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G3: Genes—Genomes—Genetics

Aaron J Sams, Adam R Boyko
Inbreeding leaves distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (> 5 megabase) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long versus short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied...
November 14, 2018: G3: Genes—Genomes—Genetics
Jeffrey W Cary, Sarah Entwistle, Timothy Satterlee, Brian M Mack, Matthew Gilbert, Perng K Chang, Leslie Scharfenstein, Yanbin Yin, Ana M Calvo
In filamentous fungi, homeobox proteins are conserved transcriptional regulators described to control conidiogenesis and fruiting body formation. Eight homeobox ( hbx ) genes are found in the genome of the aflatoxin-producing ascomycete, Aspergillus flavus While loss-of-function of seven of the eight genes had little to no effect on fungal growth and development, disruption of hbx1 , resulted in aconidial colonies and lack of sclerotial production. Furthermore, the hbx1 mutant was unable to produce aflatoxins B₁ and B₂, cyclopiazonic acid and aflatrem...
November 13, 2018: G3: Genes—Genomes—Genetics
Moses Nyine, Shichen Wang, Kian Kiani, Katherine Jordan, Shuyu Liu, Patrick Byrne, Scott Haley, Stephen Baenziger, Shiaoman Chao, Robert Bowden, Eduard Akhunov
Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS)...
November 12, 2018: G3: Genes—Genomes—Genetics
Vinci Au, Erica Li-Leger, Greta Raymant, Stephane Flibotte, George Chen, Kiana Martin, Lisa Fernando, Claudia Doell, Federico L Rosell, Su Wang, Mark L Edgley, Ann E Rougvie, Harald Hutter, Donald G Moerman
The Caenorhabditis elegans Gene Knockout Consortium is tasked with obtaining null mutations in each of the more than 20,000 open reading frames (ORFs) of this organism. To date, approximately 15,000 ORFs have associated putative null alleles. As there has been substantial success in using CRISPR/Cas9 in C. elegans , this appears to be the most promising technique to complete the task. To enhance the efficiency of using CRISPR/Cas9 to generate gene deletions in C. elegans we provide a web-based interface to access our database of guide RNAs (http://genome...
November 12, 2018: G3: Genes—Genomes—Genetics
Radhika Agarwal, Beate Schwer, Stewart Shuman
Mud1 is an inessential 298-amino acid protein subunit of the Saccharomyces cerevisiae U1 snRNP. Mud1 consists of N-terminal and C-terminal RRM domains (RRM1 and RRM2) separated by a linker domain. Synthetic lethal interactions of mud1Δ with deletions of inessential spliceosome components Nam8, Mud2, and Msl1, or missense mutations in the branchpoint-binding protein Msl5 enabled us to dissect genetically the domain requirements for Mud1 function. We find that the biological activities of Mud1 can be complemented by co-expressing separately the RRM1 (aa 1-127) and linker-RRM2 (aa 128-298) modules...
November 9, 2018: G3: Genes—Genomes—Genetics
Nicolas Svetec, Perot Saelao, Julie M Cridland, Ary A Hoffmann, David J Begun
While significant effort has been devoted to investigating the potential influence of spatially varying selection on genomic variation, relatively little effort has been devoted to experimental analysis of putative variants or genes experiencing such selection. Previous population genetic work identified an amino acid polymorphism in the Mnn1 gene as one of the most strongly latitudinally differentiated SNPs in the genome of Drosophila melanogaster in the United States and Australia. Here we report the results of our transgenic analysis of this amino acid polymorphism...
November 7, 2018: G3: Genes—Genomes—Genetics
Yanhui Hu, Richelle Sopko, Verena Chung, Marianna Foos, Romain A Studer, Sean D Landry, Daniel Liu, Leonard Rabinow, Florian Gnad, Pedro Beltrao, Norbert Perrimon
Post-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing their stability, interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, most commonly serine, threonine and tyrosine in metazoans. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that any given phosphorylation site might be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites...
November 5, 2018: G3: Genes—Genomes—Genetics
Danae Vasiliadis, Marion Hewicker-Trautwein, Daniela Klotz, Michael Fehr, Stefka Ruseva, Jennifer Arndt, Julia Metzger, Ottmar Distl
In this study, we present a detailed phenotype description and genetic elucidation of the first case of X-linked hypohidrotic ectodermal dysplasia in the shorthaired standard Dachshund. This condition is characterized by partial congenital hypotrichosis, missing and malformed teeth and a lack of eccrine sweat glands. Clinical signs including dental radiographs and histopathological findings were consistent with ectodermal dysplasia. Pedigree analysis supported an X-recessive mode of inheritance. Whole-genome sequencing of one affected puppy and his dam identified a 1-basepair deletion within the ectodysplasin-A (EDA) gene (CM000039...
November 5, 2018: G3: Genes—Genomes—Genetics
Meng-Fu Maxwell Shih, Fred Pejman Davis, Gilbert Lee Henry, Josh Dubnau
The insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The Drosophila melanogaster MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α'/β' and α/β) and 7 cell subtypes (γd, γm, α'/β'ap, α'/β'm, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity...
November 5, 2018: G3: Genes—Genomes—Genetics
James K Bull, Jullien M Flynn, Frederic J J Chain, Melania E Cristescu
In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays...
