Spotlight

A showcase of research and scholarship

in selected articles from 2018 in selected articles from 2018
A showcase of research and scholarship

Spotlight
 University of Georgia
Sue Biggins Katie Peichel
Kelly Dawe
2018/2019 GENE EXPRESSION
Fred Hutchinson University of Bern University
Editorial Board Cancer Research James A. Birchler
Christine Queitsch
Simon Fraser
Center University of Missouri
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Institutes of Health
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Executive Editor University of North University of Iowa
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University of Florida
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& Dartmouth College
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Sarah Bay Bob Goldstein
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National Laboratory
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Howard D. Lipshitz
Science Aaron P. Mitchell Rita M. Cantor Temple University
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DEVELOPMENTAL Carnegie Mellon Rob J. Kulathinal
Institute of Science Davis
AND BEHAVIORAL University
and Technology COMPLEX TRAITS GENETICS
University of California, University
Austria Joshua M. Akey Oliver J. Rando Patrick J. Brown North Carolina State
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Princeton University
USDA
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University of Toronto
Massachusetts James B. Holland
University of California, Alain Charcosset Medicine
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Medical School
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California
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Heidelberg
de la Recherche Nathan Springer University of Southern
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DKFZ & University of
Agronomique University of Susan L. Forsburg
University of Medicine at Dartmouth
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Minnesota
Wisconsin-Madison Stephen Chenoweth
University of Wyoming
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University of Toronto
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Charles Boone
University of California, Purdue University
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Livestock Research Elissa J. Chesler James A. Birchler Kansas State
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Agricultural Sciences
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Duke University
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at Irvine University of North MD Anderson Cancer Arizona
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University
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Editorial Board
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Medicine Colorado State
2018/19
University
Gustavo A. de los Timothy R. Hughes Peter L. Morrell Steve Scofield
Campos University of Toronto University of USDA-ARS
Michigan State Scott A. Jackson Minnesota
Tanja Slotte
University University of Georgia Geoffrey Morris University of
Job Dekker Mattias Jakobsson Kansas State Stockholm
University of Uppsala University University
Shavannor M. Smith
Massachusetts Chad L. Myers The University of
Medical School Jean-Luc Jannink
USDA-ARS University of Georgia
Rebecca W. Doerge Minnesota
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University Stowers Institute for
Medical Research NIDDK, National
Dina A. St. Clair
Andrew Doust Institutes of Health
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Oklahoma State Fernando Pardo- Davis
University Duke University
Manuel de Villena Lars M. Steinmetz
Aimée M. Dudley John K. Kim University of North
Johns Hopkins European Molecular
Pacific Northwest Carolina at Chapel Hill Biology Laboratory &
Diabetes Research University School of Medicine Stanford University
Institute Yuseob Kim Isobel Parkin Hidenori Tachida
Jay C. Dunlap Ewha Womans Agriculture and Agri-
University Kyushu University
Dartmouth Medical Food Canada
School Éric Lécuyer Kevin Thornton
Andrew H. Paterson University of California,
Mark Estelle Institut de recherches University of Georgia
cliniques de Montréal Irvine
University of California,
(IRCM) Stephen Pearce David W. Threadgill
San Diego
Colorado State Texas A&M University
Justin C. Fay Siu Sylvia Lee University
Washington University Cornell University Sarah A. Tishkoff
Craig S. Pikaard University of
in St. Louis Jianxin Ma Indiana University Pennsylvania
Marie-Anne Félix Purdue University
James Prendergast Olga Troyanskaya
IBENS Jun Ma University of Princeton University
Elizabeth R. Gavis Zhejiang University Edinburgh
Princeton University Stuart J. Macdonald Mike Tyers
Bruce Reed Université de Montréal
Cayetano Gonzalez The University of University of Waterloo
IRB Barcelona Kansas Joshua Udall
Nick Rhind Brigham Young
Brian D. Gregory Trudy Mackay University of
Clemson University University
University of Massachusetts
Pennsylvania Daniel Macqueen Medical School Marian Walhout
The Roslin Institute University of
David J. Gresham Jasper Rine Massachusetts
New York University Christian R. Marshall University of California, Medical School
The Hospital for Sick Berkeley
David J. Grunwald Mick Watson
The University of Utah Children Matthew Rockman University of
Sarah Mathews New York University Edinburgh
Kris Gunsalus
New York University The Commonwealth Antonis Rokas Jonathan F. Wendel
Scientific and Vanderbilt University
Ryan Hernandez Iowa State University
Industrial Research
University of California, Organisation (CSIRO) Matthew S. Sachs Randall Wisser
San Francisco Texas A&M University University of Delaware
Tara C. Matise
Jay R. Hesselberth Rutgers University Helen K. Salz José Manuel Yáñez
University of Colorado Case Western Reserve University of Chile
School of Medicine Andrew S. McCallion University
Johns Hopkins Monique Zetka
Charles S. Hoffman University School of Michael J. Scanlon McGill University
Boston College Medicine Cornell University
Ross Houston Kim S. McKim David S. Schneider
The Roslin Institute Rutgers University Stanford University
Emma Huang Todd Mockler Robert A. Sclafani
Janssen Pharma R & D Donald Danforth Plant University of Colorado
Science Center School of Medicine
Matthew Hufford
Iowa State University
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Emmanuel College

