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G3: Genes—Genomes—Genetics

Kathrin Schuldt, Christa Ehmen, Juergen Sievertsen, Jennifer Evans, Juergen May, Daniel Ansong, Birgit Muntau, Gerd Ruge, Christian Timmann, Tsiri Agbenyega, Rolf D Horstmann, Thorsten Thye
In a recent report the cellular receptor CD55 was identified as a molecule essential for the invasion of human erythrocytes by Plasmodium falciparum, the causal agent of the most severe form of malaria. As this invasion process represents a critical step during the infection with the parasite, it was hypothesized that genetic variants in the gene could affect severe malaria susceptibility. We performed high-resolution variant discovery of rare and common genetic variants in the human CD55 gene. Association testing of these variants in over 1 700 severe malaria cases and unaffected control individuals from a malaria-endemic Ashanti Region in Ghana, West Africa, were performed on the basis of single variants, combined rare variant analyses, and reconstructed haplotypes...
January 18, 2017: G3: Genes—Genomes—Genetics
Dianne M Duncan, Paula Kiefel, Ian Duncan
The death of larval salivary gland cells during metamorphosis in Drosophila melanogaster has been a key system for studying steroid controlled programmed cell death. This death is induced by a pulse of the steroid hormone ecdysone that takes place at the end of the prepupal period. For many years, it has been thought that the ecdysone direct response gene Eip93F (E93) plays a critical role in initiating salivary gland cell death. This conclusion was based largely on the finding that the three "type" alleles of E93 cause a near-complete block in salivary gland cell death...
January 18, 2017: G3: Genes—Genomes—Genetics
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Y Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arum Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly...
January 13, 2017: G3: Genes—Genomes—Genetics
Tomoyuki Furuta, Motoyuki Ashikari, Kshirod K Jena, Kazuyuki Doi, Stefan Reuscher
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species Oryza longistaminata While most GBS pipelines aim to analyze mainly homozygous populations we attempted to genotype a highly heterozygous F2 population...
January 11, 2017: G3: Genes—Genomes—Genetics
Olivia L Sabik, Juan F Medrano, Charles R Farber
Parameters of bone geometry such as width, length, and cross-sectional area are major determinants of bone strength. Though these traits are highly heritable, few genes influencing bone geometry have been identified. Here, we dissect a major quantitative trait locus (QTL) influencing femur size. This QTL was originally identified in an F2 cross between the C57BL/6J-hg/hg (HG) and CAST/EiJ strains and was referred to as femur length in high growth mice 2 (Feml2). Feml2 was located on Chromosome (Chr.) 9 at ~20 cM...
January 11, 2017: G3: Genes—Genomes—Genetics
Riyan Cheng, R W Doerge, Justin Borevitz
Multiple-trait analysis typically employs models that associate a quantitative trait locus (QTL) with all of the traits. As a result, statistical power for QTL detection may not be optimal if the QTL contributes to the phenotypic variation only in a small proportion of the traits. Excluding QTL effects that contribute little to the test statistic can improve statistical power. In this article, we show that an optimal power can be achieved when the number of QTL effects is best estimated and that a stringent criterion for QTL effect selection may improve power when the number of QTL effects is small but can reduce power otherwise...
January 6, 2017: G3: Genes—Genomes—Genetics
Piero Lamelza, Michael Ailion
How species arise is a fundamental question in biology. Species can be defined as populations of interbreeding individuals that are reproductively isolated from other such populations. Therefore, understanding how reproductive barriers evolve between populations is essential for understanding the process of speciation. Hybrid incompatibility (for example, hybrid sterility or lethality) is a common and strong reproductive barrier in nature. Here we report a lethal incompatibility between two wild isolates of the nematode Caenorhabditis nouraguensis Hybrid inviability results from the incompatibility between a maternally inherited cytoplasmic factor from each strain and a recessive nuclear locus from the other...
January 6, 2017: G3: Genes—Genomes—Genetics
Dominik Müller, Pascal Schopp, Albrecht E Melchinger
Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents (Np), but little is known about how Np affects genomic selection (GS) in RS, especially the persistency of prediction accuracy and genetic gain. Synthetics were simulated by intermating Np= 2 to 32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA) and subjected to multiple cycles of GS...
January 6, 2017: G3: Genes—Genomes—Genetics
Kyle A McElroy, Youngsook Lucy Jung, Barry M Zee, Charlotte I Wang, Peter J Park, Mitzi I Kuroda
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells which are mutant for upset We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification...
January 6, 2017: G3: Genes—Genomes—Genetics
Michael Gardner, Robert Heinz, Jianying Wang, Melissa G Mitchum
The soybean cyst nematode (SCN) Heterodera glycines is a major threat to soybean production made more challenging by the current limitations of natural resistance for managing this pathogen. The use of resistant host cultivars is effective but over time results in the generation of virulent nematode populations able to robustly parasitize the resistant host. In order to understand how virulence develops in SCN we utilized a single backcrossed BC1F2 strategy to mate a highly virulent inbred population (TN20) capable of reproducing on all current sources of resistance with an avirulent one (PA3) unable to reproduce on any of the resistant soybean lines...
January 6, 2017: G3: Genes—Genomes—Genetics
Jesse Cahill, Manoj Rajaure, Chandler O'Leary, Jordan Sloan, Armando Marrufo, Ashley Holt, Aneesha Kulkarni, Oscar Hernandez, Ry Young
Coliphage lambda proteins Rz and Rz1 are the inner membrane and outer membrane subunits of the spanin complex, a heterotetramer that bridges the periplasm and is essential for the disruption of the outer membrane during phage lysis. Recent evidence suggests the spanin complex functions by fusing the inner and outer membrane. Here we use a genetics approach to investigate and characterize determinants of spanin function. Because Rz1 is entirely embedded in the +1 reading frame of Rz, the genes were dis-embedded before using random mutagenesis to construct a library of lysis-defective alleles for both genes...
