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https://www.readbyqxmd.com/read/28728396/characterization-and-functional-inferences-of-a-genome-wide-dna-methylation-profile-in-the-loin-longissimus-dorsi-muscle-of-swine
#1
Woonsu Kim, Hyesun Park, Kang-Seok Seo, Seongwon Seo
Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates)...
May 14, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28727969/fetal-dysmorphology-still-an-essential-art-analysis-of-the-limitations-of-microarray-in-a-fetal-population-and-a-look-toward-the-genome-sequencing-era
#2
E Fletcher, M Porteous, K J McKenzie, E J Maher, M J Evans
Cytogenomic microarray allows assessment of the genome at higher resolutions than traditional karyotyping. The objective of this study is to evaluate the utility of microarray in a routine fetal autopsy setting before the advent of routine fetal exome/genome sequencing and the issues these technologies may generate. A systematic review of fetal postmortems at 12-24 weeks gestation between January 2011 and December 2014 was undertaken. Cases where there was no consent for audit, research, or genetic testing were excluded as were cases referred to the Procurator Fiscal, stillbirths, and neonatal deaths...
July 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28727939/phytohormone-and-genome-variations-in-vitis-amurensis-resistant-to-downy-mildew
#3
Ling Yin, Junjie Qu, Shuhan Deng, Shaoli Liu, Jiang Lu, Yali Zhang
Downy mildew (DM) resistance is a highly desirable agronomic trait in grape breeding. High variation in Plasmopara viticola resistance was found in Vitis cultivars. Some accessions show high P. viticola resistance even under conditions highly conducive to DM. Here, leaf disc inoculation experiments revealed that Vitis amurensis 'Zuoshaner' exhibited DM resistance with necrotic spots, whereas the V. amurensis × V. vinifera hybrid cultivar 'Zuoyouhong' was susceptible. Changes in plant hormones accumulation profiles, differed between the cultivars...
July 20, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#4
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
https://www.readbyqxmd.com/read/28727628/replication-confirms-the-association-of-loci-in-foxe1-pde8b-capzb-and-pde10a-with-thyroid-traits-a-genetics-of-diabetes-audit-and-research-tayside-study
#5
Enrique Soto-Pedre, Moneeza K Siddiqui, Alex S Doney, Colin N A Palmer, Ewan R Pearson, Graham P Leese
OBJECTIVE: Replication of associations in genome-wide association studies is desirable to ensure that such signals are potentially clinically meaningful. This study aimed to replicate associations of selected single-nucleotide polymorphisms (SNPs) with hypothyroidism and serum thyroid-stimulating hormone (TSH) using electronic medical records (EMRs). PATIENTS AND METHODS: A cross-sectional study was carried out among patients of European Caucasian ethnicity from the Genetics of Diabetes Audit and Research Tayside recruited in Tayside (Scotland, UK)...
July 19, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28727232/functional-genomic-analysis-of-corals-from-natural-co2-seeps-reveals-core-molecular-responses-involved-in-acclimatization-to-ocean-acidification
#6
C D Kenkel, A Moya, J Strahl, C Humphrey, L K Bay
Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long-term acclimatization to natural variation in pCO2 . In the coral host, only 61 genes were differentially expressed in response to pCO2 environment, but the pattern of change was highly consistent between replicate populations, likely reflecting the core expression homeostasis response to ocean acidification...
