Contents November 2015 • VOLUME 5 • ISSUE 11 • www.g3journal.org INVESTIGATIONS 2219–2227 Genes with Restricted Introgression in a Field Cricket (Gryllus firmus/Gryllus pennsylvanicus) Hybrid Zone Are Concentrated on the X Chromosome and a Single Autosome Luana S. Maroja, Erica L. Larson, Steven M. Bogdanowicz, and Richard G. Harrison Characterizing the extent of genomic differentiation between recently diverged lineages provides an important context for understanding the early stages of speciation. The authors construct a genetic linkage map for the hybridizing field crickets, Gryllus firmus and Gryllus pennsylvanicus. They show that genes that remain distinct in the face of hybridization are concentrated on the sex chromosome and in one autosomal region. The authors discuss the implications of these results for understanding the role of sex chromosomes in the origin of new species and why recently diverged species exhibit heterogeneous genomic divergence. 2229–2239 Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize Ashley N. Lough, Kaitlyn M. Faries, Dal-Hoe Koo, Abid Hussain, Leah M. Roark, Tiffany L. Langewisch, Teresa Backes, Karl A. G. Kremling, Jiming Jiang, James A. Birchler, and Kathleen J. Newton The transfer of mitochondrial DNA (mtDNA) into nuclear genomes occurs regularly. The authors examined intraspecific variation of nuclear-mtDNA sequences (NUMTs) among diverse maize inbred lines using fluorescence in situ hybridization (FISH). A large NUMT on the long arm of chromosome 9 contains a majority of the mitochondrial genome. This mtDNA insertion accounts for approximately 1% of chromosome 9 in the B73 line. However, the published nuclear genome sequence for B73 includes only part of the mtDNA sequences detected by FISH. Thus, cytogenetic analyses should be used to complement sequence searches when examining large insertions of organellar DNA into nuclear chromosomes. 2241–2255 High-Throughput Cloning of Temperature-Sensitive Caenorhabditis elegans Mutants with Adult Syncytial Germline Membrane Architecture Defects Josh Lowry, John Yochem, Chien-Hui Chuang,KenjiSugioka,AmyA.Connolly,and Bruce Bowerman The mechanisms that control the development and maintenance of the complex membrane architecture of the syncytial C. elegans germline remain poorly understood. The authors have identified temperature-sensitive mutations in 19 essential genes that cause defects in germline membrane architecture. Using whole genome sequencing, the authors identified the causal mutations in 10 of these mutants. Four of the affected genes are conserved, with orthologs known to be involved in membrane biology, and two of these are required for maintenance of the membrane architecture during adult oogenesis. This work provides a starting point for further investigation of a widely conserved feature of animal gametogenesis. Volume 5 | November 2015 | ii 2257–2266 Fine-Mapping the Wheat Snn1 Locus Conferring Sensitivity to the Parastagonospora nodorum Necrotrophic Effector SnTox1 Using an Eight Founder Multiparent Advanced Generation Inter-Cross Population James Cockram, Alice Scuderi, Toby Barber, Eiko Furuki, Keith A. Gardner, Nick Gosman, Radoslaw Kowalczyk, Huyen P. Phan, Gemma A. Rose, Kar-Chun Tan, Richard P. Oliver, and Ian J. Mackay Bread wheat is one of the world's major crops. Genetic resistance of wheat to disease is a critical factor in yield protection, and thus maintaining global food security. Disease resistance is typically a complex trait. However, the recent identification of toxic effectors secreted by fungal pathogens now allows the quantitative wheat responses to be Mendalized. Here, the authors use a multiparent advanced generation inter-cross (MAGIC) wheat population to map sensitivity loci to the effector SnTox1, produced by the necrotrophic fungus Parastagonorum nodorum. Tagging SNPs are converted to breeder-friendly markers, providing useful resources for marker-assisted breeding approaches. 2267–2274 Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci Tomoyuki Furuta, Norio Komeda, Kenji Asano, Kanako Uehara, Rico Gamuyao, Rosalyn B. Angeles-Shim, Keisuke Nagai, Kazuyuki Doi, Diane R. Wang, Hideshi Yasui, Atsushi Yoshimura, Jianzhong Wu, Susan R. McCouch, and Motoyuki Ashikari A long awn is one of the distinct morphological features of wild rice species. So far, it has not been reported how many genes are involved the formation and how genes are lost through rice domestication. The authors found three loci (RAE1, RAE2, and RAE3) that are involved in the formation of awn. The authors also showed the two cultivated rice species, Oryza sativa (Asian rice) and Oryza glaberrima (African rice), have taken different paths to become awnless. This is the first report of independent loci being selected for the same trait during crop domestication. 