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University of Calgary

ON THE COVER A tame red fox from the breeding program at the Institute of Cytology
and Genetics of the Russian Academy of Sciences in Novosibirsk, Russia. To investigate
the biological mechanisms targeted during domestication, Hekman et al. analyzed gene
expression in the anterior pituitary of tame and aggressive foxes. G3 8: 859–873. Photo:
2 Irina Pivovarova.
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3
G3: Genes | Genomes | Genetics
 GENOME REPORT

Identification of Two Distinct Classes of the

Human INO80 Complex Genome-Wide
John S. Runge, Jesse R. Raab, and Terry Magnuson
G3: Genes | Genomes | Genetics April 2018 8: 1095–1102

EDITORS’ NOTE ATP-dependent chromatin remodeling complexes

(remodelers) mediate nucleosome position at epigenomic loci. To determine
if the local chromatin landscape influences remodeler function, Runge et al.
used ChIP-seq to map members of the human INO80 remodeling complex
(INO80-C) genome-wide and to survey the chromatin landscape at its target
sites. They identified two classes of INO80-C targets with distinct chromatin
signatures and heterogeneity in the composition of the complex in each.
These data suggest INO80-C targeting may be influenced by the chromatin
landscape at its targets.

ABSTRACT Chromatin remodeling and histone modifying enzymes play

a critical role in shaping the regulatory output of a cell. Although much is
known about these classes of proteins, identifying the mechanisms by which
they coordinate gene expression programs remains an exciting topic of
investigation. One factor that may contribute to the targeting and activity of
chromatin regulators is local chromatin landscape. We leveraged genomic
approaches and publically-available datasets to characterize the chromatin
landscape at targets of the human INO80 chromatin remodeling complex
(INO80-C). Our data revealed two classes of INO80-C targets with distinct
chromatin signatures. The predominant INO80-C class was enriched for
open chromatin, H3K27ac, and representative subunits from each of the three
INO80-C modules (RUVBL1, RUVBL2, MCRS1, YY1). We named this class
Canonical INO80. Notably, we identified an unexpected class of INO80-C
targets that contained only the INO80 ATPase and harbored a repressive
chromatin signature characterized by inaccessible chromatin, H3K27me3,
and the methyltransferase EZH2. We named this class Non-Canonical
INO80 (NC-INO80). Biochemical approaches indicated that INO80-C and
the H3K27 acetyltransferase P300 physically interact, suggesting INO80-C
and P300 may jointly coordinate chromatin accessibility at Canonical INO80
sites. No interaction was detected between INO80-C and EZH2, indicating
INO80-C and EZH2 may engage in a separate form of regulatory crosstalk at
NC-INO80 targets. Our data indicate that INO80-C is more compositionally
heterogenous at its genomic targets than anticipated. Moreover, our data
suggest there is an important link between INO80-C and histone modifying
enzymes that may have consequences in developmental and pathological
contexts.

4
 MUTANT SCREEN REPORT

Ade2 Functions in the Drosophila Fat Body To

Promote Sleep
Maria E. Yurgel, Kreesha D. Shah, Elizabeth B. Brown, Carter Burns, Ryan A. Bennick,
Justin R. DiAngelo, and Alex C. Keene
G3: Genes | Genomes | Genetics November 2018 8: 3385–3395

EDITORS’ NOTE Epidemiological and genomic analyses reveal strong

interactions between disorders of sleep and metabolic state. Yurgel et al.
report the results of a genetic screen to identify genes that function within
the fat body of the fruit fly to regulate sleep. The screen identified numerous
candidate genes, and further mechanistic studies validated a sleep-
promoting role for Pfas/Ade2, which also regulates energy stores.

ABSTRACT Metabolic state is a potent modulator of sleep and circadian

behavior, and animals acutely modulate their sleep in accordance with internal
energy stores and food availability. Across phyla, hormones secreted from
adipose tissue act in the brain to control neural physiology and behavior
to modulate sleep and metabolic state. Growing evidence suggests the fat
body is a critical regulator of complex behaviors, but little is known about the
genes that function within the fat body to regulate sleep. To identify molecular
factors functioning in non-neuronal tissues to regulate sleep, we performed
an RNAi screen selectively knocking down genes in the fat body. We found
that knockdown of Phosphoribosylformylglycinamidine synthase/Pfas (Ade2),
a highly conserved gene involved the biosynthesis of purines, sleep regulation
and energy stores. Flies heterozygous for multiple Ade2 mutations are also
short sleepers and this effect is partially rescued by restoring Ade2 to the
Drosophila fat body. Targeted knockdown of Ade2 in the fat body does not
alter arousal threshold or the homeostatic response to sleep deprivation,
suggesting a specific role in modulating baseline sleep duration. Together,
these findings suggest Ade2 functions within the fat body to promote
both sleep and energy storage, providing a functional link between these
processes.

