May 2016 Table of Contents

Investigations

• The Genetic Basis of Baculum Size and Shape Variation in Mice

  Nicholas G. Schultz, Jesse Ingels, Andrew Hillhouse, Keegan Wardwell, Peter L. Chang, James M. Cheverud, Cathleen Lutz, Lu Lu, Robert W. Williams, Matthew D. Dean

  G3: Genes, Genomes, Genetics May 2016 6: 1141-1151; https://doi.org/10.1534/g3.116.027888
• Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape?

  Nicolas Navarro, A. Murat Maga

  G3: Genes, Genomes, Genetics May 2016 6: 1153-1163; https://doi.org/10.1534/g3.115.024372
• Genomic Bayesian Prediction Model for Count Data with Genotype × Environment Interaction

  Abelardo Montesinos-López, Osval A. Montesinos-López, José Crossa, Juan Burgueño, Kent M. Eskridge, Esteban Falconi-Castillo, Xinyao He, Pawan Singh, Karen Cichy

  G3: Genes, Genomes, Genetics May 2016 6: 1165-1177; https://doi.org/10.1534/g3.116.028118
• Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes

  Takashi Hamaji, Yuko Mogi, Patrick J. Ferris, Toshiyuki Mori, Shinya Miyagishima, Yukihiro Kabeya, Yoshiki Nishimura, Atsushi Toyoda, Hideki Noguchi, Asao Fujiyama, Bradley J. S. C. Olson, Tara N. Marriage, Ichiro Nishii, James G. Umen, Hisayoshi Nozaki

  G3: Genes, Genomes, Genetics May 2016 6: 1179-1189; https://doi.org/10.1534/g3.115.026229
• Comparative and Transcriptome Analyses Uncover Key Aspects of Coding- and Long Noncoding RNAs in Flatworm Mitochondrial Genomes

  Eric Ross, David Blair, Carlos Guerrero-Hernández, Alejandro Sánchez Alvarado

  G3: Genes, Genomes, Genetics May 2016 6: 1191-1200; https://doi.org/10.1534/g3.116.028175
• Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast

  Agnès Thierry, Varun Khanna, Bernard Dujon

  G3: Genes, Genomes, Genetics May 2016 6: 1201-1215; https://doi.org/10.1534/g3.115.024547
• The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

  Marie Foulongne-Oriol, Manuela Rocha de Brito, Delphine Cabannes, Aurélien Clément, Cathy Spataro, Magalie Moinard, Eustáquio Souza Dias, Philippe Callac, Jean-Michel Savoie

  G3: Genes, Genomes, Genetics May 2016 6: 1217-1226; https://doi.org/10.1534/g3.115.025718
• Staufen Negatively Modulates MicroRNA Activity in Caenorhabditis elegans

  Zhiji Ren, Isana Veksler-Lublinsky, David Morrissey, Victor Ambros

  G3: Genes, Genomes, Genetics May 2016 6: 1227-1237; https://doi.org/10.1534/g3.116.027300
• Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP) Genes in Mimulus guttatus Vernalization Response

  Jill C. Preston, Jinshun Zhong, Meghan McKeown, Meghan den Bakker, Jannice Friedman

  G3: Genes, Genomes, Genetics May 2016 6: 1239-1249; https://doi.org/10.1534/g3.115.026468
• Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes

  Dov Tiosano, Laura Audi, Sharlee Climer, Weixiong Zhang, Alan R. Templeton, Monica Fernández-Cancio, Ruth Gershoni-Baruch, José Miguel Sánchez-Muro, Mohamed El Kholy, Zèev Hochberg

  G3: Genes, Genomes, Genetics May 2016 6: 1251-1266; https://doi.org/10.1534/g3.115.026773
• Transcriptomic Analysis Identifies Candidate Genes and Gene Sets Controlling the Response of Porcine Peripheral Blood Mononuclear Cells to Poly I:C Stimulation

  Jiying Wang, Yanping Wang, Huaizhong Wang, Haifei Wang, Jian-Feng Liu, Ying Wu, Jianfeng Guo

  G3: Genes, Genomes, Genetics May 2016 6: 1267-1275; https://doi.org/10.1534/g3.116.028290
• Chicken gga-miR-103-3p Targets CCNE1 and TFDP2 and Inhibits MDCC-MSB1 Cell Migration

  Bo Han, Ling Lian, Xin Li, Chunfang Zhao, Lujiang Qu, Changjun Liu, Jiuzhou Song, Ning Yang

  G3: Genes, Genomes, Genetics May 2016 6: 1277-1285; https://doi.org/10.1534/g3.116.028498
• Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution

  Charleston W. K. Chiang, Peter Ralph, John Novembre

  G3: Genes, Genomes, Genetics May 2016 6: 1287-1296; https://doi.org/10.1534/g3.116.027581
• Mapping Challenging Mutations by Whole-Genome Sequencing

  Harold E. Smith, Amy S. Fabritius, Aimee Jaramillo-Lambert, Andy Golden

  G3: Genes, Genomes, Genetics May 2016 6: 1297-1304; https://doi.org/10.1534/g3.116.028316
• Characterization of Chicken MMP13 Expression and Genetic Effect on Egg Production Traits of Its Promoter Polymorphisms

  Zhenjie Yuan, Yuxia Chen, Qiuyue Chen, Miao Guo, Li Kang, Guiyu Zhu, Yunliang Jiang

