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G3: Genes—Genomes—Genetics

Sangmi Oh, Ichiro Kawasaki, Jae-Hyung Park, Yhong-Hee Shim
Cell division cycle 25 (cdc25) is an evolutionarily conserved phosphatase that promotes cell cycle progression. Among the four cdc25 orthologs in Caenorhabditis elegans, we found that cdc-25.4 mutant males failed to produce outcrossed progeny. This was not caused by defects in sperm development, but by defects in male mating behavior. The cdc-25.4 mutant males showed various defects during male mating, including contact response, backing, turning, and vulva location. Aberrant turning behavior was the most prominent defect in the cdc-25...
October 21, 2016: G3: Genes—Genomes—Genetics
Alexandra Asaro, Gregory Ziegler, Cathrine Ziyomo, Owen Hoekenga, Brian Dilkes, Ivan Baxter
Plants obtain soil-resident elements that support growth and metabolism from the water- flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown...
October 21, 2016: G3: Genes—Genomes—Genetics
Yanzhu Lin, Zhen-Xia Chen, Brian Oliver, Susan T Harbison
Differences in phenotype among genetically identical individuals exposed to the same environmental condition are often noted in genetic studies. Despite this commonplace observation, little is known about the causes of this variability, which has been termed microenvironmental plasticity. One possibility is that stochastic or technical sources of variance produce these differences. A second possibility is that this variation has a genetic component. We have explored gene expression robustness in the transcriptomes of 730 individual Drosophila melanogaster of 16 fixed genotypes, 9 of which are infected with Wolbachia Three replicates of flies were grown controlling for food, day/night cycles, humidity, temperature, sex, mating status, social exposure, and circadian timing of RNA extraction...
October 21, 2016: G3: Genes—Genomes—Genetics
Masayuki Onishi, John R Pringle
The unicellular green alga Chlamydomonas reinhardtii is a model organism that provides an opportunity to understand the evolution and functional biology of the lineage that includes the land plants, as well as aspects of the fundamental core biology conserved throughout the eukaryotic phylogeny. Although many tools are available to facilitate genetic, molecular biological, biochemical, and cell biological studies in Chlamydomonas, expression of unselected transgenes of interest (GOIs) has been challenging. In most methods used previously, the GOI and a selectable marker are expressed from two separate mRNAs, so that their concomitant expression is not guaranteed...
October 21, 2016: G3: Genes—Genomes—Genetics
Cristina M Crava, Sukania Ramasamy, Lino Ometto, Gianfranco Anfora, Omar Rota-Stabelli
Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D...
October 19, 2016: G3: Genes—Genomes—Genetics
Yiqin Jiang, Elise Pitmon, Jack Berry, Fred W Wolf, Zach McKenzie, Tim J Lebestky
Sleep is an essential behavioral state of rest that is regulated by homeostatic drives to ensure a balance of sleep and activity, as well as independent arousal mechanisms in the central brain. Dopamine has been identified as a critical regulator of both sleep behavior and arousal. Here we present results of a genetic screen that selectively restored the Dopamine Receptor (DopR/DopR1/dumb) to specific neuroanatomical regions of the adult Drosophila brain to assess requirements for DopR in sleep behavior. We have identified subsets of the mushroom body that utilize DopR in daytime sleep regulation...
October 19, 2016: G3: Genes—Genomes—Genetics
Rebeccah J Katzenberger, Barry Ganetzky, David A Wassarman
Outcomes of traumatic brain injury (TBI) vary because of differences in primary and secondary injuries. Primary injuries occur at the time of a traumatic event, whereas secondary injuries occur later as a result of cellular and molecular events activated in the brain and other tissues by primary injuries. We used a Drosophila melanogaster TBI model to investigate secondary injuries that cause acute mortality. By analyzing percent mortality within 24 hours of primary injuries, we previously found that age at the time of primary injuries and diet afterward affect the severity of secondary injuries...
October 17, 2016: G3: Genes—Genomes—Genetics
Jiafa Chen, Rosemary Shrestha, Junqiang Ding, Hongjian Zheng, Chunhua Mu, Jianyu Wu, George Mahuku
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance...
October 14, 2016: G3: Genes—Genomes—Genetics
Theresa L B Edelman, Katherine A McCulloch, Angela Barr, Christian Frøkjær-Jensen, Erik M Jorgensen, Ann E Rougvie
The Caenorhabditis elegans heterochronic gene pathway regulates the relative timing of events during post-embryonic development. lin-42, the worm homolog of the circadian clock gene period, is a critical element of this pathway. lin-42 function has been defined by a set of hypomorphic alleles that cause precocious phenotypes, in which later developmental events, such as the terminal differentiation of hypodermal cells, occur too early. A subset of alleles also reveals a significant role for lin-42 in molting; larval stages are lengthened and ecdysis often fails in these mutant animals...
