New in G3: Genome Reports galore, genomic prediction in cauliflower and trout, and use of a sibling subtraction method

Check out the February issue of G3!

Table of Contents

Genome Reports

Whole Genome Sequencing of Hulunbuir Short-Tailed Sheep for Identifying Candidate Genes Related to the Short-Tail Phenotype

Dafu Zhi, Lai Da, Moning Liu, Chen Cheng, Yukun Zhang, Xin Wang, Xiunan Li, Zhipeng Tian, Yanyan Yang, Tingyi He, Xin Long, Wei Wei, Guifang Cao

G3: Genes, Genomes, Genetics February 2018 8: 377-383;
DOI: https://doi.org/10.1534/g3.117.300307

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides

Genevieve M. Hoopes, John P. Hamilton, Jeongwoon Kim, Dongyan Zhao, Krystle Wiegert-Rininger, Emily Crisovan, C. Robin Buell

G3: Genes, Genomes, Genetics February 2018 8: 385-391;
DOI: https://doi.org/10.1534/g3.117.300331

Reference Quality Genome Assemblies of Three Parastagonospora nodorum Isolates Differing in Virulence on Wheat

Jonathan K. Richards, Nathan A. Wyatt, Zhaohui Liu, Justin D. Faris, Timothy L. Friesen

G3: Genes, Genomes, Genetics February 2018 8: 393-399;
DOI: https://doi.org/10.1534/g3.117.300462

Mutant Screen Report

Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice

Krista A. Geister, Andrew E. Timms, David R. Beier

G3: Genes, Genomes, Genetics February 2018 8: 401-409;
DOI: https://doi.org/10.1534/g3.117.300292

Investigations

Dissecting the Genetic Architecture of Shoot Growth in Carrot (Daucus carota L.) Using a Diallel Mating Design

Sarah D. Turner, Paul L. Maurizio, William Valdar, Brian S. Yandell, Philipp W. Simon

G3: Genes, Genomes, Genetics February 2018 8: 411-426;
DOI: https://doi.org/10.1534/g3.117.300235

Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice

Paul L. Maurizio, Martin T. Ferris, Gregory R. Keele, Darla R. Miller, Ginger D. Shaw, Alan C. Whitmore, Ande West, Clayton R. Morrison, Kelsey E. Noll, Kenneth S. Plante, Adam S. Cockrell, David W. Threadgill, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, William Valdar

G3: Genes, Genomes, Genetics February 2018 8: 427-445;
DOI: https://doi.org/10.1534/g3.117.300438

Direct Testing for Allele-Specific Expression Differences Between Conditions

Luis León-Novelo, Alison R. Gerken, Rita M. Graze, Lauren M. McIntyre, Fabio Marroni

G3: Genes, Genomes, Genetics February 2018 8: 447-460;
DOI: https://doi.org/10.1534/g3.117.300139

Selection Mapping Identifies Loci Underpinning Autumn Dormancy in Alfalfa (Medicago sativa)

Gitanshu Munjal, Jingjie Hao, Larry R. Teuber, E. Charles Brummer

G3: Genes, Genomes, Genetics February 2018 8: 461-468;
DOI: https://doi.org/10.1534/g3.117.300099

Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data

Qing-bo Zhao, Rong-rong Liao, Hao Sun, Zhe Zhang, Qi-shan Wang, Chang-suo Yang, Xiang-zhe Zhang, Yu-chun Pan

G3: Genes, Genomes, Genetics February 2018 8: 469-476;
DOI: https://doi.org/10.1534/g3.117.300382

Dependency of Heterochromatin Domains on Replication Factors

Leonie Johanna Jahn, Bethany Mason, Peter Brøgger, Tea Toteva, Dennis Kim Nielsen, Genevieve Thon

G3: Genes, Genomes, Genetics February 2018 8: 477-489;
DOI: https://doi.org/10.1534/g3.117.300341

PRC2 Is Dispensable in Vivo for ß-Catenin-Mediated Repression of Chondrogenesis in the Mouse Embryonic Cranial Mesenchyme

James Ferguson, Mahima Devarajan, Gregg DiNuoscio, Alina Saiakhova, Chia-Feng Liu, Veronique Lefebvre, Peter C. Scacheri, Radhika P. Atit

G3: Genes, Genomes, Genetics February 2018 8: 491-503;
DOI: https://doi.org/10.1534/g3.117.300311

