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https://www.readbyqxmd.com/read/28717173/liquid-phase-sequence-capture-and-targeted-re-sequencing-revealed-novel-polymorphisms-in-tomato-genes-belonging-to-the-mep-carotenoid-pathway
#1
Irma Terracciano, Concita Cantarella, Carlo Fasano, Teodoro Cardi, Giuseppe Mennella, Nunzio D'Agostino
Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent's SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28712375/imputation-of-non-genotyped-sheep-from-the-genotypes-of-their-mates-and-resulting-progeny
#2
D P Berry, N McHugh, S Randles, E Wall, K McDermott, M Sargolzaei, A C O'Brien
Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys' dams (i...
July 17, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28652263/transcriptomic-differences-in-grapevine-varieties-correlate-with-berry-anthocyanin-skin
#3
Mélanie Massonnet, Marianna Fasoli, Giovanni Battista Tornielli, Mario Altieri, Marco Sandri, Paola Zuccolotto, Paola Paci, Massimo Gardiman, Sara Zenoni, Mario Pezzotti
Grapevine berry development involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptome during berry development, most have focused on a single grapevine variety so there is a lack of comparative data representing different cultivars. Here we report the first genome-wide transcriptional analysis of 120 RNA samples corresponding to 10 Italian grapevine varieties collected at four growth stages...
June 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28645231/evolution-of-hormone-signaling-networks-in-plant-defense
#4
Matthias L Berens, Hannah M Berry, Akira Mine, Cristiana T Argueso, Kenichi Tsuda
Studies with model plants such as Arabidopsis thaliana have revealed that phytohormones are central regulators of plant defense. The intricate network of phytohormone signaling pathways enables plants to activate appropriate and effective defense responses against pathogens as well as to balance defense and growth. The timing of the evolution of most phytohormone signaling pathways seems to coincide with the colonization of land, a likely requirement for plant adaptations to the more variable terrestrial environments, which included the presence of pathogens...
June 23, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28633662/orthored-a-rapid-and-accurate-orthology-prediction-tool-with-low-computational-requirement
#5
Kai Battenberg, Ernest K Lee, Joanna C Chiu, Alison M Berry, Daniel Potter
BACKGROUND: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28626454/a-syst-omics-approach-to-ensuring-food-safety-and-reducing-the-economic-burden-of-salmonellosis
#6
Jean-Guillaume Emond-Rheault, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, Anna Colavecchio, Virginie Barrere, Brigitte Cadieux, Gitanjali Arya, Sadjia Bekal, Chrystal Berry, Elton Burnett, Camille Cavestri, Travis K Chapin, Alanna Crouse, France Daigle, Michelle D Danyluk, Pascal Delaquis, Ken Dewar, Florence Doualla-Bell, Ismail Fliss, Karen Fong, Eric Fournier, Eelco Franz, Rafael Garduno, Alexander Gill, Samantha Gruenheid, Linda Harris, Carol B Huang, Hongsheng Huang, Roger Johnson, Yann Joly, Maud Kerhoas, Nguyet Kong, Gisèle Lapointe, Line Larivière, Stéphanie Loignon, Danielle Malo, Sylvain Moineau, Walid Mottawea, Kakali Mukhopadhyay, Céline Nadon, John Nash, Ida Ngueng Feze, Dele Ogunremi, Ann Perets, Ana V Pilar, Aleisha R Reimer, James Robertson, John Rohde, Kenneth E Sanderson, Lingqiao Song, Roger Stephan, Sandeep Tamber, Paul Thomassin, Denise Tremblay, Valentine Usongo, Caroline Vincent, Siyun Wang, Joel T Weadge, Martin Wiedmann, Lucas Wijnands, Emily D Wilson, Thomas Wittum, Catherine Yoshida, Khadija Youfsi, Lei Zhu, Bart C Weimer, Lawrence Goodridge, Roger C Levesque
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28624139/applying-rigor-and-reproducibility-standards-to-assay-donor-derived-cell-free-dna-as-a-non-invasive-method-for-detection-of-acute-rejection-and-graft-injury-after-heart-transplantation
#7
Sean Agbor-Enoh, Ilker Tunc, Iwijn De Vlaminck, Ulgen Fideli, Andrew Davis, Karen Cuttin, Kenneth Bhatti, Argit Marishta, Michael A Solomon, Annette Jackson, Grace Graninger, Bonnie Harper, Helen Luikart, Jennifer Wylie, Xujing Wang, Gerald Berry, Charles Marboe, Kiran Khush, Jun Zhu, Hannah Valantine
BACKGROUND: Use of new genomic techniques in clinical settings requires that such methods are rigorous and reproducible. Previous studies have shown that quantitation of donor-derived cell-free DNA (%ddcfDNA) by unbiased shotgun sequencing is a sensitive, non-invasive marker of acute rejection after heart transplantation. The primary goal of this study was to assess the reproducibility of %ddcfDNA measurements across technical replicates, manual vs automated platforms, and rejection phenotypes in distinct patient cohorts...
