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https://www.readbyqxmd.com/read/28107818/multiple-trait-structured-antedependence-model-to-study-the-relationship-between-litter-size-and-birth-weight-in-pigs-and-rabbits
#1
Ingrid David, Hervé Garreau, Elodie Balmisse, Yvon Billon, Laurianne Canario
BACKGROUND: Some genetic studies need to take into account correlations between traits that are repeatedly measured over time. Multiple-trait random regression models are commonly used to analyze repeated traits but suffer from several major drawbacks. In the present study, we developed a multiple-trait extension of the structured antedependence model (SAD) to overcome this issue and validated its usefulness by modeling the association between litter size (LS) and average birth weight (ABW) over parities in pigs and rabbits...
January 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28097398/mapping-quantitative-trait-loci-for-root-development-under-hypoxia-conditions-in-soybean-glycine-max-l-merr
#2
Loc Van Nguyen, Ryoji Takahashi, Stephen Mwangi Githiri, Tito O Rodriguez, Nobuko Tsutsumi, Sayuri Kajihara, Takasi Sayama, Masao Ishimoto, Kyuya Harada, Keisuke Suematsu, Tomomi Abiko, Toshihiro Mochizuki
Greatest potential, QTLs for hypoxia and waterlogging tolerance in soybean roots were detected using a new phenotypic evaluation method. Waterlogging is a major environmental stress limiting soybean yield in wet parts of the world. Root development is an important indicator of hypoxia tolerance in soybean. However, little is known about the genetic control of root development under hypoxia. This study was conducted to identify quantitative trait loci (QTLs) responsible for root development under hypoxia. Recombinant inbred lines (RILs) developed from a cross between a hypoxia-sensitive cultivar, Tachinagaha, and a tolerant landrace, Iyodaizu, were used...
January 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28093066/predictive-performance-of-genomic-selection-methods-for-carcass-traits-in-hanwoo-beef-cattle-impacts-of-the-genetic-architecture
#3
Hossein Mehrban, Deuk Hwan Lee, Mohammad Hossein Moradi, Chung IlCho, Masoumeh Naserkheil, Noelia Ibáñez-Escriche
BACKGROUND: Hanwoo beef is known for its marbled fat, tenderness, juiciness and characteristic flavor, as well as for its low cholesterol and high omega 3 fatty acid contents. As yet, there has been no comprehensive investigation to estimate genomic selection accuracy for carcass traits in Hanwoo cattle using dense markers. This study aimed at evaluating the accuracy of alternative statistical methods that differed in assumptions about the underlying genetic model for various carcass traits: backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS)...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093063/whole-genome-sequence-based-genomic-prediction-in-laying-chickens-with-different-genomic-relationship-matrices-to-account-for-genetic-architecture
#4
Guiyan Ni, David Cavero, Anna Fangmann, Malena Erbe, Henner Simianer
BACKGROUND: With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher predictive ability, since such data may contain all genomic variants including causal mutations. Our objective was to compare prediction ability with high-density (HD) array data and WGS data in a commercial brown layer line with genomic best linear unbiased prediction (GBLUP) models using various approaches to weight single nucleotide polymorphisms (SNPs)...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28090408/development-of-microsatellite-markers-for-viscum-coloratum-santalaceae-and-their-application-to-wild-populations
#5
Bo-Yun Kim, Han-Sol Park, Soonok Kim, Young-Dong Kim
PREMISE OF THE STUDY: Microsatellite primers were developed for Viscum coloratum (Santalaceae), a semiparasitic medicinal plant that is known for its anticancer properties. Due to excessive human harvesting and loss of suitable habitat of its populations, it has become a potentially threatened species requiring immediate conservation efforts. METHODS AND RESULTS: Based on transcriptome data for V. coloratum, 124 primer pairs were randomly selected for initial validation, of which 19 yielded polymorphic microsatellite loci, with two to six alleles per locus...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090334/an-experimental-validation-of-genomic-selection-in-octoploid-strawberry
#6
Salvador A Gezan, Luis F Osorio, Sujeet Verma, Vance M Whitaker
The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013-2014 and 2014-2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28088213/glycine-alanine-dipeptide-repeat-protein-contributes-to-toxicity-in-a-zebrafish-model-of-c9orf72-associated-neurodegeneration
#7
Yu Ohki, Andrea Wenninger-Weinzierl, Alexander Hruscha, Kazuhide Asakawa, Koichi Kawakami, Christian Haass, Dieter Edbauer, Bettina Schmid
BACKGROUND: The most frequent genetic cause of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) is the expansion of a GGGGCC hexanucleotide repeat in a non-coding region of the chromosome 9 open reading frame 72 (C9orf72) locus. The pathological hallmarks observed in C9orf72 repeat expansion carriers are the formation of RNA foci and deposition of dipeptide repeat (DPR) proteins derived from repeat associated non-ATG (RAN) translation. Currently, it is unclear whether formation of RNA foci, DPR translation products, or partial loss of C9orf72 predominantly drive neurotoxicity in vivo...
