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https://www.readbyqxmd.com/read/28549456/association-mapping-of-loci-controlling-genetic-and-environmental-interaction-of-soybean-flowering-time-under-various-photo-thermal-conditions
#1
Tingting Mao, Jinyu Li, Zixiang Wen, Tingting Wu, Cunxiang Wu, Shi Sun, Bingjun Jiang, Wensheng Hou, Wenbin Li, Qijian Song, Dechun Wang, Tianfu Han
BACKGROUND: Soybean (Glycine max (L.) Merr.) is a short day plant. Its flowering and maturity time are controlled by genetic and environmental factors, as well the interaction between the two factors. Previous studies have shown that both genetic and environmental factors, mainly photoperiod and temperature, control flowering time of soybean. Additionally, these studies have reported gene × gene and gene × environment interactions on flowering time. However, the effects of quantitative trait loci (QTL) in response to photoperiod and temperature have not been well evaluated...
May 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28547213/evolutionary-dynamics-in-the-two-locus-two-allele-model-with-weak-selection
#2
Martin Pontz, Josef Hofbauer, Reinhard Bürger
Two-locus two-allele models are among the most studied models in population genetics. The reason is that they are the simplest models to explore the role of epistasis for a variety of important evolutionary problems, including the maintenance of polymorphism and the evolution of genetic incompatibilities. Many specific types of models have been explored. However, due to the mathematical complexity arising from the fact that epistasis generates linkage disequilibrium, few general insights have emerged. Here, we study a simpler problem by assuming that linkage disequilibrium can be ignored...
May 25, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28541468/a-fast-and-exhaustive-method-for-heterogeneity-and-epistasis-analysis-based-on-multi-objective-optimization
#3
Xiong Li
Motivation: The existing epistasis analysis approaches have been criticized mainly for their: 1) ignoring heterogeneity during epistasis analysis; 2) high computational costs; and 3) volatility of performances and results. Therefore, they will not perform well in general, leading to lack of reproducibility and low power in complex disease association studies. Method: In this work, a fast scheme is proposed to accelerate exhaustive searching based on multi-objective optimization named ESMO for concurrently analyzing heterogeneity and epistasis phenomena...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28535795/turtle-interacts-with-borderless-in-regulating-glial-extension-and-axon-ensheathment
#4
Yixu Chen, Scott Cameron, Wen-Tzu Chang, Yong Rao
Proper recognition between axons and glial processes is required for the establishment of axon ensheathment in the developing nervous system. Recent studies have begun to reveal molecular events underlying developmental control of axon-glia recognition. In our previous work, we showed that the transmembrane protein Borderless (Bdl) is specifically expressed in wrapping glia (WG), and is required for the extension of glial processes and the ensheathment of photoreceptor axons in the developing Drosophila visual system...
May 23, 2017: Molecular Brain
https://www.readbyqxmd.com/read/28535292/adaptive-radiation-of-p-fluorescens-sbw25-in-experimental-microcosms-provides-an-understanding-of-the-evolutionary-ecology-and-molecular-biology-of-a-l-interface-biofilm-formation
#5
Anna Koza, Anna Kusmierska, Kimberley McLaughlin, Olena Moshynets, Andrew J Spiers
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader. In these microcosms, the ecosystem engineering of the early wild-type colonists establish the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that de-regulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface...
