New in G3: multiparental populations, worm fat levels, and mutant screen reports

Check out the June issue of G3!

Table of Contents

Editorial

Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits

Dirk-Jan de Koning, Lauren M. McIntyre

G3: Genes, Genomes, Genetics June 2017 7: 1617-1618;

DOI: https://doi.org/10.1534/g3.117.042846

Commentary

Epistasis: Searching for Interacting Genetic Variants Using Crosses

Ian M. Ehrenreich

G3: Genes, Genomes, Genetics June 2017 7: 1619-1622;

DOI: https://doi.org/10.1534/g3.117.042770

Multiparental Populations

Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders

Daniel Oreper, Yanwei Cai, Lisa M. Tarantino, Fernando Pardo-Manuel de Villena, William Valdar

G3: Genes, Genomes, Genetics June 2017 7: 1623-1630;

DOI: https://doi.org/10.1534/g3.117.041491

Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster

Michael A. Najarro, Jennifer L. Hackett, Stuart J. Macdonald

G3: Genes, Genomes, Genetics June 2017 7: 1631-1641;

DOI: https://doi.org/10.1534/g3.117.041418

The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster

Elizabeth G. King, Anthony D. Long

G3: Genes, Genomes, Genetics June 2017 7: 1643-1652;

DOI: https://doi.org/10.1534/g3.117.041426

Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice

Lisa E. Gralinski, Vineet D. Menachery, Andrew P. Morgan, Allison L. Totura, Anne Beall, Jacob Kocher, Jessica Plante, D. Corinne Harrison-Shostak, Alexandra Schäfer, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Ralph S. Baric

G3: Genes, Genomes, Genetics June 2017 7: 1653-1663;

DOI: https://doi.org/10.1534/g3.117.041434

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross

Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Renee C. Ireton, Michael Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Shannon McWeeney, Michael Gale

G3: Genes, Genomes, Genetics June 2017 7: 1665-1682;

DOI: https://doi.org/10.1534/g3.117.041624

Identification of Ganoderma Disease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population

Sébastien Tisné, Virginie Pomiès, Virginie Riou, Indra Syahputra, Benoît Cochard, Marie Denis

G3: Genes, Genomes, Genetics June 2017 7: 1683-1692;

DOI: https://doi.org/10.1534/g3.117.041764

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

Francisco A. Cubillos, Claire Brice, Jennifer Molinet, Sebastién Tisné, Valentina Abarca, Sebastián M. Tapia, Christian Oporto, Verónica García, Gianni Liti, Claudio Martínez

G3: Genes, Genomes, Genetics June 2017 7: 1693-1705;

DOI: https://doi.org/10.1534/g3.117.042127

Pedigree-Based Analysis in a Multiparental Population of Octoploid Strawberry Reveals QTL Alleles Conferring Resistance to Phytophthora cactorum

Jozer Mangandi, Sujeet Verma, Luis Osorio, Natalia A. Peres, Eric van de Weg, Vance M. Whitaker

G3: Genes, Genomes, Genetics June 2017 7: 1707-1719;

DOI: https://doi.org/10.1534/g3.117.042119

Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population

Chitra Raghavan, Ramil Mauleon, Vanica Lacorte, Monalisa Jubay, Hein Zaw, Justine Bonifacio, Rakesh Kumar Singh, B. Emma Huang, Hei Leung

G3: Genes, Genomes, Genetics June 2017 7: 1721-1730;

DOI: https://doi.org/10.1534/g3.117.042101

Genome Report

Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines

Inge Seim, Penny L. Jeffery, Patrick B. Thomas, Colleen C. Nelson, Lisa K. Chopin

G3: Genes, Genomes, Genetics June 2017 7: 1731-1741;

DOI: https://doi.org/10.1534/g3.117.039909

Mutant Screen Reports

The Genetic Requirements for Pentose Fermentation in Budding Yeast

Karin Mittelman, Naama Barkai

G3: Genes, Genomes, Genetics June 2017 7: 1743-1752;

