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Epistasis

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https://www.readbyqxmd.com/read/28724085/quantitative-trait-loci-mapping-for-spike-characteristics-in-hexaploid-wheat
#1
Yaopeng Zhou, Benjamin Conway, Daniela Miller, David Marshall, Aaron Cooper, Paul Murphy, Shiaoman Chao, Gina Brown-Guedira, José Costa
Wheat ( L.) spike characteristics determine the number of grains produced on each spike and constitute key components of grain yield. Understanding of the genetic basis of spike characteristics in wheat, however, is limited. In this study, genotyping-by-sequencing (GBS) and the iSelect 9K assay were used on a doubled-haploid (DH) soft red winter wheat population that showed a wide range of phenotypic variation for spike traits. A genetic map spanning 2934.1 cM with an average interval length of 3.4 cM was constructed...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28720710/application-of-response-surface-methods-to-determine-conditions-for-optimal-genomic-prediction
#2
Réka Howard, Alicia L Carriquiry, William D Beavis
An epistatic genetic architecture can have a significant impact on prediction accuracies of genomic prediction (GP) methods. Machine learning methods predict traits composed of epistatic genetic architectures more accurately than statistical methods based on additive mixed linear models. The differences between these types of GP methods suggest a diagnostic for revealing genetic architectures underlying traits of interest. In addition to genetic architecture, the performance of GP methods may be influenced by the sample size of the training population, the number of QTL, and the proportion of phenotypic variability due to genotypic variability (heritability)...
July 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28720700/hitchhiking-and-epistasis-give-rise-to-cohort-dynamics-in-adapting-populations
#3
Sean W Buskirk, Ryan Emily Peace, Gregory I Lang
Beneficial mutations are the driving force of adaptive evolution. In asexual populations, the identification of beneficial alleles is confounded by the presence of genetically linked hitchhiker mutations. Parallel evolution experiments enable the recognition of common targets of selection; yet these targets are inherently enriched for genes of large target size and mutations of large effect. A comprehensive study of individual mutations is necessary to create a realistic picture of the evolutionarily significant spectrum of beneficial mutations...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28709611/the-case-epistasis-and-urolithiasis
#4
Nathalie Tabibzadeh, Lynda Cheddani, Michel Daudon, Jean-Philippe Haymann, Aurélie Toussaint, Caroline Silve, Emmanuel Letavernier
No abstract text is available yet for this article.
August 2017: Kidney International
https://www.readbyqxmd.com/read/28703322/the-drosophila-simulans-y-chromosome-interacts-with-the-autosomes-to-influence-male-fitness
#5
C Ruth Archer, Robert M Stephens, Manmohan D Sharma, David J Hosken
The Y chromosome should degenerate because it cannot recombine. However, male limited transmission increases selection efficiency for male benefit alleles on the Y, and therefore Y-chromosomes should contribute significantly to variation in male-fitness. This means that although the Drosophila Y chromosome is small and gene-poor, Y-linked genes are vital for male fertility in D. melanogaster and the Y chromosome has large male-fitness effects. It is unclear if the same pattern is seen in the closely related D...
July 13, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28703045/the-role-of-human-host-genetics-in-tuberculosis-resistance
#6
Craig Kinnear, Eileen G Hoal, Haiko Schurz, Paul D van Helden, Marlo Möller
Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations...
July 13, 2017: Expert Review of Respiratory Medicine
https://www.readbyqxmd.com/read/28694848/epiaco-a-method-for-identifying-epistasis-based-on-ant-colony-optimization-algorithm
#7
Yingxia Sun, Junliang Shang, Jin-Xing Liu, Shengjun Li, Chun-Hou Zheng
BACKGROUND: Identifying epistasis or epistatic interactions, which refer to nonlinear interaction effects of single nucleotide polymorphisms (SNPs), is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Though many works have been done for identifying epistatic interactions, due to their methodological and computational challenges, the algorithmic development is still ongoing. RESULTS: In this study, a method epiACO is proposed to identify epistatic interactions, which based on ant colony optimization algorithm...