5
 SOF T WARE & DATA RESOURCES

gQTL: A Web Application for QTL Analysis

Using the Collaborative Cross Mouse Genetic
Reference Population
Kranti Konganti, Andre Ehrlich, Ivan Rusyn, and David W. Threadgill
G3: Genes | Genomes | Genetics August 2018 8: 2559–2562

EDITORS’ NOTE The Collaborative Cross mouse genetic reference

population provides a robust opportunity for the identification of quantitative
trait loci (QTL). Until now, the software used to analyze this population was
restricted to the R platform, limiting access for many scientists. Konganti et
al. introduce gQTL, a web-based application with a simple graphical interface
designed to allow users to more easily analyze QTL mapping data from this
complex population.

ABSTRACT Multi-parental recombinant inbred populations, such as the

Collaborative Cross (CC) mouse genetic reference population, are increasingly
being used for analysis of quantitative trait loci (QTL). However specialized
analytic software for these complex populations is typically built in R that
works only on command-line, which limits the utility of these powerful
resources for many users. To overcome analytic limitations, we developed
gQTL, a web accessible, simple graphical user interface application based on
the DOQTL platform in R to perform QTL mapping using data from CC mice.

6
Mutant screen results gathering dust in your lab notebook?
WGS datasets languishing on your hard drive?
New software tools going unshared?

We’ve got an article

format for that.
Mutant Describe results of
Screen mutant screens
Reports

Describe whole
Genome genome sequence
(WGS) data of
Reports organisms and/or
strains

Software Describe novel

software for genetic
& Data data analyses and
Resources database resources

g3journal.org/content/article-types
 INVESTIG ATION

diploS/HIC: An Updated Approach to

Classifying Selective Sweeps
Andrew D. Kern and Daniel R. Schrider
G3: Genes | Genomes | Genetics June 2018 8: 1959–1970

EDITORS’ NOTE Genomes retain the marks of selection long after the
evolutionary pressures that caused them are gone. Kern and Schrider
previously designed a supervised machine learning approach called S/HIC to
identify hard and soft selective sweeps based on the patterns observed in a
particular genomic window. Here, they present diploS/HIC, which improves
upon the previous approach by using deep learning and allowing for the use
of unphased genotype data.

ABSTRACT Identifying selective sweeps in populations that have complex

demographic histories remains a difficult problem in population genetics.
We previously introduced a supervised machine learning approach, S/HIC,
for finding both hard and soft selective sweeps in genomes on the basis of
patterns of genetic variation surrounding a window of the genome. While S/
HIC was shown to be both powerful and precise, the utility of S/HIC was
limited by the use of phased genomic data as input. In this report we describe
a deep learning variant of our method, diploS/HIC, that uses unphased
genotypes to accurately classify genomic windows. diploS/HIC is shown to
be quite powerful even at moderate to small sample sizes.

8
 IN A NUTSHELL
Walnut Bayou Lane, oil on panel, © 2015 Julie B. Smiley. This painting is based on
a walnut orchard near Winters, California. Winters is the home of the USDA-ARS
National Clonal Germplasm Repository for many fruit and nut crops, including
the national walnut collection. Walnuts are a major component of California
agriculture and are a target of genomics-assisted breeding efforts. Stevens et al.
report the sequencing and assembly of six species of Juglans and one close relative,
Pterocarya stenoptera.

Genomic Variation Among and Within Six Juglans Species

Kristian A. Stevens, Keith Woeste, Sandeep Chakraborty, Marc W.
Crepeau, Charles A. Leslie, Pedro J. Martínez-García, Daniela Puiu,
Jeanne Romero-Severson, Mark Coggeshall, Abhaya M. Dandekar,
Daniel Kluepfel, David B. Neale, Steven L. Salzberg, and Charles H.
Langley
G3: Genes | Genomes | Genetics July 2018 8: 2153–2165 9
 INVESTIG ATION

Modeling the Evolution of Female Meiotic

Drive in Maize
David W. Hall and R. Kelly Dawe
G3: Genes | Genomes | Genetics January 2018 8: 123–130

EDITORS’ NOTE Autosomal drivers are examples of selfish genetic

elements that are overrepresented in gametes, thus violating Mendel’s law of
segregation. Such overrepresentation should lead to rapid fixation—unless
there are associated deleterious fitness effects. Hall and Dawe used a
mathematical model to determine the long-term behavior of autosomal drivers
that have associated deleterious fitness effects. They calculate the expected
equilibrium allele frequencies predicted by the model, given fitness estimates
for the maize abnormal chromosome 10, which is an autosomal driver. They
show that the predicted equilibrium is within the range observed in maize land
races.

ABSTRACT Autosomal drivers violate Mendel’s law of segregation in that

they are overrepresented in gametes of heterozygous parents. For drivers
to be polymorphic within populations rather than fixing, their transmission
advantage must be offset by deleterious effects on other fitness components.
In this paper, we develop an analytical model for the evolution of autosomal
drivers that is motivated by the neocentromere drive system found in maize.
In particular, we model both the transmission advantage and deleterious
fitness effects on seed viability, pollen viability, seed to adult survival mediated
by maternal genotype, and seed to adult survival mediated by offspring
genotype. We derive general, biologically intuitive conditions for the four
most likely evolutionary outcomes and discuss the expected evolution of
autosomal drivers given these conditions. Finally, we determine the expected
equilibrium allele frequencies predicted by the model given recent estimates
of fitness components for all relevant genotypes and show that the predicted
equilibrium is within the range observed in maize land races for levels of drive
at the low end of what has been observed.