DOI: https://doi.org/10.1534/g3.117.039610

Mapping the Synthetic Dosage Lethality Network of CDK1/CDC28

Christine Zimmermann, Ignacio Garcia, Manja Omerzu, Pierre Chymkowitch, Beibei Zhang, Jorrit M. Enserink

G3: Genes, Genomes, Genetics June 2017 7: 1753-1766;

DOI: https://doi.org/10.1534/g3.117.042317

Investigations

Physical Confirmation and Comparative Genomics of the Rat Mammary carcinoma susceptibility 3 Quantitative Trait Locus

Saasha Le, Zachary C. Martin, David J. Samuelson

G3: Genes, Genomes, Genetics June 2017 7: 1767-1773;

DOI: https://doi.org/10.1534/g3.117.039388

Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

Alija Bajro Mujic, Alan Kuo, Andrew Tritt, Anna Lipzen, Cindy Chen, Jenifer Johnson, Aditi Sharma, Kerrie Barry, Igor V. Grigoriev, Joseph W. Spatafora

G3: Genes, Genomes, Genetics June 2017 7: 1775-1789;

DOI: https://doi.org/10.1534/g3.117.039396

Swainsonine Biosynthesis Genes in Diverse Symbiotic and Pathogenic Fungi

Daniel Cook, Bruno G. G. Donzelli, Rebecca Creamer, Deana L. Baucom, Dale R. Gardner, Juan Pan, Neil Moore, Stuart B. Krasnoff, Jerzy W. Jaromczyk, Christopher L. Schardl

G3: Genes, Genomes, Genetics June 2017 7: 1791-1797;

DOI: https://doi.org/10.1534/g3.117.041384

NuA4 Lysine Acetyltransferase Complex Contributes to Phospholipid Homeostasis in Saccharomyces cerevisiae

Louis Dacquay, Annika Flint, James Butcher, Danny Salem, Michael Kennedy, Mads Kaern, Alain Stintzi, Kristin Baetz

G3: Genes, Genomes, Genetics June 2017 7: 1799-1809;

DOI: https://doi.org/10.1534/g3.117.041053

Quantitative Assessment of Fat Levels in Caenorhabditis elegans Using Dark Field Microscopy

Anthony D. Fouad, Shelley H. Pu, Shelly Teng, Julian R. Mark, Moyu Fu, Kevin Zhang, Jonathan Huang, David M. Raizen, Christopher Fang-Yen

G3: Genes, Genomes, Genetics June 2017 7: 1811-1818;

DOI: https://doi.org/10.1534/g3.117.040840

Genome-Wide Transcription and Functional Analyses Reveal Heterogeneous Molecular Mechanisms Driving Pyrethroids Resistance in the Major Malaria Vector Anopheles funestus Across Africa

Jacob M. Riveron, Sulaiman S. Ibrahim, Charles Mulamba, Rousseau Djouaka, Helen Irving, Murielle J. Wondji, Intan H. Ishak, Charles S. Wondji

G3: Genes, Genomes, Genetics June 2017 7: 1819-1832;

DOI: https://doi.org/10.1534/g3.117.040147

A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction

Osval A. Montesinos-López, Abelardo Montesinos-López, José Crossa, José Cricelio Montesinos-López, Francisco Javier Luna-Vázquez, Josafhat Salinas-Ruiz, José R. Herrera-Morales, Raymundo Buenrostro-Mariscal

G3: Genes, Genomes, Genetics June 2017 7: 1833-1853;

DOI: https://doi.org/10.1534/g3.117.041202

Genome-Enabled Prediction of Breeding Values for Feedlot Average Daily Weight Gain in Nelore Cattle

Adriana L. Somavilla, Luciana C. A. Regitano, Guilherme J. M. Rosa, Fabiana B. Mokry, Mauricio A. Mudadu, Polyana C. Tizioto, Priscila S. N. Oliveira, Marcela M. Souza, Luiz L. Coutinho, Danísio P. Munari

G3: Genes, Genomes, Genetics June 2017 7: 1855-1859;

DOI: https://doi.org/10.1534/g3.117.041442

SLC25 Family Member Genetic Interactions Identify a Role for HEM25 in Yeast Electron Transport Chain Stability