December 30, 2016: G3: Genes—Genomes—Genetics
Andrew T Grainger, Michael B Jones, Mei-Hua Chen, Weibin Shi
Atherosclerosis in the carotid arteries is a major cause of ischemic stroke, which accounts for 85% of all stroke cases. Genetic factors contributing to carotid atherosclerosis remain poorly understood. The aim of this study was to identify chromosomal regions harboring genes contributing to carotid atherosclerosis in mice. 228 female F2 mice were generated from an intercross between BALB/cJ (BALB) and SM/J (SM) apolipoprotein E-deficient (Apoe(-/-)) mice and fed 12 weeks of western diet. Atherosclerotic lesion sizes in the left carotid artery were quantified...
December 30, 2016: G3: Genes—Genomes—Genetics
Gemma Palomar, Freed Ahmad, Anti Vasemägi, Chikako Matsuba, Alfredo G Nicieza, José Manuel Cano
By combining 7077 SNPs and 61 microsatellites, we present the first linkage map for some of the early diverged lineages of the common frog, Rana temporaria, and the densest linkage map to date for this species. We found high homology with the published linkage maps of the Eastern and Western lineages but with differences in the order of some markers. Homology was also strong with the genome of the Tibetan frog Nanorana parkeri and we found high synteny with the clawed frog Xenopus tropicalis We confirmed marked heterochiasmy between sexes and detected non-recombining regions in several groups of the male linkage map...
December 30, 2016: G3: Genes—Genomes—Genetics
Alexandre M Harris, Michael DeGiorgio
Gene diversity, or expected heterozygosity (H), is a common statistic for assessing genetic variation within populations. Estimation of this statistic decreases in accuracy and precision when individuals are related or inbred, due to increased dependence among allele copies in the sample. The original unbiased estimator of expected heterozygosity underestimates true population diversity in samples containing relatives, as it only accounts for sample size. More recently, a general unbiased estimator of expected heterozygosity was developed that explicitly accounted for related and inbredindividuals in samples...
December 30, 2016: G3: Genes—Genomes—Genetics
Dawn E Watkins-Chow, Gaurav K Varshney, Lisa J Garrett, Zelin Chen, Erin A Jimenez, Cecilia Rivas, Kevin S Bishop, Raman Sood, Ursula L Harper, William J Pavan, Shawn M Burgess
Cpf1 has emerged as an alternative to the Cas9 RNA-guided nuclease. Here we show that gene targeting rates in mice using Cpf1 can meet or even surpass Cas9 targeting rates (approaching 100% targeting) but require higher concentrations of mRNA and guide. We also demonstrate that co-injecting two guides with close targeting sites can result in synergistic genomic cutting, even if one of the guides has minimal cutting activity.
December 30, 2016: G3: Genes—Genomes—Genetics
Charles Addo-Quaye, Elizabeth Buescher, Norman Best, Vijay Chaikam, Ivan Baxter, Brian P Dilkes
In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of EMS mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequence in wild-type siblings and heterozygous in segregating families...
December 30, 2016: G3: Genes—Genomes—Genetics
Farzad Asadi, Bidhan Chakraborty, Jim Karagiannis
As part of an earlier study aimed at uncovering gene-products with roles in defending against latrunculin A (LatA) induced cytoskeletal perturbations, we identified three members of the oxidative stress response pathway: the Pap1p AP-1 like transcription factor, the Imp1p importin-alpha, and the Caf5p efflux pump. In this report, we characterize the pathway further and show that Pap1p translocates from the cytoplasm to the nucleus in an Imp1p-dependent manner upon LatA treatment. Moreover, preventing this translocation -- through the addition of a nuclear export signal - confers the same characteristic LatA-sensitive phenotype exhibited by pap1Δ cells...
December 30, 2016: G3: Genes—Genomes—Genetics
Bryan T Welly, Michael R Miller, Jeffrey L Stott, Myra T Blanchard, Alma D Islas-Trejo, Sean M O Rourke, Amy E Young, Juan F Medrano, Alison L Van Eenennaam
Epizootic bovine abortion (EBA), or "foothill abortion", is the leading cause of beef cattle abortion in California and has also been reported in Nevada and Oregon. In the 1970's, the soft-shelled tick Ornithodoros coriaceus, or "pajaroello tick", was confirmed as the disease-transmitting vector. In 2005, a novel Deltaproteobacterium was discovered as the etiologic agent of EBA (aoEBA), recently named Pajaroellobacter abortibovis This organism cannot be grown in culture using traditional microbiological techniques; it can only be grown in experimentally-infected severe combined immunodeficient (SCID) mice...
December 30, 2016: G3: Genes—Genomes—Genetics
Julien Chaillot, Michael A Cook, Jacques Corbeil, Adnane Sellam
One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi...
December 30, 2016: G3: Genes—Genomes—Genetics
Oscar P Hurtado-Gonzales, Giseli Valentini, Thiago A S Gilio, Alexandre M Martins, Qijian Song, Marcial A Pastor-Corrales
Bean rust, caused by Uromyces appendiculatus, is a devastating disease of common bean (Phaseolus vulgaris) in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome other rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker assisted selection produce false results. We describe here the fine mapping of the Ur-3 locus for the development of highly accurate markers linked to Ur-3 An F2 population from the cross Pinto 114 (susceptible) × Aurora (resistant with Ur-3) was evaluated for its reaction to four different races of U...
December 27, 2016: G3: Genes—Genomes—Genetics
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