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https://www.readbyqxmd.com/read/28724269/association-of-human-methionine-synthase-a2756g-transition-with-prostate-cancer-a-case-control-study-and-in-silico-analysis
#1
Arezou Ebrahimi, Abasalt Hosseinzadeh Colagar, Mohammad Karimian
Methionine synthase (MTR) is one of the key enzymes of folate pathway, which play a key role in the construction, repair, and methylation of DNA. In this study, an association of MTR A2756G gene transition with prostate cancer in men populations of Kashan-Iran was investigated by a case-control study and an in silico analysis. The 200 samples including 100 patients with prostate cancer, as case group and 100 healthy men, as control group included in this study. MTR-A2756G genotyping was performed by PCR-RFLP technique...
May 2017: Acta Medica Iranica
https://www.readbyqxmd.com/read/28724083/identification-of-candidate-genes-responsible-for-stem-pith-production-using-expression-analysis-in-solid-stemmed-wheat
#2
A J Oiestad, J M Martin, J Cook, A C Varella, M J Giroux
The wheat stem sawfly (WSS) is an economically important pest of wheat in the Northern Great Plains. The primary means of WSS control is resistance associated with the single quantitative trait locus (QTL) , which controls most stem solidness variation. The goal of this study was to identify stem solidness candidate genes via RNA-seq. This study made use of 28 single nucleotide polymorphism (SNP) makers derived from expressed sequence tags (ESTs) linked to contained within a 5.13 cM region. Allele specific expression of EST markers was examined in stem tissue for solid and hollow-stemmed pairs of two spring wheat near isogenic lines (NILs) differing for the QTL...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724078/genome-wide-association-study-of-developing-leaves-heat-tolerance-during-vegetative-growth-stages-in-a-sorghum-association-panel
#3
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
#4
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
https://www.readbyqxmd.com/read/28724075/a-comprehensive-image-based-phenomic-analysis-reveals-the-complex-genetic-architecture-of-shoot-growth-dynamics-in-rice-oryza-sativa
#5
Malachy T Campbell, Qian Du, Kan Liu, Chris J Brien, Bettina Berger, Chi Zhang, Harkamal Walia
Early vigor is an important trait for many rice ( L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724074/high-resolution-genetic-and-physical-mapping-of-the-eastern-filbert-blight-resistance-region-in-jefferson-hazelnut-corylus-avellana-l
#6
Vidyasagar Sathuvalli, Shawn A Mehlenbacher, David C Smith
Eastern filbert blight (EFB), caused by the pyrenomycete (Peck) E. Müller, is a devastating disease of European hazelnut ( L) in the US Pacific Northwest. A dominant allele at a single locus from the obsolete pollenizer 'Gasaway' confers a high level of resistance to EFB. To identify the gene responsible for resistance, we initiated map-based cloning efforts in a population of 1488 seedlings that segregated for resistance. Chromosome walking was initiated using primers designed from eight previously identified random amplified polymorphic DNA markers linked to resistance...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724072/genome-wide-analysis-of-tar-spot-complex-resistance-in-maize-using-genotyping-by-sequencing-snps-and-whole-genome-prediction
#7
Shiliang Cao, Alexander Loladze, Yibing Yuan, Yongsheng Wu, Ao Zhang, Jiafa Chen, Gordon Huestis, Jingsheng Cao, Vijay Chaikam, Michael Olsen, Boddupalli M Prasanna, Felix San Vicente, Xuecai Zhang
Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724071/haplotypes-phased-from-population-transcriptomes-detecting-selection-in-the-initial-adaptation-of-miscanthus-lutarioriparius-to-stressful-environments
#8
Cai-Yun Zhu, Wei Liu, Li-Fang Kang, Qin Xu, Shi-Lai Xing, Yang-Yang Fan, Zhi-Hong Song, Juan Yan, Jian-Qiang Li, Tao Sang