2017: BioData Mining
https://www.readbyqxmd.com/read/28678836/epistasis-in-genomic-and-survival-data-of-cancer-patients
#8
Dariusz Matlak, Ewa Szczurek
Cancer aggressiveness and its effect on patient survival depends on mutations in the tumor genome. Epistatic interactions between the mutated genes may guide the choice of anticancer therapy and set predictive factors of its success. Inhibitors targeting synthetic lethal partners of genes mutated in tumors are already utilized for efficient and specific treatment in the clinic. The space of possible epistatic interactions, however, is overwhelming, and computational methods are needed to limit the experimental effort of validating the interactions for therapy and characterizing their biomarkers...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28674544/the-interactions-between-the-long-non-coding-rna-nerdl-and-its-target-gene-affect-wood-formation-in-populus-tomentosa
#9
Wan Shi, Mingyang Quan, Qingzhang Du, Deqiang Zhang
Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28659968/the-human-microbiome-and-the-missing-heritability-problem
#10
Santiago Sandoval-Motta, Maximino Aldana, Esperanza Martínez-Romero, Alejandro Frank
The "missing heritability" problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28655969/the-immunosignature-of-mother-fetus-couples-in-gestational-diabetes-mellitus-role-of-hla-g-14%C3%A2-bp-ins-del-and-papp-a-a-c-polymorphisms-in-the-uterine-inflammatory-milieu
#11
Miryam Martinetti, Fausta Beneventi, Cristina Capittini, Elena Locatelli, Margherita Simonetta, Chiara Cavagnoli, Irene De Maggio, Annalisa De Silvestri, Annamaria Pasi, Arsenio Spinillo
We enrolled 151 healthy mother/newborn couples and 26 with gestational diabetes mellitus (GDM). HLA-G and PAPP-A plasma levels were measured by ELISA at first and second trimesters, at delivery, and in cord blood. HLA-G 14 bp ins/del and PAPP-A A/C polymorphisms were genotyped. HLA-G del/del and PAPP-A C/C genotypes were more frequent among GDM mothers than controls. We observed a genetic epistasis between the two polymorphisms: the HLA-G del/del and PAPP-A C/C combination was carried by 8% of GDM mothers and 1...
2017: Disease Markers
https://www.readbyqxmd.com/read/28654546/sex-specific-effect-of-rnasel-rs486907-and-mir-146a-rs2910164-polymorphisms-interaction-as-a-susceptibility-factor-for-melanoma-skin-cancer
#12
Antonella Sangalli, Elisa Orlandi, Albino Poli, Andrea Maurichi, Mario Santinami, Morena Nicolis, Silvia Ferronato, Giovanni Malerba, Monica Rodolfo, Macarena Gomez Lira
The genetics of melanoma is complex and, in addition to environmental influences, numerous genes are involved or contribute toward melanoma predisposition. In this study, we evaluated the possible interaction between miR-146a and one of its putative targets ribonuclease L (RNASEL) in the risk of sporadic melanoma. Polymorphisms rs2910164 in miR-146a and rs486907 in the RNASEL gene have both independently been associated with the risk of different cancers, and an interaction between them has been observed in nonmelanoma skin cancer...
August 2017: Melanoma Research
https://www.readbyqxmd.com/read/28649719/regulation-of-growth-defense-balance-by-the-jasmonate-zim-domain-jaz-myc-transcriptional-module
#13
Ian T Major, Yuki Yoshida, Marcelo L Campos, George Kapali, Xiu-Fang Xin, Koichi Sugimoto, Dalton de Oliveira Ferreira, Sheng Yang He, Gregg A Howe
The plant hormone jasmonate (JA) promotes the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins to relieve repression on diverse transcription factors (TFs) that execute JA responses. However, little is known about how combinatorial complexity among JAZ-TF interactions maintains control over myriad aspects of growth, development, reproduction, and immunity. We used loss-of-function mutations to define epistatic interactions within the core JA signaling pathway and to investigate the contribution of MYC TFs to JA responses in Arabidopsis thaliana...