January 14, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28087121/upper-extremity-outcome-measures-for-collagen-vi-related-myopathy-and-lama2-related-muscular-dystrophy
#8
Roxanna M Bendixen, Jocelyn Butrum, Mina S Jain, Rebecca Parks, Bonnie Hodsdon, Carmel Nichols, Michelle Hsia, Leslie Nelson, Katherine C Keller, Michelle McGuire, Jeffrey S Elliott, Melody M Linton, Irene C Arveson, Fatou Tounkara, Ruhi Vasavada, Elizabeth Harnett, Monal Punjabi, Sandra Donkervoort, Jahannaz Dastgir, Meganne E Leach, Anne Rutkowski, Melissa Waite, James Collins, Carsten G Bönnemann, Katherine G Meilleur
Congenital muscular dystrophy (CMD) comprises a rare group of genetic muscle diseases that present at birth or early during infancy. Two common subtypes of CMD are collagen VI-related muscular dystrophy (COL6-RD) and laminin alpha 2-related dystrophy (LAMA2-RD). Traditional outcome measures in CMD include gross motor and mobility assessments, yet significant motor declines underscore the need for valid upper extremity motor assessments as a clinical endpoint. This study validated a battery of upper extremity measures in these two CMD subtypes for future clinical trials...
December 5, 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28086785/whole-genome-resequencing-reveals-diagnostic-markers-for-investigating-global-migration-and-hybridization-between-minke-whale-species
#9
Ketil Malde, Bjørghild B Seliussen, María Quintela, Geir Dahle, Francois Besnier, Hans J Skaug, Nils Øien, Hiroko K Solvang, Tore Haug, Rasmus Skern-Mauritzen, Naohisa Kanda, Luis A Pastene, Inge Jonassen, Kevin A Glover
BACKGROUND: In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An example of this can be seen in the minke whale species complex. Antarctic minke whales are genetically and morphologically distinct from the common minke found in the north Atlantic and Pacific oceans, and the two species are estimated to have been isolated from each other for 5 million years or more...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081581/differences-in-gene-expression-and-gene-associations-in-epicardial-fat-compared-to-subcutaneous-fat
#10
J Yim, S W Rabkin
Epicardial adipose tissue (EAT) plays a role in cardiac physiology and may contribute to the development of coronary artery disease. Our objective was to determine whether there was a significant difference in gene expression in EAT compared to subcutaneous adipose tissue (SAT) and to identify potential relationships. MEDLINE and EMBASE were searched using the key terms "Epicardial Adipose Tissue" or "Epicardial Fat" in combination with "RNA", "mRNA", or "gene". The entry criteria were studies that presented primary data including expression levels of mRNA in human EAT compared with SAT and an expression of variance (SD)...