10
 PAX PUNCH A one-month-old New Zealand rabbit, used for construction of
gene knockout rabbits to model human diseases. Xu et al. created a new rabbit
knockout model for PAX4, which is a key diabetes mellitus susceptibility gene
and encodes a transcription factor with an important role in mammalian pancreas
development. Photo: Hao Yu.

Generation and Phenotype Identification of PA X4 Gene Knockout

Rabbit by CRISPR/Cas9 System
Yuanyuan Xu, Yong Wang, Yuning Song, Jichao Deng, Mao Chen,
Hongsheng Ouyang, Liangxue Lai, and Zhanjun Li
G3: Genes | Genomes | Genetics August 2018 8: 2833–2840 11
Meet new collaborators and reconnect with
your community at The Allied Genetics
Conference!

TAGC 2020 will feature an even mix of topic-driven

and community sessions, plus exciting industry,
professional development, and advocacy
programming. All genetics researchers areinvited
to present, regardless of community affiliation.

GAYLORD NATIONAL RESORT & CONVENTION CENTER

APRIL 22–26, 2020 | METRO WASHINGTON, DC

GENETICS-GSA.ORG/TAGC2020
 INVESTIG ATION

Inducible Genome Editing with Conditional

CRISPR/Cas9 Mice
Alexandra Katigbak, Francis Robert, Marilène Paquet, and Jerry Pelletier
G3: Genes | Genomes | Genetics May 2018 8: 1627–1635

EDITORS’ NOTE The introduction of the CRISPR/Cas9 genome editing

system has made the engineering of specific mutations in the mouse
quicker and easier. Adding to the mouse genome editing toolbox, Katigbak
et al. report the generation of a doxycycline-regulated Cas9 allele useful for
inducible editing experimental designs. Their model allows for the controlled,
short-term production of Cas9 and introduces a new level of experimental
flexibility in Cas9 mouse models.

ABSTRACT Genetically engineered mouse models (GEMMs) are powerful

tools by which to probe gene function in vivo, obtain insight into disease
etiology, and identify modifiers of drug response. Increased sophistication
of GEMMs has led to the design of tissue-specific and inducible models in
which genes of interest are expressed or ablated in defined tissues or cellular
subtypes. Here we describe the generation of a transgenic mouse harboring
a doxycycline-regulated Cas9 allele for inducible genome engineering. This
model provides a flexible platform for genome engineering since editing is
achieved by exogenous delivery of sgRNAs and should allow for the modeling
of a range of biological and pathological processes.

13
 INVESTIG ATION

Use of a Sibling Subtraction Method

for Identifying Causal Mutations in
Caenorhabditis elegans by Whole-Genome
Sequencing
Braveen B. Joseph, Nicolas A. Blouin, and David S. Fay
G3: Genes | Genomes | Genetics February 2018 8: 669–678

EDITORS’ NOTE At the core of successful forward genetic screens is

the ability to identify causal mutations by accurately separating them from
normal variation. Joseph et al. present a new method to identify mutations in
C. elegans suppressor screens by comparing mutants to their non-mutant
siblings, thus reducing the number of candidates that must be explored.
They demonstrate the utility of their method by identifying suppressors of two
NimA-related kinases in C. elegans.

ABSTRACT Whole-genome sequencing (WGS) is an indispensable tool

for identifying causal mutations obtained from genetic screens. To reduce
the number of causal mutation candidates typically uncovered by WGS,
Caenorhabditis elegans researchers have developed several strategies. One
involves crossing N2-background mutants to the polymorphic Hawaiian (HA)
strain, which can be used to simultaneously identify mutant strain variants
and obtain high-density mapping information. This approach, however, is not
well suited for uncovering mutations in complex genetic backgrounds, and HA
polymorphisms can alter phenotypes. Other approaches make use of DNA
variants present in the initial background or introduced by mutagenesis. This
information is used to implicate genomic regions with high densities of DNA
lesions that persist after backcrossing, but these methods can provide lower
resolution than HA mapping. To identify suppressor mutations using WGS,
we developed an approach termed the sibling subtraction method (SSM).
This method works by eliminating variants present in both mutants and their
non-mutant siblings, thus greatly reducing the number of candidates. We
used this method with two members of the C. elegans NimA-related kinase
family, nekl-2 and nekl-3. Combining weak aphenotypic alleles of nekl-2 and
nekl-3 leads to penetrant molting defects and larval arrest. We isolated ~50
suppressors of nekl-2; nekl-3 synthetic lethality using F1 clonal screening
methods and a peel-1–based counterselection strategy. When applied to five
of the suppressors, SSM led to only one to four suppressor candidates per
strain. Thus SSM is a powerful approach for identifying causal mutations in
any genetic background and provides an alternative to current methods.

