New in G3: heat shocked worms and CRISPRed chickens

Check out the April issue of G3!

Meeting Report

Evolution of Plant Phenotypes, from Genomes to Traits

Josep M. Casacuberta, Scott Jackson, Olivier Panaud, Michael Purugganan, and Jonathan Wendel

G3 April 2016 6:775-778; Early Online February 11, 2016

doi:10.1534/g3.115.025502

Full Text | Full Text (PDF)

Investigations

Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici

Megan C. McDonald, Lachlan McGinness, James K. Hane, Angela H. Williams, Andrew Milgate, and Peter S. Solomon

G3 April 2016 6:779-791; Early Online February 2, 2016

doi:10.1534/g3.115.025197

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing

Richard S. Fletcher, David Herrmann, Jack L. Mullen, Qinfei Li, Daniel R. Schrider, Nicholas Price, Junjiang Lin, Kelsi Grogan, Andrew Kern, and John K. McKay

G3 April 2016 6:793-803; Early Online January 22, 2016

doi:10.1534/g3.115.021279

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility

Pavle Vrljicak, Shijie Tao, Gaurav K. Varshney, Helen Ngoc Bao Quach, Adita Joshi, Matthew C. LaFave, Shawn M. Burgess, and Karuna Sampath

G3 April 2016 6:805-817; Early Online January 27, 2016

doi:10.1534/g3.115.026849

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Drak Is Required for Actomyosin Organization During Drosophila Cellularization

Ashish B. Chougule, Mary C. Hastert, and Jeffrey H. Thomas

G3 April 2016 6:819-828; Early Online January 27, 2016

doi:10.1534/g3.115.026401

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish

Fernando Fuentes, Eric Reynolds, Stephen W. Lewellis, Gayatri Venkiteswaran, and Holger Knaut

G3 April 2016 6:829-834; Early Online January 27, 2016

doi:10.1534/g3.115.026344

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

Justin E. Anderson, Thomas J. Y. Kono, Robert M. Stupar, Michael B. Kantar, and Peter L. Morrell

G3 April 2016 6:835-843; Early Online January 27, 2016

doi:10.1534/g3.116.026914

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes

Yong-Bi Fu, Gregory W. Peterson, and Yibo Dong

G3 April 2016 6:845-856; Early Online January 27, 2016

doi:10.1534/g3.115.025775

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

Nicholas A. Tinker, Wubishet A. Bekele, and Jiro Hattori

G3 April 2016 6:857-863; Early Online January 27, 2016

doi:10.1534/g3.115.024596

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton

Duke Pauli, Pedro Andrade-Sanchez, A. Elizabete Carmo-Silva, Elodie Gazave, Andrew N. French, John Heun, Douglas J. Hunsaker, Alexander E. Lipka, Tim L. Setter, Robert J. Strand, Kelly R. Thorp, Sam Wang, Jeffrey W. White, and Michael A. Gore

G3 April 2016 6:865-879; Early Online January 27, 2016

doi:10.1534/g3.115.023515

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes

Anna Sliva, Zheng Kuang, Pamela B. Meluh, and Jef D. Boeke

G3 April 2016 6:881-892; Early Online February 2, 2016

doi:10.1534/g3.115.026757

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

Hyunjin Shim, Stefan Laurent, Sebastian Matuszewski, Matthieu Foll, and Jeffrey D. Jensen

G3 April 2016 6:893-904; Early Online February 11, 2016

doi:10.1534/g3.115.023200

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis

Matthew J. Markert, Ying Zhang, Metewo S. Enuameh, Steven M. Reppert, Scot A. Wolfe, and Christine Merlin

G3 April 2016 6:905-915; Early Online February 2, 2016

doi:10.1534/g3.116.027029

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Efficient Genome Editing in Chicken DF-1 Cells Using the CRISPR/Cas9 System

Yichun Bai, Linjie He, Pengcheng Li, Kun Xu, Simin Shao, Chonghua Ren, Zhongtian Liu, Zehui Wei, and Zhiying Zhang

G3 April 2016 6:917-923; Early Online February 11, 2016

doi:10.1534/g3.116.027706

Abstract | Full Text | Full Text (PDF)

Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation

Daniele Rosellini, Nicoletta Ferradini, Stefano Allegrucci, Stefano Capomaccio, Elisa Debora Zago, Paola Leonetti, Bachir Balech, Riccardo Aversano, Domenico Carputo, Lara Reale, and Fabio Veronesi

G3 April 2016 6:925-938; Early Online February 8, 2016

doi:10.1534/g3.115.026021

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genetically Determined Variation in Lysis Time Variance in the Bacteriophage X174

Christopher W. Baker, Craig R. Miller, Tanayott Thaweethai, Jeffrey Yuan, Meghan Hollibaugh Baker, Paul Joyce, and Daniel M. Weinreich

G3 April 2016 6:939-955; Early Online February 26, 2016

doi:10.1534/g3.115.024075

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae

Anthony R. Borneman, Angus H. Forgan, Radka Kolouchova, James A. Fraser, and Simon A. Schmidt

G3 April 2016 6:957-971; Early Online February 11, 2016

doi:10.1534/g3.115.025692

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome

Junchen Gu, Michael Stevens, Xiaoyun Xing, Daofeng Li, Bo Zhang, Jacqueline E. Payton, Eugene M. Oltz, James N. Jarvis, Kaiyu Jiang, Theodore Cicero, Joseph F. Costello, and Ting Wang

