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Walid Korani, Ye Chu, C Corley Holbrook, Peggy Ozias-Akins
Post-harvest aflatoxin contamination is a challenging issue that affects peanut quality. Aflatoxin is produced by fungi belonging to the Aspergilli group, and is known as an acutely toxic, carcinogenic and immune-suppressing class of mycotoxins. Evidence for several host genetic factors that may impact aflatoxin contamination has been reported, e.g. , genes for lipoxygenase (PnLOX1 and PnLOX2/PnLOX3 that showed either positive or negative regulation with Aspergillus infection), ROS, and WRKY (highly associated with or differentially expressed upon infection of maize with A...
March 15, 2018: Genetics
Tim Beissinger, Jochen Kruppa, David Cavero, Ngoc-Thuy Ha, Malena Erbe, Henner Simianer
Important traits in agricultural, natural, and human populations are increasingly being shown to be under the control of many genes that individually contribute only a small proportion of genetic variation. However, the majority of modern tools in quantitative and population genetics, including genome wide association studies and selection mapping protocols, are designed to identify individual genes with large effects. We have developed an approach to identify traits that have been under selection and are controlled by large numbers of loci...
March 15, 2018: Genetics
Charlotte Wang, Jung-Ying Tzeng, Pei-Zhen Wu, Martin Preisig, Chuhsing Kate Hsiao
A properly designed distance-based measure can capture informative genetic differences among individuals with different phenotypes and be used to detect variants responsible for the phenotypes. To detect associated variants, various tests have been designed to contrast genetic dis/similarity scores of certain subject groups in different ways, among which the most widely used strategy is to quantify the difference between the within-group genetic dis/similarities (i.e., case-case and control-control similarities) and the between-group dis/similarities (i...
March 15, 2018: Genetics
Heather Dionne, Karen L Hibbard, Amanda Cavallaro, Jui-Chun Kao, Gerald M Rubin
The ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity...
March 13, 2018: Genetics
Yoann Anciaux, Luis-Miguel Chevin, Ophélie Ronce, Guillaume Martin
Evolutionary rescue describes a situation where adaptive evolution prevents the extinction of a population facing a stressing environment. Models of evolutionary rescue could in principle be used to predict the level of stress beyond which extinction becomes likely for species of conservation concern, or conversely the treatment levels most likely to limit the emergence of resistant pests or pathogens. Stress levels are known to affect both the rate of population decline (demographic effect) and the speed of adaptation (evolutionary effect), but the latter aspect has received less attention...
March 13, 2018: Genetics
Miriam Ratliff, Katherine L Hill-Harfe, Elizabeth J Gleason, Huiping Ling, Tim L Kroft, Steven W L'Hernault
Covalent attachment of ubiquitin to substrate proteins changes their function or marks them for proteolysis, and specificity of ubiquitin attachment is mediated by the numerous E3 ligases encoded by animals. Mind Bomb is an essential E3 ligase during Notch pathway signaling in insects and vertebrates. While C. elegans encodes a Mind Bomb homolog ( mib-1 ), it has never been recovered in the extensive Notch suppressor/enhancer screens that have identified numerous pathway components. Here, we show that C. elegans mib-1 null mutants have a spermatogenesis-defective phenotype that results in a heterogeneous mixture of arrested spermatocytes, defective spermatids and motility-impaired spermatozoa...
March 12, 2018: Genetics
John F Wolters, Guillaume Charron, Alec Gaspary, Christian R Landry, Anthony C Fiumera, Heather L Fiumera
Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mitonuclear interactions...
March 12, 2018: Genetics
Martin Johnsson, Rie Henriksen, Jesper Fogelholm, Andrey Höglund, Per Jensen, Dominic Wright
The identification of genes affecting sociality can give insights into the maintenance and development of sociality and personality. In this study, we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social reinstatement, a social and anxiety-related behavior. A total of 24 social reinstatement QTL were identified and overlaid with over 600 eQTL obtained from the same birds using hypothalamic tissue...
March 12, 2018: Genetics
Anne P Lutz, Sarah Schladebeck, Christian Renicke, Roberta Spadaccini, Hans-Ulrich Mösch, Christof Taxis
The ubiquitin-proteasome system (UPS) controls cellular functions by maintenance of a functional proteome and degradation of key regulatory proteins. Central to the UPS is the proteasome that adjusts the abundance of numerous proteins, thereby safeguarding their activity or initiating regulatory events. Here, we demonstrate that the essential Saccharomyces cerevisiae protein Yjr141w/Ipa1 (Important for cleavage and PolyAdenylation) belongs to the HECT_2 (homologous to E6-AP carboxyl terminus_2) family. We found that five cysteine residues within the HECT_2 family signature and the C-terminus are essential for Ipa1 activity...
March 8, 2018: Genetics
Hao Cheng, Kadir Kizilkaya, Jian Zeng, Dorian Garrick, Rohan Fernando
Bayesian multiple-regression methods incorporating different mixture priors for marker effects are widely used in genomic prediction. Improvement in prediction accuracies from using those methods, such as BayesB, BayesC and BayesCπ, have been shown in single-trait analyses with both simulated and real data. These methods have been extended to multi-trait analyses, but only under the restrictive assumption that a locus simultaneously affects all the traits or none of them. This assumption is not biologically meaningful, especially in multi-trait analyses involving many traits...