January 12, 2017: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
https://www.readbyqxmd.com/read/28073972/awareness-and-attitude-regarding-reproductive-options-of-persons-carrying-a-brca-mutation-and-their-partners
#11
J J G Gietel-Habets, C E M de Die-Smulders, I A P Derks-Smeets, A Tibben, V C G Tjan-Heijnen, R van Golde, E Gomez-Garcia, C M Kets, L A D M van Osch
STUDY QUESTION: To what extent are BRCA mutation carriers and their partners in the Netherlands aware about preimplantation genetic diagnosis (PGD) and prenatal diagnosis (PND) as reproductive options and what is their attitude towards these options? SUMMARY ANSWER: Awareness of PGD (66%) and PND (61%) among BRCA mutation carriers and their partners is relatively high and 80% and 26%, respectively, of BRCA carriers and their partners find offering PGD and PND for hereditary breast and ovarian cancer (HBOC) acceptable...
January 9, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28062449/context-sensitive-network-based-disease-genetics-prediction-and-its-implications-in-drug-discovery
#12
Yang Chen, Rong Xu
MOTIVATION: Disease phenotype networks play an important role in computational approaches to identifying new disease-gene associations. Current disease phenotype networks often model disease relationships based on pairwise similarities, therefore ignore the specific context on how two diseases are connected. In this study, we propose a new strategy to model disease associations using context-sensitive networks (CSNs). We developed a CSN-based phenome-driven approach for disease genetics prediction, and investigated the translational potential of the predicted genes in drug discovery...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28054352/impact-of-il13-genetic-polymorphism-arg130gln-on-total-serum-ige-levels-and-ifn-%C3%AE-gene-expression
#13
Bozena Smolkova, Jana Tulinska, Lubica Palkovicova Murinova, Verona Buocikova, Aurelia Liskova, Katarina Rausova, Miroslava Kuricova, Henrieta Patayova, Maria Sustrova, Eva Neubauerova Svorcova, Silvia Ilavska, Michaela Szabova, Tomas Nemessanyi, Eva Jahnova, Maria Dusinska, Peter Ciznar, Laurence Fuortes
This cross-sectional study was designed to investigate the extent of genetic susceptibility by targeting variants in IL-4/IL-13 signalling pathways leading to atopic disease in early childhood. We evaluated involvement of five single nucleotide polymorphisms IL4 C-590T, IL13 C-1055T, IL13 Arg130Gln, IL4RA Ile50Val and IL4RA Ser478Pro, in the control of serum total and antigen-specific IgE levels. Furthermore, we analyzed their association with changes in gene expression of five cytokines having key roles in inflammatory and anti-inflammatory immune response (IL-4, IL-13, IFN-γ, IL-8 and IL-10)...
January 5, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28052106/a-prediction-algorithm-for-drug-response-in-patients-with-mesial-temporal-lobe-epilepsy-based-on-clinical-and-genetic-information
#14
Mariana S Silva-Alves, Rodrigo Secolin, Benilton S Carvalho, Clarissa L Yasuda, Elizabeth Bilevicius, Marina K M Alvim, Renato O Santos, Claudia V Maurer-Morelli, Fernando Cendes, Iscia Lopes-Cendes
Mesial temporal lobe epilepsy is the most common form of adult epilepsy in surgical series. Currently, the only characteristic used to predict poor response to clinical treatment in this syndrome is the presence of hippocampal sclerosis. Single nucleotide polymorphisms (SNPs) located in genes encoding drug transporter and metabolism proteins could influence response to therapy. Therefore, we aimed to evaluate whether combining information from clinical variables as well as SNPs in candidate genes could improve the accuracy of predicting response to drug therapy in patients with mesial temporal lobe epilepsy...
2017: PloS One
https://www.readbyqxmd.com/read/28049703/pathway-structured-predictive-model-for-cancer-survival-prediction-a-two-stage-approach
#15
Xinyan Zhang, Yan Li, Tomi Akinyemiju, Akinyemi I Ojesina, Phillip Buckhaults, Nianjun Liu, Bo Xu, Nengjun Yi
Heterogeneity in terms of tumor characteristics, prognosis, and survival among cancer patients has been a persistent problem for many decades. Currently, prognosis and outcome predictions are made based on clinical factors and/or by incorporating molecular profiling data. However, inaccurate prognosis and prediction may result by using only clinical or molecular information directly. One of the main shortcomings of past studies is the failure to incorporate prior biological information into the predictive model, given strong evidence of the pathway-based genetic nature of cancer, i...