  G3: Genes, Genomes, Genetics May 2016 6: 1305-1312; https://doi.org/10.1534/g3.116.027755
• Genomic Selection in Multi-environment Crop Trials

  Helena Oakey, Brian Cullis, Robin Thompson, Jordi Comadran, Claire Halpin, Robbie Waugh

  G3: Genes, Genomes, Genetics May 2016 6: 1313-1326; https://doi.org/10.1534/g3.116.027524
• The SEB-1 Transcription Factor Binds to the STRE Motif in Neurospora crassa and Regulates a Variety of Cellular Processes Including the Stress Response and Reserve Carbohydrate Metabolism

  Fernanda Zanolli Freitas, Stela Virgilio, Fernanda Barbosa Cupertino, David John Kowbel, Mariana Fioramonte, Fabio Cesar Gozzo, N. Louise Glass, Maria Célia Bertolini

  G3: Genes, Genomes, Genetics May 2016 6: 1327-1343; https://doi.org/10.1534/g3.116.028506
• Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes

  Silvia N. Kariuki, John D. Blischak, Shigeki Nakagome, David B. Witonsky, Anna Di Rienzo

  G3: Genes, Genomes, Genetics May 2016 6: 1345-1355; https://doi.org/10.1534/g3.116.028712
• Gene Regulatory Evolution During Speciation in a Songbird

  John H. Davidson, Christopher N. Balakrishnan

  G3: Genes, Genomes, Genetics May 2016 6: 1357-1364; https://doi.org/10.1534/g3.116.027946
• The HIST1 Locus Escapes Reprogramming in Cloned Bovine Embryos

  Byungkuk Min, Sunwha Cho, Jung Sun Park, Kyuheum Jeon, Yong-Kook Kang

  G3: Genes, Genomes, Genetics May 2016 6: 1365-1371; https://doi.org/10.1534/g3.115.026666
• Preparing for Winter: The Transcriptomic Response Associated with Different Day Lengths in Drosophila montana

  Darren J. Parker, Michael G. Ritchie, Maaria Kankare

  G3: Genes, Genomes, Genetics May 2016 6: 1373-1381; https://doi.org/10.1534/g3.116.027870
• The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram

  Michael J. Prigge, Kathleen Greenham, Yi Zhang, Aaron Santner, Cristina Castillejo, Andrew M. Mutka, Ronan C. O’Malley, Joseph R. Ecker, Barbara N. Kunkel, Mark Estelle

  G3: Genes, Genomes, Genetics May 2016 6: 1383-1390; https://doi.org/10.1534/g3.115.025585
• Multiple Targets on the Gln3 Transcription Activator Are Cumulatively Required for Control of Its Cytoplasmic Sequestration

  Rajendra Rai, Jennifer J. Tate, Terrance G. Cooper

  G3: Genes, Genomes, Genetics May 2016 6: 1391-1408; https://doi.org/10.1534/g3.116.027615
• Genetic Background, Maternal Age, and Interaction Effects Mediate Rates of Crossing Over in Drosophila melanogaster Females

  Chad M. Hunter, Matthew C. Robinson, David L. Aylor, Nadia D. Singh

  G3: Genes, Genomes, Genetics May 2016 6: 1409-1416; https://doi.org/10.1534/g3.116.027631
• A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing

  Jinpeng Wang, Li Li, Guofan Zhang

  G3: Genes, Genomes, Genetics May 2016 6: 1417-1426; https://doi.org/10.1534/g3.116.026971
• Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster

  Janani Iyer, Qingyu Wang, Thanh Le, Lucilla Pizzo, Sebastian Grönke, Surendra S. Ambegaokar, Yuzuru Imai, Ashutosh Srivastava, Beatriz Llamusí Troisí, Graeme Mardon, Ruben Artero, George R. Jackson, Adrian M. Isaacs, Linda Partridge, Bingwei Lu, Justin P. Kumar, Santhosh Girirajan

  G3: Genes, Genomes, Genetics May 2016 6: 1427-1437; https://doi.org/10.1534/g3.116.027060
• The Sorghum Gene for Leaf Color Changes upon Wounding (P) Encodes a Flavanone 4-Reductase in the 3-Deoxyanthocyanidin Biosynthesis Pathway

  Hiroyuki Kawahigashi, Shigemitsu Kasuga, Yuji Sawada, Jun-ichi Yonemaru, Tsuyu Ando, Hiroyuki Kanamori, Jianzhong Wu, Hiroshi Mizuno, Mitsuru Momma, Zui Fujimoto, Masami Yokota Hirai, Takashi Matsumoto

  G3: Genes, Genomes, Genetics May 2016 6: 1439-1447; https://doi.org/10.1534/g3.115.026104
• Organ Length Control by an ADAMTS Extracellular Protease in Caenorhabditis elegans

  Yukimasa Shibata, Yuri Kawakado, Noriyoshi Hori, Kota Tanaka, Ryo Inoue, Tomomi Takano, Yukihiko Kubota, Kiyoji Nishiwaki

  G3: Genes, Genomes, Genetics May 2016 6: 1449-1457; https://doi.org/10.1534/g3.116.028019
• Pollen Killer Gene S35 Function Requires Interaction with an Activator That Maps Close to S24, Another Pollen Killer Gene in Rice

  Takahiko Kubo, Atsushi Yoshimura, Nori Kurata

  G3: Genes, Genomes, Genetics May 2016 6: 1459-1468; https://doi.org/10.1534/g3.116.027573