Pas de deux: An Intricate Dance of Anther Smut and Its Host

Su San Toh, Zehua Chen, Eric C. Rouchka, David J. Schultz, Christina A. Cuomo, Michael H. Perlin

G3: Genes, Genomes, Genetics February 2018 8: 505-518;
DOI: https://doi.org/10.1534/g3.117.300318

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population

Alencar Xavier, Diego Jarquin, Reka Howard, Vishnu Ramasubramanian, James E. Specht, George L. Graef, William D. Beavis, Brian W. Diers, Qijian Song, Perry B. Cregan, Randall Nelson, Rouf Mian, J. Grover Shannon, Leah McHale, Dechun Wang, William Schapaugh, Aaron J. Lorenz, Shizhong Xu, William M. Muir, Katy M. Rainey

G3: Genes, Genomes, Genetics February 2018 8: 519-529;
DOI: https://doi.org/10.1534/g3.117.300300

Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs

Gavriel Y. Matt, James G. Umen

G3: Genes, Genomes, Genetics February 2018 8: 531-550;
DOI: https://doi.org/10.1534/g3.117.300253

Powerful Inference with the D-Statistic on Low-Coverage Whole-Genome Data

Samuele Soraggi, Carsten Wiuf, Anders Albrechtsen

G3: Genes, Genomes, Genetics February 2018 8: 551-566;
DOI: https://doi.org/10.1534/g3.117.300192

Growth of Caenorhabditis elegans in Defined Media Is Dependent on Presence of Particulate Matter

Matthew R. Flavel, Adam Mechler, Mahdi Shahmiri, Elizabeth R. Mathews, Ashley E. Franks, Weisan Chen, Damien Zanker, Bo Xian, Shan Gao, Jing Luo, Surafel Tegegne, Christian Doneski, Markandeya Jois

G3: Genes, Genomes, Genetics February 2018 8: 567-575;
DOI: https://doi.org/10.1534/g3.117.300325

A 12.3-kb Duplication Within the VWF Gene in Pigs Affected by Von Willebrand Disease Type 3

Stefanie Lehner, Mahnaz Ekhlasi-Hundrieser, Carsten Detering, Hanna Allerkamp, Christiane Pfarrer, Mario von Depka Prondzinski

G3: Genes, Genomes, Genetics February 2018 8: 577-585;
DOI: https://doi.org/10.1534/g3.117.300432

Dosage-Dependent Expression Variation Suppressed on the Drosophila Male XChromosome

Hangnoh Lee, Dong-Yeon Cho, Damian Wojtowicz, Susan T. Harbison, Steven Russell, Brian Oliver, Teresa M. Przytycka

G3: Genes, Genomes, Genetics February 2018 8: 587-598;
DOI: https://doi.org/10.1534/g3.117.300400

Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example

Yanyan Liu, Sican Xiong, Wei Sun, Fei Zou

G3: Genes, Genomes, Genetics February 2018 8: 599-605;
DOI: https://doi.org/10.1534/g3.117.300483

Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources

Xiaoqing Rong-Mullins, Michael C. Ayers, Mahmoud Summers, Jennifer E. G. Gallagher

G3: Genes, Genomes, Genetics February 2018 8: 607-619;
DOI: https://doi.org/10.1534/g3.117.300138

In Vivo Functional Analysis of Drosophila Robo1 Fibronectin Type-III Repeats

Haley E. Brown, Marie C. Reichert, Timothy A. Evans

G3: Genes, Genomes, Genetics February 2018 8: 621-630;
DOI: https://doi.org/10.1534/g3.117.300418

Zinc Detoxification: A Functional Genomics and Transcriptomics Analysis inDrosophila melanogaster Cultured Cells

Stephanie E. Mohr, Kirstin Rudd, Yanhui Hu, Wei Roc Song, Quentin Gilly, Michael Buckner, Benjamin E. Housden, Colleen Kelley, Jonathan Zirin, Rong Tao, Gabriel Amador, Katarzyna Sierzputowska, Aram Comjean, Norbert Perrimon

G3: Genes, Genomes, Genetics February 2018 8: 631-641;
DOI: https://doi.org/10.1534/g3.117.300447

Had1 Is Required for Cell Wall Integrity and Fungal Virulence in Cryptococcus neoformans