January 2017: Genetics
https://www.readbyqxmd.com/read/28046178/using-single-step-genomic-best-linear-unbiased-predictor-to-enhance-the-mitigation-of-seasonal-losses-due-to-heat-stress-in-pigs
#16
B O Fragomeni, D A L Lourenco, S Tsuruta, H L Bradford, K A Gray, Y Huang, I Misztal
The purposes of this study were to analyze the impact of seasonal losses due to heat stress in pigs from different breeds raised in different environments and to evaluate the accuracy improvement from adding genomic information to genetic evaluations. Data were available for 2 different swine populations: purebred Duroc animals raised in Texas and North Carolina and commercial crosses of Duroc and F females (Landrace × Large White) raised in Missouri and North Carolina; pedigrees provided links for animals from different states...
December 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/28040800/identification-introgression-and-validation-of-fruit-volatile-qtls-from-a-red-fruited-wild-tomato-species
#17
José L Rambla, Aurora Medina, Asun Fernández-Del-Carmen, Walter Barrantes, Silvana Grandillo, Maria Cammareri, Gloria López-Casado, Guillermo Rodrigo, Arancha Alonso, Santiago García-Martínez, Jaime Primo, Juan J Ruiz, Rafael Fernández-Muñoz, Antonio J Monforte, Antonio Granell
Volatile organic compounds (VOCs) are major determinants of fruit flavor, a primary objective in tomato breeding. A recombinant inbred line (RIL) population consisting of 169 lines derived from a cross between Solanum lycopersicum and a red-fruited wild tomato species Solanum pimpinellifolium accession (SP) was characterized for VOCs in three different seasons. Correlation and hierarchical cluster analyses were performed on the 52 VOCs identified, providing a tool for the putative assignation of individual compounds to metabolic pathways...
December 30, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28040779/forward-genetics-by-sequencing-ems-variation-induced-inbred-lines
#18
Charles Addo-Quaye, Elizabeth Buescher, Norman Best, Vijay Chaikam, Ivan Baxter, Brian P Dilkes
In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of EMS mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequence in wild-type siblings and heterozygous in segregating families...
December 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28031058/assessment-of-knowledge-attitude-and-practice-towards-consanguineous-marriages-among-a-cohort-of-multiethnic-health-care-providers-in-saudi-arabia
#19
Dhekra Alnaqeb, Hanan Hamamy, Amira M Youssef, Khalid Al-Rubeaan
This study aimed to assess knowledge, attitude and practice related to consanguinity among multiethnic health care providers in the Kingdom of Saudi Arabia. Using a cross-sectional study design, a validated, self-administered close-ended questionnaire was randomly distributed to health care providers in different health institutions in the country between 1st August 2012 and 31st July 2013. A total of 1235 health care providers completed the study questionnaire. Of the 892 married participants (72.23% of total), 11...
December 29, 2016: Journal of Biosocial Science
https://www.readbyqxmd.com/read/28028694/a-new-model-of-flavonoids-affinity-towards-p-glycoprotein-genetic-algorithm-support-vector-machine-with-features-selected-by-a-modified-particle-swarm-optimization-algorithm
#20
Ying Cui, Qinggang Chen, Yaxiao Li, Ling Tang
Flavonoids exhibit a high affinity for the purified cytosolic NBD (C-terminal nucleotide-binding domain) of P-glycoprotein (P-gp). To explore the affinity of flavonoids for P-gp, quantitative structure-activity relationship (QSAR) models were developed using support vector machines (SVMs). A novel method coupling a modified particle swarm optimization algorithm with random mutation strategy and a genetic algorithm coupled with SVM was proposed to simultaneously optimize the kernel parameters of SVM and determine the subset of optimized features for the first time...
December 27, 2016: Archives of Pharmacal Research
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