May 23, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28533810/tc003132-is-essential-for-the-follicle-stem-cell-lineage-in-telotrophic-tribolium-oogenesis
#6
Matthias Teuscher, Nadi Ströhlein, Markus Birkenbach, Dorothea Schultheis, Michael Schoppmeier
BACKGROUND: Stem cells are undifferentiated cells with a potential for self-renewal, which are essential to support normal development and homeostasis. To gain insight into the molecular mechanisms underlying adult stem cell biology and organ evolution, we use the telotrophic ovary of the beetle Tribolium. To this end, we participated in a large-scale RNAi screen in the red flour beetle Tribolium, which identified functions in embryonic and postembryonic development for more than half of the Tribolium genes...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28531234/directed-evolution-to-improve-the-catalytic-efficiency-of-urate-oxidase-from-bacillus-subtilis
#7
Wenjie Li, Shouteng Xu, Biao Zhang, Yelin Zhu, Yan Hua, Xin Kong, Lianhong Sun, Jiong Hong
Urate oxidase is a key enzyme in purine metabolism and catalyzes the oxidation of uric acid to allantoin. It is used to treat hyperuricemia and gout, and also in a diagnostic kit. In this study, error-prone polymerase chain reaction and staggered extension process was used to generate a mutant urate oxidase with improved enzyme activity from Bacillus subtilis. After several rounds of mutagenesis and screening, two mutants 6E9 and 8E279 were obtained which exhibited 2.99 and 3.43 times higher catalytic efficiency, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28528644/bypassing-negative-epistasis-on-yield-in-tomato-imposed-by-a-domestication-gene
#8
Sebastian Soyk, Zachary H Lemmon, Matan Oved, Josef Fisher, Katie L Liberatore, Soon Ju Park, Anna Goren, Ke Jiang, Alexis Ramos, Esther van der Knaap, Joyce Van Eck, Dani Zamir, Yuval Eshed, Zachary B Lippman
Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing "jointless" fruit stems that reduced fruit dropping and facilitated mechanical harvesting...
May 15, 2017: Cell
https://www.readbyqxmd.com/read/28522540/orthogonal-estimates-of-variances-for-additive-dominance-and-epistatic-effects-in-populations
#9
Z G Vitezica, A Legarra, M A Toro, L Varona
Genomic prediction methods based on multiple markers have potential to include non-additive effects in prediction and analysis of complex traits. However, most developments assume Hardy-Weinberg equilibrium (HWE). Statistical approaches for genomic selection that account for dominance and epistasis in a general context, without assuming HWE (e.g. crosses or homozygous lines), are therefore needed. Our method expands the NOIA orthogonal approach, that builds incidence matrices based on genotypic (not allelic) frequencies, to include genome-wide epistasis for an arbitrary number of interacting loci in a genomic evaluation context...
May 18, 2017: Genetics
https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#10
Kelin Xu, Li Jin, Momiao Xiong
BACKGROUND: Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28518057/on-the-mechanistic-nature-of-epistasis-in-a-canonical-cis-regulatory-element
#11
Mato Lagator, Tiago Paixao, Nick Barton, Jonathan P Bollback, Călin C Guet
Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites...
May 18, 2017: ELife
https://www.readbyqxmd.com/read/28512086/two-loci-contribute-epistastically-to-heterospecific-pollen-rejection-a-postmating-isolating-barrier-between-species
#12
Jennafer A P Hamlin, Natasha A Sherman, Leonie C Moyle
Recognition and rejection of heterospecific male gametes occurs in a broad range of taxa, although the complexity of mechanisms underlying these components of postmating cryptic female choice is poorly understood. In plants, the arena for postmating interactions is the female reproductive tract (pistil), within which heterospecific pollen tube growth can be arrested via active molecular recognition and rejection. Unilateral incompatibility (UI) is one such postmating barrier in which pollen arrest occurs in only one direction of an interspecific cross...
May 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28510293/a-test-for-y-linked-additive-and-epistatic-effects-on-surviving-bacterial-infections-in-drosophila-melanogaster
#13
Ian C Kutch, Kenneth M Fedorka
Y and W chromosomes offer a theoretically powerful way for sexual dimorphism to evolve. Consistent with this possibility, Drosophila melanogaster Y-chromosomes can influence gene regulation throughout the genome; particularly immune-related genes. In order for Y-linked regulatory variation (YRV) to contribute to adaptive evolution it must be comprised of additive genetic variance, such that variable Ys induce consistent phenotypic effects within the local gene pool. We assessed the potential for Y-chromosomes to adaptively shape gram-negative and gram-positive bacterial defense by introgressing Ys across multiple genetic haplotypes from the same population...
May 16, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28510252/assessing-non-additive-effects-in-gblup-model
#14
I C Vieira, J P R Dos Santos, L P M Pires, B M Lima, F M A Gonçalves, M Balestre
Understanding non-additive effects in the expression of quantitative traits is very important in genotype selection, especially in species where the commercial products are clones or hybrids. The use of molecular markers has allowed the study of non-additive genetic effects on a genomic level, in addition to a better understanding of its importance in quantitative traits. Thus, the purpose of this study was to evaluate the behavior of the GBLUP model in different genetic models and relationship matrices and their influence on the estimates of genetic parameters...