October 14, 2016: G3: Genes—Genomes—Genetics
Ferdouse Begum, Reshmi Chowdhury, Vivian Cheung, Stephanie Sherman, Eleanor Feingold
Meiotic recombination is an essential step in gametogenesis and is one that also generates genetic diversity. Genome-wide association and molecular studies have identified genes that influence of human meiotic recombination. RNF212 is associated with total or average number of recombination events, and PRDM9 is associated with the locations of hotspots, or sequences where crossing over appears to cluster. In addition, a common inversion on chromosome 17 is strongly associated with recombination. Other genes have been identified by GWAS, but those results have not been replicated...
October 12, 2016: G3: Genes—Genomes—Genetics
Toby Fountain, Mark Ravinet, Richard Naylor, Klaus Reinhardt, Roger K Butlin
The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread...
October 12, 2016: G3: Genes—Genomes—Genetics
Tanaka Kenta, Jessica E M Edwards, Roger K Butlin, Terry Burke, W Paul Quick, Peter Urwin, Matthew P Davey
Whilst genotype-environment interaction is increasingly receiving attention by ecologists and evolutionary biologists, such studies need genetically homogeneous replicates-a challenging hurdle in outcrossing plants. This could potentially be overcome by using tissue culture techniques. However, plants regenerated from tissue culture may show aberrant phenotypes and "somaclonal" variation. Here we examined the somaclonal variation due to tissue culturing using the response to cold treatment of the photosynthetic efficiency (chlorophyll fluorescence measurements for Fv/Fm, Fv'/Fm' and ΦPSII, representing maximum efficiency of photosynthesis for dark- and light-adapted leaves, and the actual electron transport operating efficiency, respectively, which are reliable indicators of photoinhibition and damage to the photosynthetic electron transport system)...
October 11, 2016: G3: Genes—Genomes—Genetics
Jose Maria Carvajal-Gonzalez, Sonia Mulero-Navarro, Michael Smith, Marek Mlodzik
Most mutant alleles in the Fz-PCP pathway genes were discovered in classic Drosophila screens looking for recessive loss-of-function mutations. Nonetheless, although Fz-PCP signaling is sensitive to increased doses of PCP gene products, not many screens have been performed in the wing under genetically engineered Fz over-expression conditions, mostly because the Fz phenotypes were strong and/or not easy to score and quantify. Here we present a screen based on an unexpected mild Frizzled gain-of-function phenotype...
October 11, 2016: G3: Genes—Genomes—Genetics
Gregory P Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L Fridley, Gottfried E Konecny, Ellen L Goode, Casey S Greene, Jennifer A Doherty
Four gene expression subtypes of high-grade serous ovarian cancer (HGSC) have been previously described. In these early studies, a fraction of samples that did not fit well into the four subtype classifications were excluded. Therefore, we sought to systematically determine the concordance of transcriptomic HGSC subtypes across populations without removing any samples. We created a bioinformatics pipeline to independently cluster the five largest mRNA expression datasets using k-means and non-negative matrix factorization (NMF)...
October 11, 2016: G3: Genes—Genomes—Genetics
Ratan Chopra, Gloria Burow, Charles E Simpson, Jennifer Chagoya, Joann Mudge, Mark D Burow
To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of twenty-two Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues and de novo assembly wasperformed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 bi-allelic SNPs. Among ten naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs...
October 11, 2016: G3: Genes—Genomes—Genetics
Wanlong Li, Ghana S Challa, Huilan Zhu, Wenjie Wei
Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species including diploid wheat and rye, by comparative mapping and comparative analysis of the draft genome and chromosome survey sequences of the Triticeae species...
October 11, 2016: G3: Genes—Genomes—Genetics
Yongxia Cui, Beng Kah Song, Lin-Feng Li, Ya-Ling Li, Zhongyun Huang, Ana L Caicedo, Yulin Jia, Kenneth M Olsen
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation...
October 11, 2016: G3: Genes—Genomes—Genetics
Yasir Ahmed-Braimah
Understanding the genetic basis of speciation is a central problem in evolutionary biology. Studies of reproductive isolation have provided several insights into the genetic causes of speciation, especially in taxa that lend themselves to detailed genetic scrutiny. Reproductive barriers have usually been divided into those that occur before zygote formation (prezygotic) and after (postzygotic), with the latter receiving a great deal of attention over several decades. Reproductive barriers that occur after mating but before zygote formation (postmating prezygotic) are especially understudied at the genetic level...
October 11, 2016: G3: Genes—Genomes—Genetics
Andrew P Morgan, John P Didion, Anthony G Doran, James M Holt, Leonard McMillan, Thomas M Keane, Fernando Pardo-Manuel de Villena
Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14X and 18X coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains...
October 7, 2016: G3: Genes—Genomes—Genetics
Dianne Velasco, Josh Hough, Mallikarjuna Aradhya, Jeffrey Ross-Ibarra
The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originate on opposite sides of Asia and were independently domesticated approximately 5000 years ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has ~7X the genetic diversity of peach, and high genome-wide FST values support their status as separate species...
October 5, 2016: G3: Genes—Genomes—Genetics
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