14
 FINE FEATHERS The rock pigeon was domesticated thousands of years ago,
and intensive selective breeding has produced over 350 modern breeds. Charles
Darwin was a pigeon aficionado and referenced pigeon breeding as an example of
how selection produces spectacular variation. The breed depicted here is the Jacobin,
which is distinguished by an elaborate hood of feathers on its head and neck. Holt
et al. report an updated genome assembly, annotation, and linkage map for the rock
pigeon, a species that continues to be widely studied in genetics, ecology, physiology,
behavior, and evolutionary biology.
Photo: Mike Shapiro.

Improved Genome Assembly and Annotation for the Rock Pigeon

(Columba livia)
Carson Holt, Michael Campbell, David A. Keays, Nathaniel Edelman,
Aurélie Kapusta, Emily Maclary, Eric T. Domyan, Alexander Suh,
Wesley C. Warren, Mark Yandell, M. Thomas P. Gilbert, and Michael D.
Shapiro
G3: Genes | Genomes | Genetics May 2018 8: 1391–1398 15
 INVESTIG ATION

RAD Sequencing and a Hybrid Antarctic

Fur Seal Genome Assembly Reveal Rapidly
Decaying Linkage Disequilibrium, Global
Population Structure and Evidence for
Inbreeding
Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório,
Jaume Forcada, Ann-Christin Polikeit, Simon D. Goldsworthy, Michael E. Goebel,
Jörn Kalinowski, Jochen B. W. Wolf, and Joseph I. Hoffman
G3: Genes | Genomes | Genetics August 2018 8: 2709–2722

EDITORS’ NOTE Humble et al. generated a large restriction site associated

DNA (RAD) sequence dataset for the Antarctic fur seal, which—combined
with an improved genome assembly—shows evidence of rapid linkage
disequilibrium decay, appreciable variation in inbreeding, and the presence
of global population structure. These findings enrich our understanding of
an important marine top predator, providing insights into both the impact of
commercial hunting and the subsequent recovery of the species.

ABSTRACT Recent advances in high throughput sequencing have

transformed the study of wild organisms by facilitating the generation of
high quality genome assemblies and dense genetic marker datasets. These
resources have the potential to significantly advance our understanding
of diverse phenomena at the level of species, populations and individuals,
ranging from patterns of synteny through rates of linkage disequilibrium (LD)
decay and population structure to individual inbreeding. Consequently, we
used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus
gazella) genome assembly and genotyped 83 individuals from six populations
using restriction site associated DNA (RAD) sequencing. The resulting hybrid
genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided
clear evidence for the conservation of large chromosomal segments between
the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively
sampled population of South Georgia, we found that LD decayed rapidly,
reaching the background level by around 400 kb, consistent with other
vertebrates but at odds with the notion that fur seals experienced a strong
historical bottleneck. We also found evidence for population structuring, with
four main Antarctic island groups being resolved. Finally, appreciable variance
in individual inbreeding could be detected, reflecting the strong polygyny and
site fidelity of the species. Overall, our study contributes important resources
for future genomic studies of fur seals and other pinnipeds while also
providing a clear example of how high throughput sequencing can generate
diverse biological insights at multiple levels of organization.

16
GENOME DIVE A young Antarctic fur seal (Arctocephalus gazella) playing in the
waters of Bird Island, South Georgia during the 2016 breeding season.
Photo: John Dickens.

17
 MULTIPARENTAL POPUL ATIONS

Coping-Style Behavior Identified by a Survey of

Parent-of-Origin Effects in the Rat
Carme Mont, Polinka Hernandez-Pliego, Toni Cañete, Ignasi Oliveras, Cristóbal Río-
Álamos, Gloria Blázquez, Regina López-Aumatell, Esther Martínez-Membrives, Adolf
Tobeña, Jonathan Flint, Alberto Fernández-Teruel, and Richard Mott
G3: Genes | Genomes | Genetics October 2018 8: 3283–3291

EDITORS’ NOTE Mont et al. show that the heritability of most complex
traits in outbred laboratory rats contain a component that can be attributed
to parent-of-origin effects. In particular, behaviors relating to coping style
are particularly enriched for such effects. The authors confirm these findings
through an independent experiment involving a reciprocal cross of divergent
rat strains. Their results suggest evaluating parent-of-origin effects on coping-
style behavior could be warranted in other species, including humans.

ABSTRACT In this study we investigate the effects of parent of origin on

complex traits in the laboratory rat, with a focus on coping style behavior in
stressful situations. We develop theory, based on earlier work, to partition
heritability into a component due to a combination of parent of origin,
maternal, paternal and shared environment, and another component
that estimates classical additive genetic variance. We use this theory to
investigate the effects on heritability of the parental origin of alleles in 798
outbred heterogeneous stock rats across 199 complex traits. Parent-of-
origin-like heritability was on average 2.7 fold larger than classical additive
heritability. Among the phenotypes with the most enhanced parent-of-origin
heritability were 10 coping style behaviors, with average 3.2 fold heritability
enrichment. To confirm these findings on coping behavior, and to eliminate the
possibility that the parent of origin effects are due to confounding with shared
environment, we performed a reciprocal F1 cross between the behaviorally
divergent RHA and RLA rat strains. We observed parent-of-origin effects on
F1 rat anxiety/coping-related behavior in the Elevated Zero Maze test. Our
study is the first to assess genetic parent-of-origin effects in rats, and confirm
earlier findings in mice that such effects influence coping and impulsive
behavior, and suggest these effects might be significant in other mammals,
including humans.