Adaptation is a characteristic that enhances the survival or reproduction of organisms; selection is the critical process leading to adaptive evolution. Therefore, detecting selection is important in studying evolutionary biology. Changes in allele frequency are fundamental to adaptive evolution. The allele frequency of entire genes at the genomic scale is more intensive and precise for analyzing selection effects, compared with simple sequence repeat and single nucleotide polymorphism (SNP) alleles from nuclear gene fragments...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724070/marker-trait-association-analysis-of-iron-and-zinc-concentration-in-lentil-lens-culinaris-medik-seeds
#9
Hamid Khazaei, Rajib Podder, Carolyn T Caron, Shudhangshu S Kundu, Marwan Diapari, Albert Vandenberg, Kirstin E Bett
Lentil ( Medik.) seeds are relatively rich in iron (Fe) and zinc (Zn), making lentil a potential crop to aid in the global battle against human micronutrient deficiency. Understanding the genetic basis for uptake of seed Fe and Zn is required to increase sustainable concentrations of these minerals in seeds. The objectives of this study were to characterize genetic variation in seed Fe and Zn concentration and to identify molecular markers associated with these traits across diverse lentil accessions. A set of 138 cultivated lentil accessions from 34 countries were evaluated in four environments (2 sites × 2 yr) in Saskatchewan, Canada...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724069/a-distinct-genetic-cluster-in-cultivated-chickpea-as-revealed-by-genome-wide-marker-discovery-and-genotyping
#10
Stefano Pavan, Concetta Lotti, Angelo R Marcotrigiano, Rosa Mazzeo, Nicoletta Bardaro, Valentina Bracuto, Francesca Ricciardi, Francesca Taranto, Nunzio D'Agostino, Adalgisa Schiavulli, Claudio De Giovanni, Cinzia Montemurro, Gabriella Sonnante, Luigi Ricciardi
The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea ( L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724068/genome-wide-association-mapping-of-qualitatively-inherited-traits-in-a-germplasm-collection
#11
Nonoy B Bandillo, Aaron J Lorenz, George L Graef, Diego Jarquin, David L Hyten, Randall L Nelson, James E Specht
Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ∼13,000 soybean [ (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724065/comparative-mapping-and-targeted-capture-sequencing-of-the-gametocidal-loci-in-aegilops-sharonensis
#12
Surbhi Grewal, Laura-Jayne Gardiner, Barbora Ndreca, Emilie Knight, Graham Moore, Ian P King, Julie King
Gametocidal (Gc) chromosomes or elements in species such as Eig are preferentially transmitted to the next generation through both the male and female gametes when introduced into wheat ( L.). Furthermore, any genes, such as genes that control agronomically important traits, showing complete linkage with Gc elements, are also transmitted preferentially to the next generation without the need for selection. The mechanism for the preferential transmission of the Gc elements appears to occur by the induction of extensive chromosome damage in any gametes that lack the Gc chromosome in question...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724064/genetic-characterization-of-the-soybean-nested-association-mapping-population
#13
Qijian Song, Long Yan, Charles Quigley, Brandon D Jordan, Edward Fickus, Steve Schroeder, Bao-Hua Song, Yong-Qiang Charles An, David Hyten, Randall Nelson, Katy Rainey, William D Beavis, Jim Specht, Brian Diers, Perry Cregan
A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [ (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724063/evaluation-of-genetic-diversity-and-host-resistance-to-stem-rust-in-usda-nsgc-durum-wheat-accessions
#14
Shiaoman Chao, Matthew N Rouse, Maricelis Acevedo, Agnes Szabo-Hever, Harold Bockelman, J Michael Bonman, Elias Elias, Daryl Klindworth, Steven Xu
The USDA-ARS National Small Grains Collection (NSGC) maintains germplasm representing global diversity of small grains and their wild relatives. To evaluate the utility of the NSGC durum wheat ( L. ssp. ) accessions, we assessed genetic diversity and linkage disequilibrium (LD) patterns in a durum core subset containing 429 lines with spring growth habit originating from 64 countries worldwide. Genetic diversity estimated using wheat single-nucleotide polymorphism (SNP) markers showed considerable diversity captured in this collection...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724061/multi-locus-mixed-model-analysis-of-stem-rust-resistance-in-winter-wheat