J. Noelia Dufay, J. Pedro Fernández-Murray, Christopher R. McMaster

G3: Genes, Genomes, Genetics June 2017 7: 1861-1873;

DOI: https://doi.org/10.1534/g3.117.041194

Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species

Qun-Jie Zhang, Li-Zhi Gao

G3: Genes, Genomes, Genetics June 2017 7: 1875-1885;

DOI: https://doi.org/10.1534/g3.116.037572

Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses

Laura R. Serbus, Brian Garcia Rodriguez, Zinat Sharmin, A. J. M. Zehadee Momtaz, Steen Christensen

G3: Genes, Genomes, Genetics June 2017 7: 1887-1898;

DOI: https://doi.org/10.1534/g3.117.042184

Adaptive Roles of SSY1 and SIR3 During Cycles of Growth and Starvation in Saccharomyces cerevisiae Populations Enriched for Quiescent or Nonquiescent Cells

Dominika M. Wloch-Salamon, Katarzyna Tomala, Dimitra Aggeli, Barbara Dunn

G3: Genes, Genomes, Genetics June 2017 7: 1899-1911;

DOI: https://doi.org/10.1534/g3.117.041749

Genetic Architecture of a Rice Nested Association Mapping Population

Christopher A. Fragoso, Maria Moreno, Zuoheng Wang, Christopher Heffelfinger, Lady J. Arbelaez, John A. Aguirre, Natalia Franco, Luz E. Romero, Karine Labadie, Hongyu Zhao, Stephen L. Dellaporta, Mathias Lorieux

G3: Genes, Genomes, Genetics June 2017 7: 1913-1926;

DOI: https://doi.org/10.1534/g3.117.041608

A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae

Sheina B. Sim, Scott M. Geib

G3: Genes, Genomes, Genetics June 2017 7: 1927-1940;

DOI: https://doi.org/10.1534/g3.117.040170

Evolutionary Conservation and Emerging Functional Diversity of the Cytosolic Hsp70:J Protein Chaperone Network of Arabidopsis thaliana

Amit K. Verma, Danish Diwan, Sandeep Raut, Neha Dobriyal, Rebecca E. Brown, Vinita Gowda, Justin K. Hines, Chandan Sahi

G3: Genes, Genomes, Genetics June 2017 7: 1941-1954;

DOI: https://doi.org/10.1534/g3.117.042291

RNAseq Analysis of the Drosophila Response to the Entomopathogenic Nematode Steinernema

Shruti Yadav, Sean Daugherty, Amol Carl Shetty, Ioannis Eleftherianos

G3: Genes, Genomes, Genetics June 2017 7: 1955-1967;

DOI: https://doi.org/10.1534/g3.117.041004

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci

Sarah Milbredt, Torsten Waldminghaus

G3: Genes, Genomes, Genetics June 2017 7: 1969-1977;

DOI: https://doi.org/10.1534/g3.117.040782

Genome-Wide Exome Analysis of Cmv5-Disparate Mouse Strains that Differ in Host Resistance to Murine Cytomegalovirus Infection

Alyssa Gillespie, Heather Lee, Catherine Robertson, Maya Cabot, Michael G. Brown

G3: Genes, Genomes, Genetics June 2017 7: 1979-1984;

DOI: https://doi.org/10.1534/g3.117.042531

HDAC Inhibitors Disrupt Programmed Resistance to Apoptosis During Drosophila Development

Yunsik Kang, Khailee Marischuk, Gina D. Castelvecchi, Arash Bashirullah

G3: Genes, Genomes, Genetics June 2017 7: 1985-1993;

DOI: https://doi.org/10.1534/g3.117.041541

Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction

Massaine Bandeira e Sousa, Jaime Cuevas, Evellyn Giselly de Oliveira Couto, Paulino Pérez-Rodríguez, Diego Jarquín, Roberto Fritsche-Neto, Juan Burgueño, Jose Crossa

G3: Genes, Genomes, Genetics June 2017 7: 1995-2014;

DOI: https://doi.org/10.1534/g3.117.042341