May 20, 2017: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/28618374/proteomic-profiling-of-german-dornfelder-grape-berries-using-data-independent-acquisition
#8
Matthias Riebel, Petra Fronk, Ute Distler, Stefan Tenzer, Heinz Decker
Grapevine is one of the most important fruit plants throughout the world. Sequencing of the grape genome in 2007 enabled in-depth analyses of the grape proteome. Whereas many studies addressed changes in proteomic composition of grapes during ripening, we focused on the proteome of mature grape berries from Dornfelder, a characteristic red wine grape for Germany. Current data-independent acquisition proteomics technology enables the analysis of proteomic compositions in a degree of accuracy that was unreachable only a few years ago...
June 7, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28559906/drawing-links-from-transcriptome-to-metabolites-the-evolution-of-aroma-in-the-ripening-berry-of-moscato-bianco-vitis-vinifera-l
#9
Laura Costantini, Christian D Kappel, Massimiliano Trenti, Juri Battilana, Francesco Emanuelli, Maddalena Sordo, Marco Moretto, Céline Camps, Roberto Larcher, Serge Delrot, Maria S Grando
Monoterpenes confer typical floral notes to "Muscat" grapevine varieties and, to a lesser extent, to other aromatic non-Muscat varieties. Previous studies have led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are largely unknown. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28553296/use-of-natural-diversity-and-biotechnology-to-increase-the-quality-and-nutritional-content-of-tomato-and-grape
#10
REVIEW
Quentin Gascuel, Gianfranco Diretto, Antonio J Monforte, Ana M Fortes, Antonio Granell
Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28515004/animal-breeding-strategies-can-improve-meat-quality-attributes-within-entire-populations
#11
D P Berry, S Conroy, T Pabiou, A R Cromie
The contribution of animal breeding to changes in animal performance is well documented across a range of species. Once genetic variation in a trait exists, then breeding to improve the characteristics of that trait is possible, if so desired. Considerable genetic variation exists in a range of meat quality attributes across a range of species. The genetic variation that exists for meat quality is as large as observed for most performance traits; thus, within a well-structured breeding program, rapid genetic gain for meat quality could be possible...
April 21, 2017: Meat Science
https://www.readbyqxmd.com/read/28512461/transcriptional-responses-to-pre-flowering-leaf-defoliation-in-grapevine-berry-from-different-growing-sites-years-and-genotypes
#12
Sara Zenoni, Silvia Dal Santo, Giovanni B Tornielli, Erica D'Incà, Ilaria Filippetti, Chiara Pastore, Gianluca Allegro, Oriana Silvestroni, Vania Lanari, Antonino Pisciotta, Rosario Di Lorenzo, Alberto Palliotti, Sergio Tombesi, Matteo Gatti, Stefano Poni
Leaf removal is a grapevine canopy management technique widely used to modify the source-sink balance and/or microclimate around berry clusters to optimize fruit composition. In general, the removal of basal leaves before flowering reduces fruit set, hence achieving looser clusters, and improves grape composition since yield is generally curtailed more than proportionally to leaf area itself. Albeit responses to this practice seem quite consistent, overall vine performance is affected by genotype, environmental conditions, and severity of treatment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28499415/discrimination-of-candidate-subgenome-specific-loci-by-linkage-map-construction-with-an-s1-population-of-octoploid-strawberry-fragaria%C3%A2-%C3%A3-%C3%A2-ananassa
#13
Soichiro Nagano, Kenta Shirasawa, Hideki Hirakawa, Fumi Maeda, Masami Ishikawa, Sachiko N Isobe
BACKGROUND: The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers...