Won-Hee Jung, Ye-Eun Son, Sang-Hun Oh, Ci Fu, Hye Shin Kim, Jin-Hwan Kwak, Maria E. Cardenas, Joseph Heitman, Hee-Soo Park

G3: Genes, Genomes, Genetics February 2018 8: 643-652;
DOI: https://doi.org/10.1534/g3.117.300444

Highly Efficient Site-Specific Mutagenesis in Malaria Mosquitoes Using CRISPR

Ming Li, Omar S. Akbari, Bradley J. White

G3: Genes, Genomes, Genetics February 2018 8: 653-658;
DOI: https://doi.org/10.1534/g3.117.1134

Sequencing of Linkage Region on Chromosome 12p11 Identifies PKP2 as a Candidate Gene for Left Ventricular Mass in Dominican Families

Nicole D. Dueker, Shengru Guo, Ashley Beecham, Liyong Wang, Susan H. Blanton, Marco R. Di Tullio, Tatjana Rundek, Ralph L. Sacco

G3: Genes, Genomes, Genetics February 2018 8: 659-668;
DOI: https://doi.org/10.1534/g3.117.300358

Use of a Sibling Subtraction Method for Identifying Causal Mutations in Caenorhabditis elegans by Whole-Genome Sequencing

Braveen B. Joseph, Nicolas A. Blouin, David S. Fay

G3: Genes, Genomes, Genetics February 2018 8: 669-678;
DOI: https://doi.org/10.1534/g3.117.300135

Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

Thomas D. Brekke, Katherine A. Steele, John F. Mulley

G3: Genes, Genomes, Genetics February 2018 8: 679-686;
DOI: https://doi.org/10.1534/g3.117.300495

Differential Regulation of Zfp30 Expression in Murine Airway Epithelia Through Altered Binding of ZFP148 to rs51434084

Lucas T. Laudermilk, Joseph M. Thomas, Samir N. Kelada

G3: Genes, Genomes, Genetics February 2018 8: 687-693;
DOI: https://doi.org/10.1534/g3.117.300507

Genetic Identification of Separase Regulators in Caenorhabditis elegans

Michael Melesse, Dillon E. Sloan, Joseph T. Benthal, Quincey Caylor, Krishen Gosine, Xiaofei Bai, Joshua N. Bembenek

G3: Genes, Genomes, Genetics February 2018 8: 695-705;
DOI: https://doi.org/10.1534/g3.117.300298

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

Patrick Thorwarth, Eltohamy A. A. Yousef, Karl J. Schmid

G3: Genes, Genomes, Genetics February 2018 8: 707-718;
DOI: https://doi.org/10.1534/g3.117.300199

Genomic Prediction Accuracy for Resistance Against Piscirickettsia salmonis in Farmed Rainbow Trout

Grazyella M. Yoshida, Rama Bangera, Roberto Carvalheiro, Katharina Correa, René Figueroa, Jean P. Lhorente, José M. Yáñez

G3: Genes, Genomes, Genetics February 2018 8: 719-726;
DOI: https://doi.org/10.1534/g3.117.300499

Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in RiceYuka Kitomi, Emari Nakao, Sawako Kawai, Noriko Kanno, Tsuyu Ando, Shuichi Fukuoka, Kenji Irie, Yusaku Uga

G3: Genes, Genomes, Genetics February 2018 8: 727-735;
DOI: https://doi.org/10.1534/g3.117.300147

Genetic Evidence for Roles of Yeast Mitotic Cyclins at Single-Stranded Gaps Created by DNA Replication Laurence Signon

G3: Genes, Genomes, Genetics February 2018 8: 737-752;
DOI: https://doi.org/10.1534/g3.117.300537

Corrigendum

Corrigendum

G3: Genes, Genomes, Genetics February 2018 8: 753;
DOI: https://doi.org/10.1534/g3.117.300500

Retraction

Role of Translesion Synthesis DNA Polymerases in DNA Replication in the Presence of a Weak DNA Polymerase d in Saccharomyces cerevisiae

Likui Zhang, Yanchao Huang, Xinyuan Zhu, Yuxiao Wang, Haoqiang Shi, Min Chen, Kunming Dong, Xiaojian Zhou

G3: Genes, Genomes, Genetics February 2018 8: 754;
DOI: https://doi.org/10.1534/g3.117.300097