June 26, 2017: New Phytologist
https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#14
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28636612/laminin-211-inhibits-protein-kinase-a-in-schwann-cells-to-modulate-neuregulin-1-type-iii-driven-myelination
#15
Monica Ghidinelli, Yannick Poitelon, Yoon Kyoung Shin, Dominique Ameroso, Courtney Williamson, Cinzia Ferri, Marta Pellegatta, Kevin Espino, Amit Mogha, Kelly Monk, Paola Podini, Carla Taveggia, Klaus-Armin Nave, Lawrence Wrabetz, Hwan Tae Park, Maria Laura Feltri
Myelin is required for proper nervous system function. Schwann cells in developing nerves depend on extrinsic signals from the axon and from the extracellular matrix to first sort and ensheathe a single axon and then myelinate it. Neuregulin 1 type III (Nrg1III) and laminin α2β1γ1 (Lm211) are the key axonal and matrix signals, respectively, but how their signaling is integrated and if each molecule controls both axonal sorting and myelination is unclear. Here, we use a series of epistasis experiments to show that Lm211 modulates neuregulin signaling to ensure the correct timing and amount of myelination...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28634159/a-role-for-the-nonsense-mediated-mrna-decay-pathway-in-maintaining-genome-stability-in-caenorhabditis-elegans
#16
Víctor González-Huici, Bin Wang, Anton Gartner
Ionizing radiation (IR) is commonly used in cancer therapy and is a main source of DNA double-strand-breaks (DSBs), one of the most toxic forms of DNA damage. We have used Caenorhabditis elegans as an invertebrate model to identify novel factors required for repair of DNA damage inflicted by IR. We have performed an unbiased genetic screen, finding that smg-1 mutations confer strong hypersensitivity to IR. SMG-1 is a phosphoinositide-3 kinase (PI3K) kinase involved in mediating nonsense-mediated mRNA decay (NMD) of transcripts containing premature stop codons and related to the ATM and ATR kinases which are at the apex of DNA damage signalling pathways...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28619819/yorkie-and-hedgehog-independently-restrict-bmp-production-in-escort-cells-to-permit-germline-differentiation-in-the-drosophila-ovary
#17
Jianhua Huang, Amy Reilein, Daniel Kalderon
Multiple signaling pathways guide the behavior and differentiation of both germline stem cells (GSCs) and somatic stem cells (FSCs) in the Drosophila germarium, necessitating careful control of signal generation, range and responses. Signal integration involves Escort Cells (ECs), which promote differentiation of the GSC derivatives they envelop, provide niche signals for FSCs and derive directly from FSCs in adults. Hedgehog (Hh) signaling induces the Hippo pathway effector Yorkie (Yki) to promote proliferation and maintenance of FSCs but Hh also signals to ECs, which are quiescent...
June 15, 2017: Development
https://www.readbyqxmd.com/read/28618270/diversity-of-functionally-permissive-sequences-in-the-receptor-binding-site-of-influenza-hemagglutinin
#18
Nicholas C Wu, Jia Xie, Tianqing Zheng, Corwin M Nycholat, Geramie Grande, James C Paulson, Richard A Lerner, Ian A Wilson
Influenza A virus hemagglutinin (HA) initiates viral entry by engaging host receptor sialylated glycans via its receptor-binding site (RBS). The amino acid sequence of the RBS naturally varies across avian and human influenza virus subtypes and is also evolvable. However, functional sequence diversity in the RBS has not been fully explored. Here, we performed a large-scale mutational analysis of the RBS of A/WSN/33 (H1N1) and A/Hong Kong/1/1968 (H3N2) HAs. Many replication-competent mutants not yet observed in nature were identified, including some that could escape from an RBS-targeted broadly neutralizing antibody...
June 14, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28608555/epistasis-%C3%A3-environment-interactions-among-arabidopsis-thaliana-glucosinolate-genes-impact-complex-traits-and-fitness-in-the-field
#19
Rachel E Kerwin, Julie Feusier, Alise Muok, Catherine Lin, Brandon Larson, Daniel Copeland, Jason A Corwin, Matthew J Rubin, Marta Francisco, Baohua Li, Bindu Joseph, Cynthia Weinig, Daniel J Kliebenstein
Despite the growing number of studies showing that genotype × environment and epistatic interactions control fitness, the influences of epistasis × environment interactions on adaptive trait evolution remain largely uncharacterized. Across three field trials, we quantified aliphatic glucosinolate (GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation...
June 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28607034/tctex-1-controls-ciliary-resorption-by-regulating-branched-actin-polymerization-and-endocytosis
#20
Masaki Saito, Wataru Otsu, Kuo-Shun Hsu, Jen-Zen Chuang, Teruyuki Yanagisawa, Vincent Shieh, Taku Kaitsuka, Fan-Yan Wei, Kazuhito Tomizawa, Ching-Hwa Sung
The primary cilium is a plasma membrane-protruding sensory organelle that undergoes regulated assembly and resorption. While the assembly process has been studied extensively, the cellular machinery that governs ciliary resorption is less well understood. Previous studies showed that the ciliary pocket membrane is an actin-rich, endocytosis-active periciliary subdomain. Furthermore, Tctex-1, originally identified as a cytoplasmic dynein light chain, has a dynein-independent role in ciliary resorption upon phosphorylation at Thr94...
June 12, 2017: EMBO Reports
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