May 10, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28508485/-conversion-of-epistatic-into-additive-genetic-variance-in-finite-populations-and-possible-impact-on-long-term-selection-response
#15
W G Hill
The role of epistasis in understanding the genetic architecture and variation of quantitative traits and its role, if any, in artificial selection and livestock improvement more generally has a long and sometimes controversial history. Its presence has been clearly demonstrated in, for example, laboratory experiments, but the amount of variation it contributes is likely to be small in outbred populations. In a finite population, although additive x additive epistatic variance is lost by genetic drift, it also contributes by conversion to additive variance through drift sampling and therefore has a potential indirect role in medium and long-term selection response, with superficial similarity to and hard to distinguish from mutation...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28507069/saers-is-responsive-to-cellular-respiratory-status-and-regulates-fermentative-biofilm-formation-in-staphylococcus-aureus
#16
Ameya A Mashruwala, Casey M Gries, Tyler D Scherr, Tammy Kielian, Jeffrey M Boyd
Biofilms are multicellular communities of microorganisms living as a quorum rather than as individual cells. The bacterial human pathogen Staphylococcus aureus uses oxygen as a terminal electron acceptor during respiration. Infected human tissues are hypoxic or anoxic. We recently reported that impaired respiration elicits a programmed cell lysis (PCL) phenomenon in S. aureus leading to the release of cellular polymers that are utilized to form biofilms. PCL is dependent upon the AtlA murein hydrolase and is regulated, in part, by the SrrAB two-component regulatory system (TCRS)...
May 15, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28506960/familial-analysis-of-epistatic-and-sex-dependent-association-of-genes-of-the-renin-angiotensin-aldosterone-system-and-blood-pressure
#17
Katrina J Scurrah, Angela Lamantia, Justine A Ellis, Stephen B Harrap
BACKGROUND: Renin-angiotensin-aldosterone system genes have been inconsistently associated with blood pressure, possibly because of unrecognized influences of sex-dependent genetic effects or gene-gene interactions (epistasis). METHODS AND RESULTS: We tested association of systolic blood pressure with single-nucleotide polymorphisms (SNPs) at renin (REN), angiotensinogen (AGT), angiotensin-converting enzyme (ACE), angiotensin II type 1 receptor (AGTR1), and aldosterone synthase (CYP11B2), including sex-SNP or SNP-SNP interactions...
June 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28506208/a-strategy-to-apply-quantitative-epistasis-analysis-on-developmental-traits
#18
Marta K Labocha, Wang Yuan, Boanerges Aleman-Meza, Weiwei Zhong
BACKGROUND: Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. METHODS: In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28505183/high-order-epistasis-shapes-evolutionary-trajectories
#19
Zachary R Sailer, Michael J Harms
High-order epistasis-where the effect of a mutation is determined by interactions with two or more other mutations-makes small, but detectable, contributions to genotype-fitness maps. While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories, the evolutionary consequences of high-order epistasis remain poorly understood. To determine the effect of high-order epistasis on evolutionary trajectories, we computationally removed high-order epistasis from experimental genotype-fitness maps containing all binary combinations of five mutations...
May 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28493873/modeling-of-a-negative-feedback-mechanism-explains-antagonistic-pleiotropy-in-reproduction-in-domesticated-caenorhabditis-elegans-strains
#20
Edward E Large, Raghavendra Padmanabhan, Kathie L Watkins, Richard F Campbell, Wen Xu, Patrick T McGrath
Most biological traits and common diseases have a strong but complex genetic basis, controlled by large numbers of genetic variants with small contributions to a trait or disease risk. The effect-size of most genetic variants is not absolute and is instead dependent upon multiple factors such as the age and genetic background of an organism. In order to understand the mechanistic basis of these changes, we characterized heritable trait differences between two domesticated strains of C. elegans. We previously identified a major effect locus, caused in part by a mutation in a component of the NURF chromatin remodeling complex, that regulates reproductive output in an age-dependent manner...
May 2017: PLoS Genetics
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