effects of malate salts and culture on growth performance, carcass quality, ruminal fermentation products, and blood metabolites in heifers raised under southern Europe practical farm conditions. A total of 108 Charolaise cross heifers (214 ± 27.3 kg BW and 6.4 ± 1.1 mo of age) were housed in 18 pens of 6 animals each and used in a 114-d feedlot study. There was a totally randomized experimental design, and 6 pens were assigned to each of the following experimental diets: a control (no supplementation), the control plus 4 g of disodium/calcium malate mixture per kilogram of concentrate (2...
October 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898835/genomic-prediction-of-barley-hybrid-performance
#7
Norman Philipp, Guozheng Liu, Yusheng Zhao, Sang He, Monika Spiller, Gunther Stiewe, Klaus Pillen, Jochen C Reif, Zuo Li
Hybrid breeding in barley ( L.) offers great opportunities to accelerate the rate of genetic improvement and to boost yield stability. A crucial requirement consists of the efficient selection of superior hybrid combinations. We used comprehensive phenotypic and genomic data from a commercial breeding program with the goal of examining the potential to predict the hybrid performances. The phenotypic data were comprised of replicated grain yield trials for 385 two-way and 408 three-way hybrids evaluated in up to 47 environments...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898834/the-triticeae-toolbox-combining-phenotype-and-genotype-data-to-advance-small-grains-breeding
#8
Victoria C Blake, Clay Birkett, David E Matthews, David L Hane, Peter Bradbury, Jean-Luc Jannink
The Triticeae Toolbox (; T3) is the database schema enabling plant breeders and researchers to combine, visualize, and interrogate the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP). T3 enables users to define specific data sets for download in formats compatible with the external tools TASSEL, Flapjack, and R; or to use by software residing on the T3 server for operations such as Genome Wide Association and Genomic Prediction. New T3 tools to assist plant breeders include a Selection Index Generator, analytical tools to compare phenotype trials using common or user-defined indices, and a histogram generator for nursery reports, with applications using the Android OS, and a Field Plot Layout Designer in development...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898833/a-cluster-of-nucleotide-binding-site-leucine-rich-repeat-genes-resides-in-a-barley-powdery-mildew-resistance-quantitative-trait-loci-on-7hl
#9
Carlos P Cantalapiedra, Bruno Contreras-Moreira, Cristina Silvar, Dragan Perovic, Frank Ordon, María Pilar Gracia, Ernesto Igartua, Ana M Casas
Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898828/population-structure-in-the-model-grass-is-highly-correlated-with-flowering-differences-across-broad-geographic-areas
#10
Ludmila Tyler, Scott J Lee, Nelson D Young, Gregory A DeIulio, Elena Benavente, Michael Reagon, Jessica Sysopha, Riccardo M Baldini, Angelo Troìa, Samuel P Hazen, Ana L Caicedo
The small, annual grass (L.) Beauv., a close relative of wheat ( L.) and barley ( L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 , seven , and three accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898822/genomic-prediction-of-manganese-efficiency-in-winter-barley
#11
Florian Leplat, Just Jensen, Per Madsen
Manganese efficiency is a quantitative abiotic stress trait controlled by several genes each with a small effect. Manganese deficiency leads to yield reduction in winter barley ( L.). Breeding new cultivars for this trait remains difficult because of the lack of visual symptoms and the polygenic features of the trait. Hence, Mn efficiency is a potential suitable trait for a genomic selection (GS) approach. A collection of 248 winter barley varieties was screened for Mn efficiency using Chlorophyll (Chl ) fluorescence in six environments prone to induce Mn deficiency...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898767/genotyping-by-sequencing-on-pooled-samples-and-its-use-in-measuring-segregation-bias-during-the-course-of-androgenesis-in-barley
#12
Sébastien Bélanger, Patricio Esteves, Isabelle Clermont, Martine Jean, François Belzile
Estimation of allelic frequencies is often required in breeding but genotyping many individuals at many loci can be expensive. We have developed a genotyping-by-sequencing (GBS) approach for estimating allelic frequencies on pooled samples (Pool-GBS) and used it to examine segregation distortion in doubled haploid (DH) populations of barley ( L.). In the first phase, we genotyped each line individually and exploited these data to explore a strategy to call single nucleotide polymorphisms (SNPs) on pooled reads...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898766/genomic-regions-influencing-seminal-root-traits-in-barley
#13
Hannah Robinson, Lee Hickey, Cecile Richard, Emma Mace, Alison Kelly, Andrew Borrell, Jerome Franckowiak, Glen Fox
Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley ( L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898761/transplant-resources-for-triticeae-genomic-data
#14
Manuel Spannagl, Michael Alaux, Matthias Lange, Daniel M Bolser, Kai C Bader, Thomas Letellier, Erik Kimmel, Raphael Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer, Christoph Grabmuller, Jinbo Chen, Christian Colmsee, Sebastian Beier, Martin Mascher, Thomas Schmutzer, Daniel Arend, Anil Thanki, Ricardo Ramirez-Gonzalez, Martin Ayling, Sarah Ayling, Mario Caccamo, Klaus F X Mayer, Uwe Scholz, Delphine Steinbach, Hadi Quesneville, Paul J Kersey
The genome sequences of many important Triticeae species, including bread wheat ( L.) and barley ( L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898286/a-conserved-puccinia-striiformis-protein-interacts-with-wheat-npr1-and-reduces-induction-of-pathogenesis-related-genes-in-response-to-pathogens
#15
Xiaodong Wang, Baoju Yang, Kun Li, Zhensheng Kang, Dario Cantu, Jorge Dubcovsky
In Arabidopsis, NPR1 is a key transcriptional co-regulator of systemic acquired resistance. Upon pathogen challenge, NPR1 translocates from the cytoplasm to the nucleus, where it interacts with TGA-bZIP transcription factors to activate the expression of several Pathogenesis-Related (PR) genes. In a screen of a yeast two-hybrid library from wheat leaves infected with Puccinia striiformis f. sp. tritici, we identified a conserved rust protein that interacts with wheat NPR1 and named it Puccinia NPR1 interactor (PNPi)...