18
 discover

SERIES
at the GSA Journals
MULTIPARENTAL GENOMIC
POPULATIONS PREDICTION

The basic idea is simple: combine the
strength of the experimental system
with the genetic diversity of the target
population. Rather than choose two
inbred lines or two phenotypically divergent
individuals as founders of a genetic
reference panel, choose eight—or
twenty-five. We refer to this broad set of
genetic reference panels as multiparental
populations. This collection fosters
discussion about the genetic inferences
made from MPPs, including the best ways
to analyze the data and how to extend
these inferences to natural populations.
Genomic Prediction as a field was
launched by a landmark GENETICS
paper authored by Meuwissen, Hayes,
and Goddard in 2001. The premise was
to use genotypic information to predict
breeding values for particular phenotypes
without specific knowledge of the
individual genes contributing to that trait.
These methodologies have since been
used in human genetics to predict disease
risk and other phenotypic outcomes. The
goal of the collection is to stimulate
discussion about the different techniques
used in the community and to examine
data that would further the discussions.

These cross-journal, ongoing series feature methodologies,

datasets, and insights on exciting topics in complex trait
research. Both collections accept submissions on a rolling
basis, so submit your paper today.
genetics.org/content/multiparental_populations
genetics.org/content/genomic-prediction 19
 MULTIPARENTAL POPUL ATIONS

A Genomic Reference Panel for Drosophila

serrata
Adam J. Reddiex, Scott L. Allen, and Stephen F. Chenoweth
G3: Genes | Genomes | Genetics April 2018 8: 1335–1346

EDITORS’ NOTE The availability of robust genomic references for different

species of Drosophila paves the way for greater understanding of population
genetics and evolutionary biology. Reddiex et al. present a collection of
110 resequenced inbred lines of the Australian Drosophila serrata. Their
sequencing work gives insight into the population structure within this species
and allows for future genome-wide association studies to be performed,
expanding the population genomic and quantitative genetic studies possible
in the Drosophila genus.

ABSTRACT Here we describe a collection of re-sequenced inbred lines

of Drosophila serrata, sampled from a natural population situated deep
within the species endemic distribution in Brisbane, Australia. D. serrata is
a member of the speciose montium group whose members inhabit much of
south east Asia and has been well studied for aspects of climatic adaptation,
sexual selection, sexual dimorphism, and mate recognition. We sequenced
110 lines that were inbred via 17-20 generations of full-sib mating at an
average coverage of 23.5x with paired-end Illumina reads. 15,228,692 biallelic
SNPs passed quality control after being called using the Joint Genotyper for
Inbred Lines (JGIL). Inbreeding was highly effective and the average levels of
residual heterozygosity (0.86%) were well below theoretical expectations. As
expected, linkage disequilibrium decayed rapidly, with r2 dropping below 0.1
within 100 base pairs. With the exception of four closely related pairs of lines
which may have been due to technical errors, there was no statistical support
for population substructure. Consistent with other endemic populations of
other Drosophila species, preliminary population genetic analyses revealed
high nucleotide diversity and, on average, negative Tajima’s D values. A
preliminary GWAS was performed on a cuticular hydrocarbon trait, 2-Me-
C28 revealing 4 SNPs passing Bonferroni significance residing in or near
genes. One gene Cht9 may be involved in the transport of CHCs from the
site of production (oenocytes) to the cuticle. Our panel will facilitate broader
population genomic and quantitative genetic studies of this species and
serve as an important complement to existing D. melanogaster panels that
can be used to test for the conservation of genetic architectures across the
Drosophila genus.

20
 GENOMIC PREDICTION

DEEP LEARNING Maize ears from the International Maize and Wheat
Improvement Center’s (CIMMYT) maize germplasm bank. Montesinos-López et
al. used deep learning neural network methods for genomic predictions of maize
and wheat plant breeding data. They conclude that the deep learning methods can
be a powerful complement of classic genomic-enabled prediction tools and other
analysis strategies.
Photo: CIMMYT.