G3 April 2016 6:973-986; Early Online February 17, 2016

doi:10.1534/g3.115.025437

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A HAND2 Loss-of-Function Mutation Causes Familial Ventricular Septal Defect and Pulmonary Stenosis

Yu-Min Sun, Jun Wang, Xing-Biao Qiu, Fang Yuan, Ruo-Gu Li, Ying-Jia Xu, Xin-Kai Qu, Hong-Yu Shi, Xu-Min Hou, Ri-Tai Huang, Song Xue, and Yi-Qing Yang

G3 April 2016 6:987-992; Early Online February 10, 2016

doi:10.1534/g3.115.026518

Abstract | Full Text | Full Text (PDF)

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

Timothy Hoggard, Ivan Liachko, Cassaundra Burt, Troy Meikle, Katherine Jiang, Gheorghe Craciun, Maitreya J. Dunham, and Catherine A. Fox

G3 April 2016 6:993-1012; Early Online February 10, 2016

doi:10.1534/g3.116.027904

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives

Aiko Iwata-Otsubo, Brittany Radke, Seth Findley, Brian Abernathy, C. Eduardo Vallejos, and Scott A. Jackson

G3 April 2016 6:1013-1022; Early Online February 10, 2016

doi:10.1534/g3.115.024984

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data

Jaleal S. Sanjak, Anthony D. Long, and Kevin R. Thornton

G3 April 2016 6:1023-1030; Early Online February 10, 2016

doi:10.1534/g3.115.026013

Abstract | Full Text | Full Text (PDF) | Supplemental Material

The Stress Granule RNA-Binding Protein TIAR-1 Protects Female Germ Cells from Heat Shock in Caenorhabditis elegans

Gabriela Huelgas-Morales, Carlos Giovanni Silva-García, Laura S. Salinas, David Greenstein, and Rosa E. Navarro

G3 April 2016 6:1031-1047; Early Online February 10, 2016

doi:10.1534/g3.115.026815

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium

Guillaume P. Ramstein, Joseph Evans, Shawn M. Kaeppler, Robert B. Mitchell, Kenneth P. Vogel, C. Robin Buell, and Michael D. Casler

G3 April 2016 6:1049-1062; Early Online February 11, 2016

doi:10.1534/g3.115.024950

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species

Paul P. Jung, Anastasie Sigwalt, Shinsuke Ohnuki, Jacky de Montigny, Yoshikazu Ohya, and Joseph Schacherer

G3 April 2016 6:1063-1071; Early Online February 17, 2016

doi:10.1534/g3.115.026682

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Embryonal Control of Yellow Seed Coat Locus ECY1 Is Related to Alanine and Phenylalanine Metabolism in the Seed Embryo of Brassica napus

Fulin Wang, Jiewang He, Jianghua Shi, Tao Zheng, Fei Xu, Guanting Wu, Renhu Liu, and Shengyi Liu

G3 April 2016 6:1073-1081; Early Online February 19, 2016

doi:10.1534/g3.116.027110

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Neurofibromin Loss of Function Drives Excessive Grooming in Drosophila

Lanikea B. King, Marta Koch, Keith R. Murphy, Yoheilly Velazquez, William W. Ja, and Seth M. Tomchik

G3 April 2016 6:1083-1093; Early Online February 19, 2016

doi:10.1534/g3.115.026484

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Genetic Map for the Only Self-Fertilizing Vertebrate

Akira Kanamori, Yosuke Sugita, Yasufumi Yuasa, Takamasa Suzuki, Kouichi Kawamura, Yoshinobu Uno, Katsuyasu Kamimura, Yoichi Matsuda, Catherine A. Wilson, Angel Amores, John H. Postlethwait, Koushirou Suga, and Yoshitaka Sakakura

G3 April 2016 6:1095-1106; Early Online February 10, 2016

doi:10.1534/g3.115.022699

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Mutant Screen Reports

A Simultaneous Genetic Screen for Zygotic and Sterile Mutants in a Hermaphroditic Vertebrate (Kryptolebias marmoratus)

Sofia Sucar, Ginger L. Moore, Melissa E. Ard, and Brian C. Ring

G3 April 2016 6:1107-1119; Early Online January 22, 2016

doi:10.1534/g3.115.022475

Abstract | Full Text | Full Text (PDF) | Supplemental Material

MEC-10 and MEC-19 Reduce the Neurotoxicity of the MEC-4(d) DEG/ENaC Channel in Caenorhabditis elegans

Yushu Chen, Shashank Bharill, Robert O’Hagan, Ehud Y. Isacoff, and Martin Chalfie

G3 April 2016 6:1121-1130; doi:10.1534/g3.115.023507

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Microarray Analysis of Gene Expression in Saccharomyces cerevisiae kap108 Mutants upon Addition of Oxidative Stress

Kenneth D. Belanger, Nathaniel Larson, Jonathan Kahn, Dmitry Tkachev, and Ahmet Ay

G3 April 2016 6:1131-1139; Early Online February 17, 2016

doi:10.1534/g3.116.027011

Abstract | Full Text | Full Text (PDF) | Supplemental Material