November 29, 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27895852/protein-protein-interaction-network-of-celiac-disease
#16
Mona Zamanian Azodi, Hassan Peyvandi, Mohammad Rostami-Nejad, Akram Safaei, Kamran Rostami, Reza Vafaee, Mohammadhossein Heidari, Mostafa Hosseini, Mohammad Reza Zali
AIM: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. BACKGROUND: Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease...
2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/27891136/characterization-of-salinity-tolerance-of-transgenic-rice-lines-harboring-hscbl8-of-wild-barley-hordeum-spontanum-line-from-qinghai-tibet-plateau
#17
Wanli Guo, Tianlong Chen, Nazim Hussain, Guoping Zhang, Lixi Jiang
Rice is more sensitive to salinity, particularly at its early vegetative and later productive stages. Wild plants growing in harsh environments such as wild barley from Qinghai-Tibet Plateau adapt to the adverse environment with allelic variations at the loci responsible for stressful environment, which could be used for rice genetic improvement. In this study, we overexpressed HsCBL8 encoding a calcium-sensor calcineurin B-like (CBL) protein in rice. The gene was isolated from XZ166, a wild-barley (Hordeum spontanum) line originated from Qinghai-Tibet Plateau...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27889933/development-and-field-performance-of-nitrogen-use-efficient-rice-lines-for-africa
#18
Michael Gomez Selvaraj, Milton Orlando Valencia, Satoshi Ogawa, Yingzhi Lu, Liying Wu, Christopher Downs, Wayne Skinner, Zhongjin Lu, Jean C Kridl, Manabu Ishitani, Jos van Boxtel
Nitrogen (N) fertilizers are a major input cost in rice production and its excess application leads to major environmental pollution. Development of rice varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Here, we report the results of field evaluations of marker-free transgenic NERICA4 (New Rice for Africa 4) rice lines over-expressing barley alanine amino transferase (HvAlaAT) under the control of a rice stress-inducible promoter (pOsAnt1). Field evaluations over three growing seasons and two rice growing ecologies (lowland and upland) revealed that grain yield of pOsAnt1:HvAlaAT transgenic events was significantly higher than sibling nulls and wild type controls under different N application rates...
November 27, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27889125/analysis-of-pasture-supplementation-strategies-by-means-of-a-mechanistic-model-of-ruminal-digestion-and-metabolism-in-the-dairy-cow
#19
J P McNamara, M J Auldist, L C Marett, P J Moate, W J Wales
Effective pasture supplementation is critical to the efficiency of resource management in milk production. We understand a great deal about ruminal and metabolic processes in dairy cattle that control efficiency but we need to improve our ability to predict effects of practical feeding strategies based on the basic biological processes of the cow. Therefore, a large-scale pasture supplementation study was used to explore the details of both practical management and the underlying biological principles and processes involved...
November 23, 2016: Journal of Dairy Science
https://www.readbyqxmd.com/read/27888554/a-high-resolution-genetic-map-of-the-cereal-crown-rot-pathogen-fusarium-pseudograminearum-provides-a-near-complete-genome-assembly
#20
Donald M Gardiner, Aurelie H Benfield, Jiri Stiller, Stuart Stephen, Karen Aitken, Chunji Liu, Kemal Kazan
Fusarium pseudograminearum is an important pathogen of wheat and barley, particularly in semi-arid environments. Previous genome assemblies for this organism were based entirely on short read data and are highly fragmented. In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals. The genetic map, along with long read scaffolding of a short read-based genome assembly, was used to give a near complete assembly of the four F. pseudograminearum chromosomes...
November 26, 2016: Molecular Plant Pathology
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