March 7, 2018: Genetics
Jeffrey B Endelman, Cari A Schmitz Carley, Paul C Bethke, Joseph J Coombs, Mark E Clough, Washington L da Silva, Walter S De Jong, David S Douches, Curtis M Frederick, Kathleen G Haynes, David G Holm, J Creighton Miller, Patricio R Muñoz, Felix M Navarro, Richard G Novy, Jiwan P Palta, Gregory A Porter, Kyle T Rak, Vidyasagar R Sathuvalli, Asunta L Thompson, G Craig Yencho
As one of the world's most important food crops, potato ( Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including the use of SNP arrays to determine allele dosage at thousands of markers. By combining genotype and pedigree information with phenotype data for economically important traits, the objectives of this study were to (1) partition the genetic variance into additive vs. non-additive components, and (2) determine the accuracy of genome-wide prediction. Between 2012 and 2017, a training population of 571 clones was evaluated for total yield, specific gravity, and chip fry color...
March 7, 2018: Genetics
Xulong Wang, Vivek M Philip, Guruprasad Ananda, Charles C White, Ankit Malhotra, Paul J Michalski, Krishna R Murthy Karuturi, Sumana R Chintalapudi, Casey Acklin, Michael Sasner, David A Bennett, Philip L De Jager, Gareth R Howell, Gregory W Carter
Recent technical and methodological advances have greatly enhanced genome-wide association studies (GWAS). The advent of low-cost whole-genome sequencing facilitates high-resolution variant identification, and the development of linear mixed models (LMM) allows improved identification of putatively causal variants. While essential for correcting false positive associations due to sample relatedness and population stratification, LMMs have commonly been restricted to quantitative variables. However, phenotypic traits in association studies are often categorical, coded as binary case-control or ordered variables describing disease stages...
March 5, 2018: Genetics
Nuno R Nené, Alistair S Dunham, Christopher J R Illingworth
A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference...
March 2, 2018: Genetics
Charlene H Emerson, Christopher R Lopez, Albert Ribes-Zamora, Erica J Polleys, Christopher L Williams, Lythou Yeo, Jacques E Zaneveld, Rui Chen, Alison A Bertuch
The Ku heterodimer acts centrally in non-homologous end-joining (NHEJ) of DNA double strand breaks (DSB). Saccharomyces cerevisiae Ku, like mammalian Ku, binds and recruits NHEJ factors to DSB ends. Consequently, NHEJ is virtually absent in yeast Ku null ( yku 70Δ or yku80Δ ) strains. Previously, we unexpectedly observed imprecise NHEJ proficiency in a yeast Ku mutant with impaired DNA end-binding (DEB). However, how DEB impairment supported imprecise NHEJ was unknown. Here, we found imprecise NHEJ proficiency to be a feature of a panel of DEB-impaired Ku mutants and that DEB impairment resulted in a deficiency in precise NHEJ...
March 2, 2018: Genetics
Catherine R Linnen, Claire T O'Quin, Taylor Shackleford, Connor R Sears, Carita Lindstedt
Pigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand the existing sample of color loci, we performed quantitative trait locus (QTL) mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly ( Neodiprion lecontei ): carotenoid-based yellow body color and melanin-based spotting pattern...
March 1, 2018: Genetics
Alexandre Blanckaert, Joachim Hermisson
By encompassing the whole continuum between allopatric and sympatric scenarios, parapatric speciation includes many potential scenarios for the evolution of new species. Here, we investigate how a genetic barrier to gene flow, that relies on a single postzygotic genetic incompatibility, may further evolve under ongoing migration. We consider a continent island model with three loci involved in pairwise Dobzhansky-Muller incompatibilities (DMIs). Using an analytic approach, we derive the conditions for invasion of a new mutation and its consequences for the strength and stability of the initial genetic barrier...
March 1, 2018: Genetics
David I Schlipalius, Andrew G Tuck, Rajeswaran Jagadeesan, Tam Nguyen, Ramandeep Kaur, Sabtharishi Subramanian, Roberto Barrero, Manoj Nayak, Paul R Ebert
Next-generation sequencing methods enable identification of the genetic basis of traits in species that have no prior genomic information available. The combination of next generation sequencing, variant analysis and linkage is a powerful way of identifying candidate genes for a trait of interest. Here we used a comparative transcriptomics (RNAseq) and genetic linkage analysis approach to identify the rph1 gene. rph1 variants are responsible for resistance to the fumigant phosphine (PH3 ) that is used to control insect pests of stored grain...
March 1, 2018: Genetics
Andrew Lloyd, Chris Morgan, Chris Franklin, Kirsten Bomblies
Meiotic recombination shuffles genetic information from sexual species into gametes to create novel combinations in offspring. Thus, recombination is an important factor in inheritance, adaptation and responses to selection. However, recombination is not a static parameter - meiotic recombination rate is sensitive to variation in the environment, especially temperature. That recombination rates change in response to both increases and decreases in temperature was reported in Drosophila a century ago, and since then in several other species...
March 1, 2018: Genetics
Carin A Loewen, Barry Ganetzky
Proper mitochondrial activity depends upon proteins encoded by genes in the nuclear and mitochondrial genomes that must interact functionally and physically in a precisely coordinated manner. Consequently, mito-nuclear allelic interactions are thought to be of crucial importance on an evolutionary scale, as well as for manifestation of essential biological phenotypes, including those directly relevant to human disease. Nonetheless, detailed molecular understanding of mito-nuclear interactions is still lacking, and definitive examples of such interactions in vivo are sparse...
March 1, 2018: Genetics
Timothy P Bilton, Matthew R Schofield, Michael A Black, David Chagné, Phillip L Wilcox, Ken G Dodds
Next generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high density genetic linkage maps, which facilitate the development of non-model species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth...
February 27, 2018: Genetics
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