November 2, 2018: G3: Genes—Genomes—Genetics
Robert W Corty, William Valdar
We present vqtl, an R package for mean-variance QTL mapping. This QTL mapping approach tests for genetic loci that influence the mean of the phenotype, termed mean QTL, the variance of the phenotype, termed variance QTL, or some combination of the two, termed mean-variance QTL. It is unique in its ability to correct for variance heterogeneity arising not only from the QTL itself but also from nuisance factors, such as sex, batch, or housing. This package provides functions to conduct genome scans, run permutations to assess the statistical significance, and make informative plots to communicate results...
November 2, 2018: G3: Genes—Genomes—Genetics
Robert W Corty, William Valdar
Standard QTL mapping procedures seek to identify genetic loci affecting the phenotypic mean while assuming that all individuals have the same residual variance. But when the residual variance differs systematically between groups, perhaps due to a genetic or environmental factor, such standard procedures can falter: in testing for QTL associations, they attribute too much weight to observations that are noisy and too little to those that are precise, resulting in reduced power and and increased susceptibility to false positives...
November 2, 2018: G3: Genes—Genomes—Genetics
Robert W Corty, Vivek Kumar, Lisa M Tarantino, Joseph S Takahashi, William Valdar
We illustrate, through two case studies, that "mean-variance QTL mapping"-QTL mapping that models effects on the mean and the variance simultaneously-can discover QTL that traditional interval mapping cannot. Mean-variance QTL mapping is based on the double generalized linear model, which extends the standard linear model used in interval mapping by incorporating not only a set of genetic and covariate effects for mean but also set of such effects for the residual variance. Its potential for use in QTL mapping has been described previously, but it remains underutilized, with certain key advantages undemonstrated until now...
November 2, 2018: G3: Genes—Genomes—Genetics
Julia Wittes, Trudi Schüpbach
The Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) and epidermal growth factor receptor (EGFR) signaling pathways are conserved regulators of tissue patterning, morphogenesis, and other cell biological processes. During Drosophila oogenesis, these pathways determine the fates of epithelial follicle cells (FCs). JAK/STAT and EGFR together specify a population of cells called the posterior follicle cells (PFCs), which signal to the oocyte to establish the embryonic axes. In this study, whole genome expression analysis was performed to identify genes activated by JAK/STAT and/or EGFR...
November 1, 2018: G3: Genes—Genomes—Genetics
Desiree DeMille, Jenny A Pape, Benjamin T Bikman, Majid Ghassemian, Julianne H Grose
PAS kinase 1 (Psk1) is a key regulator of respiration in Saccharomyces cerevisiae Herein the molecular mechanisms of this regulation are explored through the characterization of its substrate, Centromere binding factor 1 (Cbf1). CBF1 -deficient yeast displayed a significant decrease in cellular respiration, while PAS kinase-deficient yeast, or yeast harboring a Cbf1 phosphosite mutant (T211A) displayed a significant increase. Transmission electron micrographs showed an increased number of mitochondria in PAS kinase-deficient yeast consistent with the increase in respiration...
October 31, 2018: G3: Genes—Genomes—Genetics
Yun-Song Lai, Wei Zhang, Xiaohui Zhang, Di Shen, Haiping Wang, Yang Qiu, Jiangping Song, Xixiang Li
The cucumber ( Cucumis sativus ) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7%-52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes...
October 30, 2018: G3: Genes—Genomes—Genetics
Jessica P Lao, Katie M Ulrich, Jeffrey R Johnson, Billy W Newton, Ajay A Vashisht, James A Wohlschlegel, Nevan J Krogan, David P Toczyski
The highly conserved DNA damage response (DDR) pathway monitors the genomic integrity of the cell and protects against genotoxic stresses. The apical kinases, Mec1 and Tel1 (ATR and ATM in human, respectively), initiate the DNA damage signaling cascade through the effector kinases, Rad53 and Chk1, to regulate a variety of cellular processes including cell cycle progression, DNA damage repair, chromatin remodeling, and transcription. The DDR also regulates other cellular pathways, but direct substrates and mechanisms are still lacking...
October 30, 2018: G3: Genes—Genomes—Genetics
Renaud Rincent, Jean-Paul Charpentier, Patricia Faivre-Rampant, Etienne Paux, Jacques Le Gouis, Catherine Bastien, Vincent Segura
Genomic selection - the prediction of breeding values using DNA polymorphisms - is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in the different layers between the genome and the phenotype...
October 29, 2018: G3: Genes—Genomes—Genetics
Alfred Ozimati, Robert Kawuki, Williams Esuma, Ismail Siraj Kayondo, Marnin Wolfe, Roberto Lozano, Ismail Rabbi, Peter Kulakow, Jean-Luc Jannink
Cassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector ( Bemisia tabaci ) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined...
October 29, 2018: G3: Genes—Genomes—Genetics
Mana Ohkura, Peter J Cotty, Marc J Orbach
Aspergillus flavus , the primary causal agent for aflatoxin contamination on crops, consists of isolates with two distinct morphologies: isolates of the S morphotype produce numerous <u>s</u>mall sclerotia and lower numbers of conidia while isolates of the L morphotype produce fewer <u>l</u>arge sclerotia and abundant conidia. The morphotypes also differ in aflatoxin production with S isolates consistently producing high concentrations of aflatoxin, whereas L isolates range from atoxigenic to highly toxigenic...
October 25, 2018: G3: Genes—Genomes—Genetics
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