Multi-environment Genomic Prediction of Plant Traits Using Deep

Learners With Dense Architecture
Abelardo Montesinos-López, Osval A. Montesinos-López, Daniel
Gianola, José Crossa, and Carlos M. Hernández-Suárez
G3: Genes | Genomes | Genetics December 2018 8: 3813–3828 21
 INVESTIG ATION

Comparative Genomics of Aspergillus flavus S

and L Morphotypes Yield Insights into Niche
Adaptation
Mana Ohkura, Peter J. Cotty, and Marc J. Orbach
G3: Genes | Genomes | Genetics December 2018 8: 3915–3930

EDITORS’ NOTE Aspergillus flavus is the causal agent for aflatoxin crop
contamination and consists of isolates with two distinct morphologies—S
and L—that also differ in toxigenicity. Ohkura et al. identified structural and
gene content differences between the morphotypes, including a >530 kb
inversion, as well as differences in proteins involved in nutrient metabolism,
nutrient acquisition, antimicrobial defense, and evasion of host immunity.
Their findings indicate the genomes of the two morphotypes differ beyond
developmental genes and have diverged to adapt to different niches. Based
on the differences in morphology and genomic content, they hypothesize the
S and L morphotypes are adapted to the soil and phyllosphere, respectively.

ABSTRACT Aspergillus flavus, the primary causal agent for aflatoxin

contamination on crops, consists of isolates with two distinct morphologies:
isolates of the S morphotype produce numerous small sclerotia and lower
numbers of conidia while isolates of the L morphotype produce fewer large
sclerotia and abundant conidia. The morphotypes also differ in aflatoxin
production with S isolates consistently producing high concentrations of
aflatoxin, whereas L isolates range from atoxigenic to highly toxigenic. The
production of abundant sclerotia by the S morphotype suggests adaptation
for long-term survival in the soil, whereas the production of abundant
conidia by the L morphotype suggests adaptation for aerial dispersal to the
phyllosphere. To identify genomic changes that support differential niche
adaptation, the sequences of three S and three L morphotype isolates
were compared. Differences in genome structure and gene content were
identified between the morphotypes. A >530 kb inversion between the
morphotypes affect a secondary metabolite gene cluster and a cutinase
gene. The morphotypes also differed in proteins predicted to be involved
in carbon/nitrogen metabolism, iron acquisition, antimicrobial defense, and
evasion of host immunity. The S morphotype genomes contained more intact
secondary metabolite clusters indicating there is higher selection pressure
to maintain secondary metabolism in the soil and that it is not limited to
aflatoxin production. The L morphotype genomes were enriched in amino
acid transporters, suggesting efficient nitrogen transport may be critical in the
nutrient limited phyllosphere. These findings indicate the genomes of the two
morphotypes differ beyond developmental genes and have diverged as they
adapted to their respective niches.

22
 ZOMBIE ENTRY Unidentified dead fly infected with the insect-pathogenic
fungus Entomophthora muscae s.l. (Subphylum Entomophthoromycotina: order
Entomophthorales). The fungus has taken over the behavior of the fly just before
death and forced it to bite on to the substrate and lift its wings unnaturally away
from the abdomen. The fungus can be seen as the white mass growing out from the
swollen abdomen where conidiophores are forcibly discharging infective conidia
that can infect new flies. Arnesen et al. investigate the presence of subtilisin-like
serine proteases in such species, which are enzymes that allow fungi to penetrate the
host cuticle and gain entry to the soft tissues inside.
Photo: Jens H. Petersen.

Early Diverging Insect-Pathogenic Fungi of the Order

Entomophthorales Possess Diverse and Unique Subtilisin-Like
Serine Proteases
Jonathan A. Arnesen, Joanna Małagocka, Andrii Gryganskyi, Igor V.
Grigoriev, Kerstin Voigt, Jason E. Stajich, and Henrik H. De Fine Licht
G3: Genes | Genomes | Genetics October 2018 8: 3311–3319
23
 INVESTIG ATION

Hierarchical Assessment of Mutation Properties

in Daphnia magna
Sarah Eberle, Djeneba Dezoumbe, Rhegan McGregor, Shane Kinzer, Whitney Raver,
Sarah Schaack, and Leigh C. Latta
G3: Genes | Genomes | Genetics November 2018 8: 3481–3487

EDITORS’ NOTE Spontaneous mutations are the ultimate source of genetic

variation, but our understanding of the context-dependence of mutation
parameters is still limited. Eberle et al. investigated genotypic and trait-specific
variation in susceptibility to the effects of mutation in Daphnia magna. They
found that behavioral traits are particularly susceptible to deleterious mutation
accumulation. Additionally, the ancestral selection history of a population
influences the susceptibility of individual genotypes to deleterious mutation
accumulation. Their results suggest susceptibility to mutation accumulation
may vary widely at several levels of biological hierarchy.

ABSTRACT Understanding the context dependence of spontaneous

mutations is crucial to predicting evolutionary trajectories. In this experiment,
the impact of genetic background and trait type on mutational susceptibility
was investigated. Mutant and non-mutant lines of six unique genotypes from
two populations of Daphnia magna were phenotypically assayed using a
common-garden experiment. Morphological, life-history, and behavioral traits
were measured, and estimates of the mutation parameters were generated.
The mutation parameters varied between the populations and among
genotypes, suggesting differential susceptibility to mutation depending upon
genomic background. Traits also varied in their susceptibility to mutation, with
behavioral traits evolving more rapidly than life-history and morphological
traits. These results may reflect the unique selection histories of these
populations.