May 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28464096/the-impact-of-multi-generational-genotype-imputation-strategies-on-imputation-accuracy-and-subsequent-genomic-predictions
#14
M M Judge, D C Purfield, R D Sleator, D P Berry
The objective of the present study was to quantify, using simulations, the impact of successive generations of genotype imputation on genomic predictions. The impact of using a small reference population of true genotypes versus a larger reference population of imputed genotypes on the accuracy of genomic predictions was also investigated. After construction of a founder population, high-density (HD) genotypes ( = 43,500 single nucleotide polymorphisms, SNP) were simulated across 25 generations ( = 46,800 per generation); a low-density genotype panel ( = 3,000 SNP) was developed from these HD genotypes, which was then used to impute genotypes using 7 alternative imputation strategies...
April 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28463982/the-distribution-of-runs-of-homozygosity-and-selection-signatures-in-six-commercial-meat-sheep-breeds
#15
Deirdre C Purfield, Sinead McParland, Eamon Wall, Donagh P Berry
Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH...
2017: PloS One
https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#16
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28380529/characterization-of-an-x-chromosomal-non-mosaic-monosomy-59-x0-dairy-heifer-detected-using-routinely-available-single-nucleotide-polymorphism-genotype-data
#17
D P Berry, A Wolfe, J O'Donovan, N Byrne, R G Sayers, K G Dodds, J C McEwan, R E O'Connor, M McClure, D C Purfield
Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive performance. Despite this, cytogenetic analyses of cattle, especially females, are not routinely undertaken. Genome-wide single nucleotide polymorphism (SNP) genotype data are now, however, routinely being generated in many species globally at a relatively low cost. The objective of the present study was to evaluate the potential of routinely available SNP genotype data to identify sex-chromosome aberrations using X chromosome monosomy 59,X0 as a case study for illustration...
March 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28370629/a-group-of-grapevine-myba-transcription-factors-located-in-chromosome-14-control-anthocyanin-synthesis-in-vegetative-organs-with-different-specificities-compared-with-the-berry-color-locus
#18
José Tomás Matus, Erika Cavallini, Rodrigo Loyola, Janine Höll, Laura Finezzo, Silvia Dal Santo, Sandrine Vialet, Mauro Commisso, Federica Roman, Andrea Schubert, José Antonio Alcalde, Jochen Bogs, Agnès Ageorges, Giovanni Battista Tornielli, Patricio Arce-Johnson
Grapevine organs accumulate anthocyanins in a cultivar-specific and environmentally induced manner. The MYBA1-A2 genes within the berry color locus in chromosome 2 represent the major genetic determinants of fruit color. The simultaneous occurrence of transposon insertions and point mutations in these genes is responsible for most white-skinned phenotypes; however, the red pigmentation found in vegetative organs suggests the presence of additional regulators. This work describes a genomic region of chromosome 14 containing three closely related R2R3-MYB genes, named MYBA5, MYBA6 and MYBA7...
April 2, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28344990/inspiired-a-pipeline-for-quantitative-analysis-of-sites-of-new-dna-integration-in-cellular-genomes
#19
Eric Sherman, Christopher Nobles, Charles C Berry, Emmanuelle Six, Yinghua Wu, Anatoly Dryga, Nirav Malani, Frances Male, Shantan Reddy, Aubrey Bailey, Kyle Bittinger, John K Everett, Laure Caccavelli, Mary J Drake, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344988/inspiired-quantification-and-visualization-tools-for-analyzing-integration-site-distributions
#20
Charles C Berry, Christopher Nobles, Emmanuelle Six, Yinghua Wu, Nirav Malani, Eric Sherman, Anatoly Dryga, John K Everett, Frances Male, Aubrey Bailey, Kyle Bittinger, Mary J Drake, Laure Caccavelli, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to genomic features and that support numerous user-defined statistical tests...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
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