April 2016 Table of Contents

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, Peter S. Solomon

  G3: Genes, Genomes, Genetics April 2016 6: 779-791; https://doi.org/10.1534/g3.115.025197
• 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, John K. McKay

  G3: Genes, Genomes, Genetics April 2016 6: 793-803; https://doi.org/10.1534/g3.115.021279
• 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, Karuna Sampath

  G3: Genes, Genomes, Genetics April 2016 6: 805-817; https://doi.org/10.1534/g3.115.026849
• Drak Is Required for Actomyosin Organization During Drosophila Cellularization

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

  G3: Genes, Genomes, Genetics April 2016 6: 819-828; https://doi.org/10.1534/g3.115.026401
• A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish

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

  G3: Genes, Genomes, Genetics April 2016 6: 829-834; https://doi.org/10.1534/g3.115.026344
• 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, Peter L. Morrell

  G3: Genes, Genomes, Genetics April 2016 6: 835-843; https://doi.org/10.1534/g3.116.026914
• Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes

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

  G3: Genes, Genomes, Genetics April 2016 6: 845-856; https://doi.org/10.1534/g3.115.025775
• Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

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

  G3: Genes, Genomes, Genetics April 2016 6: 857-863; https://doi.org/10.1534/g3.115.024596
• 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, Michael A. Gore

  G3: Genes, Genomes, Genetics April 2016 6: 865-879; https://doi.org/10.1534/g3.115.023515
• Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes

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

  G3: Genes, Genomes, Genetics April 2016 6: 881-892; https://doi.org/10.1534/g3.115.026757
• Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

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

  G3: Genes, Genomes, Genetics April 2016 6: 893-904; https://doi.org/10.1534/g3.115.023200
• 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, Christine Merlin

  G3: Genes, Genomes, Genetics April 2016 6: 905-915; https://doi.org/10.1534/g3.116.027029
• 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, Zhiying Zhang

  G3: Genes, Genomes, Genetics April 2016 6: 917-923; https://doi.org/10.1534/g3.116.027706
• 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, Fabio Veronesi

  G3: Genes, Genomes, Genetics April 2016 6: 925-938; https://doi.org/10.1534/g3.115.026021
• Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174

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

  G3: Genes, Genomes, Genetics April 2016 6: 939-955; https://doi.org/10.1534/g3.115.024075
• 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, Simon A. Schmidt

  G3: Genes, Genomes, Genetics April 2016 6: 957-971; https://doi.org/10.1534/g3.115.025692
• 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, Ting Wang

  G3: Genes, Genomes, Genetics April 2016 6: 973-986; https://doi.org/10.1534/g3.115.025437
• 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, Yi-Qing Yang

  G3: Genes, Genomes, Genetics April 2016 6: 987-992; https://doi.org/10.1534/g3.115.026518
• 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, Catherine A. Fox

  G3: Genes, Genomes, Genetics April 2016 6: 993-1012; https://doi.org/10.1534/g3.116.027904
• 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, Scott A. Jackson

  G3: Genes, Genomes, Genetics April 2016 6: 1013-1022; https://doi.org/10.1534/g3.115.024984
• Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data

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

  G3: Genes, Genomes, Genetics April 2016 6: 1023-1030; https://doi.org/10.1534/g3.115.026013
• 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, Rosa E. Navarro

  G3: Genes, Genomes, Genetics April 2016 6: 1031-1047; https://doi.org/10.1534/g3.115.026815
• 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, Michael D. Casler

  G3: Genes, Genomes, Genetics April 2016 6: 1049-1062; https://doi.org/10.1534/g3.115.024950
• 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, Joseph Schacherer

  G3: Genes, Genomes, Genetics April 2016 6: 1063-1071; https://doi.org/10.1534/g3.115.026682
• 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, Shengyi Liu

  G3: Genes, Genomes, Genetics April 2016 6: 1073-1081; https://doi.org/10.1534/g3.116.027110
• Neurofibromin Loss of Function Drives Excessive Grooming in Drosophila

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

  G3: Genes, Genomes, Genetics April 2016 6: 1083-1093; https://doi.org/10.1534/g3.115.026484
• 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, Yoshitaka Sakakura

  G3: Genes, Genomes, Genetics April 2016 6: 1095-1106; https://doi.org/10.1534/g3.115.022699