July 20, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28727049/association-of-udder-traits-with-single-nucleotide-polymorphisms-in-crossbred-bos-indicus-bos-taurus-cows
#7
M W Tolleson, C A Gill, A D Herring, P K Riggs, J E Sawyer, J O Sanders, D G Riley
The size, support, and health of udders limit the productive life of beef cows, especially those with background, because, in general, such cows have a reputation for problems with udders. Genomic association studies of bovine udder traits have been conducted in dairy cattle and recently in Continental European beef breeds but not in cows with background. The objective of this study was to determine associations of SNP and udder support scores, teat length, and teat diameter in half (Nellore), half (Angus) cows...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28727016/genomewide-association-mapping-and-pathway-analysis-of-meat-tenderness-in-polled-nellore-cattle
#8
L M Castro, G J M Rosa, F B Lopes, L C A Regitano, A J M Rosa, C U Magnabosco
Brazil is one of the world's largest beef exporters, although the product has a low price due to quality issues. The meat exported by Brazil is considered medium and low quality by international buyers, mainly due to lack of tenderness. The predominant Zebu breeds (80% Nellore) are known for producing tougher beef than taurine breeds. Nonetheless, some studies have shown that there is substantial genetic variability for tenderness within the Nellore breed, although it is a difficult trait to improve by conventional selection methods...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28727006/genetic-analysis-of-semen-production-traits-of-japanese-black-and-holstein-bulls-genome-wide-marker-based-estimation-of-genetic-parameters-and-environmental-effect-trends
#9
Y Atagi, A Onogi, M Kinukawa, A Ogino, K Kurogi, K Uchiyama, T Yasumori, K Adachi, K Togashi, H Iwata
The semen production traits of bulls from 2 major cattle breeds in Japan, Holstein and Japanese Black, were analyzed comprehensively using genome-wide markers. Weaker genetic correlations were observed between the 2 age groups (1 to 3 yr old and 4 to 6 yr old) regarding semen volume and sperm motility compared with those observed for sperm number and motility after freeze-thawing. The preselection of collected semen for freezing had a limited effect. Given the increasing importance of bull proofs at a young age because of genomic selection and the results from preliminary studies, we used a multiple-trait model that included motility after freeze-thawing with records collected at young ages...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726721/identification-and-validation-of-new-alleles-of-falsiflora-and-compound-inflorescence-genes-controlling-the-number-of-branches-in-tomato-inflorescence
#10
Huan Zheng, Saneyuki Kawabata
The architecture of inflorescences shows extensive diversity in both branching frequency and flower number, which eventually, determines agricultural productivity. In this study, F₂ (second filial) populations derived from a cross between Solanum lycopersicum 10AS111A (highly-branched inflorescence) and the S. pimpinellifolium PI124039 (inflorescence having a single branch) were used to decipher the genetic control of branch number (BN) of inflorescence in plants bearing small-sized tomato fruits. The segregation ratio of single- and moderately-branched types to the highly-branched type was significantly different from 3:1 but not different from 15:1 at p < 0...
July 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28726125/nitrogen-assimilation-in-denitrifier-bacillus-azotoformans-lmg-9581-t
#11
Yihua Sun, Paul De Vos, Anne Willems
Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO3(-))/nitrite (NO2(-)) reduction to ammonium (NH4(+)) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581(T) shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene...
July 19, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28725363/bridging-two-scholarly-islands-enriches-both-coi-dna-barcodes-for-species-identification-versus-human-mitochondrial-variation-for-the-study-of-migrations-and-pathologies
#12
David S Thaler, Mark Y Stoeckle
DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28725028/detection-and-quantitation-of-copy-number-variation-in-the-voltage-gated-sodium-channel-gene-of-the-mosquito-culex-quinquefasciatus
#13
Walter Fabricio Silva Martins, Krishanthi Subramaniam, Keith Steen, Henry Mawejje, Triantafillos Liloglou, Martin James Donnelly, Craig Stephen Wilding
Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724956/mapping-resistance-responses-to-sclerotinia-infestation-in-introgression-lines-of-brassica-juncea-carrying-genomic-segments-from-wild-brassicaceae-b-fruticulosa
#14
Kusum Rana, Chhaya Atri, Mehak Gupta, Javed Akhatar, Prabhjodh S Sandhu, Nitin Kumar, Ravinder Jaswal, Martin J Barbetti, Surinder S Banga
Sclerotinia stem rot (Sclerotinia sclerotiorum) is a major disease of Brassica oilseeds. As suitable donors to develop resistant cultivars are not available in crop Brassicas, we introgressed resistance from a wild Brassicaceae species, B. fruticulosa. We produced 206 B. juncea-B. fruticulosa introgression lines (ILs). These were assessed for pollen grain fertility, genome size variations and resistance responses to Sclerotinia following stem inoculations under disease-conducive conditions. Of these, 115 ILs showing normal fertility and genome size were selected for cytogenetic characterization using florescent genomic in situ hybridization (Fl-GISH)...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724489/population-genetic-structure-of-the-cayo-santiago-colony-of-rhesus-macaques-macaca-mulatta
#15
Sreetharan Kanthaswamy, Robert F Oldt, Jillian Ng, Angelina V Ruiz-Lambides, Elizabeth Maldonado, Melween I Martínez, Carlos A Sariol
The rhesus macaque population at Cayo Santiago increases annually and is in urgent need of control. In-depth assessments of the colony's population genetic and pedigree structures provide a starting point for improving the colony's long-term management program. We evaluated the degree of genetic variation and coefficients of inbreeding and kinship of the Cayo Santiago colony by using pedigree and short tandem repeat (STR) data from 4738 rhesus macaques, which represent 7 extant social groups and a group of migrant males...