#15
Paul D Mihalyov, Virginia A Nichols, Peter Bulli, Matthew N Rouse, Michael O Pumphrey
Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With the improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method of mining populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus f. sp. is a devastating disease that threatens wheat ( L.) production worldwide. Here, we explored the genetic basis of stem rust resistance in a global collection of 1411 hexaploid winter wheat accessions genotyped with 5390 single nucleotide polymorphism markers...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724060/genome-wide-association-mapping-of-crown-rust-resistance-in-oat-elite-germplasm
#16
Kathy Esvelt Klos, Belayneh A Yimer, Ebrahiem M Babiker, Aaron D Beattie, J Michael Bonman, Martin L Carson, James Chong, Stephen A Harrison, Amir M H Ibrahim, Frederic L Kolb, Curt A McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J Paul Murphy, Nicholas A Tinker
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724058/search-for-dq2-5-and-dq8-alleles-using-a-lower-cost-technique-in-patients-with-type-1-diabetes-and-celiac-disease-in-a-population-of-southern-brazil
#17
Marília D Bastos, Thayne W Kowalski, Márcia Puñales, Balduíno Tschiedel, Luiza M Mariath, Ana Luiza G Pires, Lavínia S Faccini, Themis R Silveira
Objective: To evaluate the frequency of DQ2.5 and DQ8 alleles using the Tag-single-nucleotide polymorphism (Tag-SNP) technique in individuals with type 1 diabetes mellitus (T1DM) and celiac disease (CD) in southern Brazil. Materials and methods: In a prospective design, we performed the search for DQA1*0501 and DQB1*0201 alleles for DQ2.5 and DQB1*0302 for DQ8 through Real-Time Polymerase Chain Reaction (RT-PCR) technique, using TaqMan Genotyping Assays (Applied Biosystems, USA)...
July 13, 2017: Archives of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28723925/immunologic-response-to-vaccine-challenge-in-pregnant-ptpn22-r620w-carriers-and-non-carriers
#18
Shelly H Tien, Juliet N Crabtree, Heather L Gray, Erik J Peterson
OBJECTIVES: Influenza infection is a significant cause of respiratory morbidity among pregnant women. Seasonal influenza vaccination engages innate immune receptors to promote protective immunity. A coding polymorphism (R620W) in PTPN22 imparts elevated risk for human infection and autoimmune disease, predisposes to diminished innate immune responses, and associates with reduced immunization responses. We sought to quantify the effects of PTPN22-R620W on humoral and cell-mediated immune responses to the inactivated influenza vaccine among healthy pregnant women...
2017: PloS One
https://www.readbyqxmd.com/read/28723901/2b-rad-genotyping-for-population-genomic-studies-of-chagas-disease-vectors-rhodnius-ecuadoriensis-in-ecuador
#19
Luis E Hernandez-Castro, Marta Paterno, Anita G Villacís, Björn Andersson, Jaime A Costales, Michele De Noia, Sofía Ocaña-Mayorga, Cesar A Yumiseva, Mario J Grijalva, Martin S Llewellyn
BACKGROUND: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses...
July 19, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28723867/prediction-of-severe-toxicity-in-adult-patients-under-treatment-with-5-fluorouracil-a-prospective-cohort-study
#20
Carolina Vázquez, María Orlova, Federico Angriman, José N Minatta, Paula Scibona, María A Verzura, Esteban G Jáuregui, Heidy Díaz de Arce, María G Pallotta, Waldo H Belloso
5-Fluorouracil (5-FU) has long been used for the treatment of gastrointestinal tumors harboring interindividual variability in both the pharmacokinetic and the pharmacogenetic profiles, which in turn may lead to life-threatening toxicities. We carried out a prospective cohort study of adult patients initiating treatment with 5-FU between 2013 and 2015. Primary exposures of interest were the methylenetetrahydrofolate reductase single nucleotide polymorphism in exons 4 and 7 and 5'-untranslated region-thymidylate synthase VNTR genotypes, in addition to baseline clinical and demographic variables...
July 18, 2017: Anti-cancer Drugs
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