2275–2283 Evolutionary Fate of the Androgen Receptor2Signaling Pathway in Ray-Finned Fishes with a Special Focus on Cichlids Thibault Lorin, Walter Salzburger, and Astrid Böhne The authors investigate for the first time the genetic composition of the androgen receptor–signaling pathway in ray-finned fish genomes characterizing gene duplications and losses, with a special focus on paralogs derived from the teleost-specific whole genome duplication (TSGD) using the spotted gar as reference. One particular lineage, the cichlids, shows differing selection pressures acting on TSGD duplicates. In cichlids from East African Lake Tanganyika, the authors find that gene duplicates differ in their expression pattern on the tissue and species level. The authors explore in more detail indications of a neofunctionalization event for the rac1 GTPase in cichlids. 2285–2290 SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean Qijian Song, Gaofeng Jia, David L. Hyten, Jerry Jenkins, Eun-Young Hwang, Steven G. Schroeder, Juan M. Osorno, Jeremy Schmutz, Scott A. Jackson, Phillip E. McClean, and Perry B. Cregan These authors identified SNP DNA markers based on a diverse set of common bean cultivars via next generation sequencing technologies; developed Illumina Infinium BeadChip assays containing SNPs with high polymorphism within and between common bean market classes; created high density genetic linkage maps; anchored and oriented large common bean sequence scaffolds generated by the Joint Genome Institute, Department of Energy; and designed a BARCBean6K_3 BeadChip with a core set of 6,000 highly informative SNP markers. The BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad. 2291–2298 Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis Jeanine M. Refsnider, Thomas J. Poorten, Penny F. Langhammer, Patricia A. Burrowes, and Erica Bree Rosenblum Understanding the genetic basis of virulence shifts for emerging pathogens is critical. The fungus Batrachochytrium dendrobatidis (Bd) causes a lethal skin disease in amphibians and is responsible for amphibian declines around the world. The authors compared full genomes of two Bd samples. Both originated from the same source, but one decreased in virulence over 30 generations in the lab. Virulence attenuation was associated with loss of chromosomal segments and mutations in specific protease genes. These results demonstrate that genomic processes, like changes in chromosomal copy number, can occur over extremely short timescales and may contribute to virulence shifts in emerging pathogens. iii | Contents 2299–2306 Persistent Activation of the Innate Immune Response in Adult Drosophila Following Radiation Exposure During Larval Development Lisa J. Sudmeier, Sai-Suma Samudrala, Steven P. Howard, and Barry Ganetzky Cranial radiation therapy is an effective treatment for pediatric central nervous system malignancies, but survivors often suffer from long-term neurological and neurocognitive side effects. Here the authors show that the innate immune response is activated in the adult Drosophila brain following radiation exposure during larval development and that this response is sustained in adult flies weeks after radiation exposure. The authors also present preliminary data suggesting that innate immunity is radioprotective during Drosophila development. Together, these data suggest that activation of the innate immune response may be beneficial initially following radiation exposure. However, chronic inflammation may eventually lead to impaired neuronal function and viability. 2307–2321 Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea Carrie A. Whittle and Cassandra G. Extavour Codon and amino acid usage have been correlated with expression level in some animals, and may be shaped by selection for efficient and accurate translation. Research on codon usage, and particularly amino acid frequency, remains focused on a few traditional animal models, but insights can be gained by expanding studies to a broader range of organisms. Here the authors use transcriptomes of three emerging model arthropods to reveal that highly expressed genes favor specific synonymous codons, moderate-cost amino acids, shorter proteins, and are preferentially involved in cell cycling and protein synthesis. These findings suggest translational selection operates across divergent Pancrustacea.