July 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28724449/novel-promoters-and-coding-first-exons-in-dlg2-linked-to-developmental-disorders-and-intellectual-disability
#16
Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
BACKGROUND: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play...
July 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28724409/hybrid-assembly-with-long-and-short-reads-improves-discovery-of-gene-family-expansions
#17
Jason R Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P Walenz, Junqi Liu, Robert M Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G Maron, Susan R McCouch, W Richard McCombie, Michael C Schatz, Peter Tiffin, Nevin D Young, Kevin A T Silverstein
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724398/whole-genome-sequencing-identifies-a-novel-alms1-gene-mutation-in-two-chinese-siblings-with-alstr%C3%A3-m-syndrome
#18
Lin Yang, Zixiu Li, Mei Mei, Xiaomei Fan, Guodong Zhan, Huijun Wang, Guoying Huang, Mingbang Wang, Weidong Tian, Wenhao Zhou
BACKGROUND: Alström syndrome is a rare multi-systemic disorder with a broad spectrum of symptoms. This syndrome is characterized by childhood retinal degeneration; sensorineural hearing loss; obesity; type 2 diabetes mellitus; cardiomyopathy; systemic fibrosis; and pulmonary, hepatic, and renal failure. CASE PRESENTATION: A Chinese quartet family with two siblings predominantly affected by cone-rod dystrophy and short stature were recruited. The craniofacial dysmorphism and on-set age-of-cone-rod dystrophy in the proband showed a minor intrafamilial variability...
July 19, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28724078/genome-wide-association-study-of-developing-leaves-heat-tolerance-during-vegetative-growth-stages-in-a-sorghum-association-panel
#19
Junping Chen, Ratan Chopra, Chad Hayes, Geoffrey Morris, Sandeep Marla, John Burke, Zhanguo Xin, Gloria Burow
Heat stress reduces grain yield and quality worldwide. Enhancing heat tolerance of crops at all developmental stages is one of the essential strategies required for sustaining agricultural production especially as frequency of temperature extremes escalates in response to climate change. Although heat tolerance mechanisms have been studied extensively in model plant species, little is known about the genetic control underlying heat stress responses of crop plants at the vegetative stage under field conditions...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724076/gbs-based-genomic-selection-for-pea-grain-yield-under-severe-terminal-drought
#20
Paolo Annicchiarico, Nelson Nazzicari, Luciano Pecetti, Massimo Romani, Barbara Ferrari, Yanling Wei, E Charles Brummer
Terminal drought is the main stress that limits pea ( L.) grain yield in Mediterranean-climate regions. This study provides an unprecedented assessment of the predictive ability of genomic selection (GS) for grain yield under severe terminal drought using genotyping-by-sequencing (GBS) data. Additional aims were to assess the GS predictive ability for different GBS data quality filters and GS models, comparing intrapopulation with interpopulation GS predictive ability and to perform genome-wide association (GWAS) studies...
July 2017: Plant Genome
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