24
 GENOME REPORT

Highly Contiguous Genome Assemblies of 15

Drosophila Species Generated Using Nanopore
Sequencing
Danny E. Miller, Cynthia Staber, Julia Zeitlinger, and R. Scott Hawley
G3: Genes | Genomes | Genetics October 2018 8: 3131–3141

EDITORS’ NOTE Miller et al. used Oxford Nanopore single-molecule

sequencing technology to sequence and assemble the genomes of fifteen
Drosophila species. This approach resulted in highly-contiguous genome
assemblies with relative ease and low expense, at an average cost of $1,000
(USD) per genome. The resulting assemblies spanned a substantial number
of gaps in currently published reference genomes.

ABSTRACT The Drosophila genus is a unique group containing a wide

range of species that occupy diverse ecosystems. In addition to the most
widely studied species, Drosophila melanogaster, many other members
in this genus also possess a well-developed set of genetic tools. Indeed,
high-quality genomes exist for several species within the genus, facilitating
studies of the function and evolution of cis-regulatory regions and proteins
by allowing comparisons across at least 50 million years of evolution. Yet,
the available genomes still fail to capture much of the substantial genetic
diversity within the Drosophila genus. We have therefore tested protocols
to rapidly and inexpensively sequence and assemble the genome from
any Drosophila species using single-molecule sequencing technology
from Oxford Nanopore. Here, we use this technology to present highly
contiguous genome assemblies of 15 Drosophila species: 10 of the 12
originally sequenced Drosophila species (ananassae, erecta, mojavensis,
persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba),
four additional species that had previously reported assemblies (biarmipes,
bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria).
Genomes were generated from an average of 29x depth-of-coverage data
that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent
alignment of contigs from the published reference genomes demonstrates
that our assemblies could be used to close over 60% of the gaps present in
the currently published reference genomes. Importantly, the materials and
reagents cost for each genome was approximately $1,000 (USD). This study
demonstrates the power and cost-effectiveness of long-read sequencing for
genome assembly in Drosophila and provides a framework for the affordable
sequencing and assembly of additional Drosophila genomes.

25
 INVESTIG ATION

A High-Resolution Genetic Map for the

Laboratory Rat
John Littrell, Shirng-Wern Tsaih, Amelie Baud, Pasi Rastas, Leah Solberg-Woods,
and Michael J. Flister
G3: Genes | Genomes | Genetics July 2018 8: 2241–2248

EDITORS’ NOTE Studying complex traits requires an accurate genetic map

of the organism in question. Previously, the available genetic map for rat was
low-resolution, far less complete than human and mouse maps, and ill-suited
for complex trait studies. Littrell et al. present a much higher-resolution
genetic map, along with sex-specific genetic maps. This updated map will
facilitate the study of complex traits and recombination rates in the rat.

ABSTRACT An accurate and high-resolution genetic map is critical for

mapping complex traits, yet the resolution of the current rat genetic map
is far lower than human and mouse, and has not been updated since the
original Jensen-Seaman map in 2004. For the first time, we have refined
the rat genetic map to sub-centimorgan (cM) resolution (<0.02 cM) by using
95,769 genetic markers and 870 informative meioses from a cohort of 528
heterogeneous stock (HS) rats. Global recombination rates in the revised
sex-averaged map (0.66 cM/Mb) did not differ compared to the historical map
(0.65 cM/Mb); however, substantial refinement was made to the localization of
highly recombinant regions within the revised map. Also for the first time, sex-
specific rat genetic maps were generated, which revealed both genomewide
and fine-scale variation in recombination rates between male and female
rats. Reanalysis of multiple quantitative trait loci (QTL) using the historical and
refined rat genetic maps demonstrated marked changes to QTL localization,
shape, and effect size. As a resource to the rat research community, we have
provided revised centimorgan positions for all physical positions within the
rat genome and commonly used genetic markers for trait mapping, including
44,828 SSLP markers and the RATDIV genotyping array. Collectively, this
study provides a substantial improvement to the rat genetic map and an
unprecedented resource for analysis of complex traits and recombination in
the rat.

26
 Black lion tamarins from São Paulo Zoo. This endangered species is a New World
monkey endemic to the Atlantic rainforest of São Paulo State, Brazil. It is estimated
that there are just a thousand wild individuals, and reproducing the species in
captivity is reportedly difficult. Domingues de Freitas et al. report genomic data for
the black lion tamarin and a Callitrichidae phylogeny. Such data can help address
important biological and conservation questions and may assist in establishing an
integrated conservation program for this primate species.
Photo: Paulo Gil; Courtesy of FPZSP (São Paulo Zoological Park Foundation).

Next-Generation Sequencing of the Complete Mitochondrial

Genome of the Endangered Species Black Lion Tamarin
Leontopithecus chrysopygus (Primates) and Mitogenomic
Phylogeny Focusing on the Callitrichidae Family
Patrícia Domingues de Freitas, Fernando Luis Mendez, Karla Chávez-
Congrains, Pedro Manoel Galetti, Luiz Lehmann Coutinho, Alcides
Pissinatti, and Carlos Daniel Bustamante
27
G3: Genes | Genomes | Genetics June 2018 8: 1985–1991