!"#$ !

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A showcase of research and scho|arsh|p
|n se|ected art|c|es from 2013
EDITOR-IN-CHIEF
Brenda J. Andrews
University of Toronto
EXECUTIVE EDITOR
Tracey DePellegrin
DEPUTY EDITOR-
IN-CHIEF, COMPLEX
TRAITS
Dirk-Jan de Koning
Swedish University of
Agricultural Sciences
DEPUTY EDITOR-
IN-CHIEF, HUMAN
GENETICS
Stephen W. Scherer
The Hospital for Sick
Children & University
of Toronto
SENIOR EDITORS
Katrien M. Devos
University of Georgia
Susan L. Forsburg
University of Southern
California
R. Scott Hawley
Stowers lnstitute for
Medical Research
Stephen l. Wright
University of Toronto
ASSISTANT EDITOR
Cristy Gelling
ASSISTANT
MANAGING EDITOR
Ruth lsaacson
2013/2014
Ed|tor|a| Board
ASSOCIATE EDITORS
Danika L. Bannasch
University of California,
Davis
Judith Berman
University of Minnesota
& Tel Aviv University
James A. Birchler
University of Missouri
Charles Boone
University of Toronto
Michael Boutros
DKFZ & University of
Heidelberg
Rachel Brem
Buck lnstitute for
Research on Aging
Julie Brill
The Hospital for Sick
Children
David T. Burke
University of Michigan
Medical School
Rita M. Cantor
University of California,
Los Angeles
Susan Celniker
Lawrence Berkeley
National Laboratory
Aravinda Chakravarti
Johns Hopkins
University School of
Medicine
J. Michael Cherry
Stanford University
Barak A. Cohen
Washington University
School of Medicine
Josep M. Comeron
University of lowa
Gloria M. Coruzzi
New York University
William S. Davidson
Simon Fraser
University
Kelly Dawe
University of Georgia
Job Dekker
University of
Massachusetts
Medical School
Fred S. Dietrich
Duke University
Medical Center
Rebecca W. Doerge
Purdue University
Aime M. Dudley
Pacifc Northwest
Diabetes Research
lnstitute
Jay C. Dunlap
Dartmouth Medical
School
Mark Estelle
University of California,
San Diego
Justin D. Faris
USDA-ARS Cereal
Crops Research Unit
David S. Fay
University of Wyoming
Justin C. Fay
Washington University
in St. Louis
Audrey Gasch
University of
Wisconsin-Madison
Bikram S. Gill
Kansas State
University
David J. Gresham
New York University
David J. Grunwald
The University of Utah
Kris Gunsalus
New York University
lra M. Hall
University of virginia
Jay R. Hesselberth
University of Colorado
School of Medicine
Charles S. Hoffman
Boston College
James B. Holland
USDA & North Carolina
State University
Emma Huang
CSlRO
Timothy R. Hughes
University of Toronto
Scott A. Jackson
University of Georgia
Sue L. Jaspersen
Stowers lnstitute for
Medical Research
Stephen L. Johnson
Washington University
School of Medicine
Nicholas Katsanis
Duke University
Cynthia Kenyon
University of California,
San Francisco
John K. Kim
University of Michigan
Yuseob Kim
Ewha Womans
University
Rob J. Kulathinal
Temple University
Siu Sylvia Lee
Cornell University
Howard D. Lipshitz
University of Toronto
Andrew S. McCallion
Johns Hopkins
University School of
Medicine
John H. McCusker
Duke University
Medical Center
Kim S. McKim
Rutgers University
Donald G. Moerman
University of British
Columbia
Corey Nislow
The University of
British Columbia
Andrew H. Paterson
University of Georgia
Peter Pfaffelhuber
University of Freiburg
Patrick C. Phillips
University of Oregon
Eric M. Phizicky
University of Rochester
Medical Center
Craig S. Pikaard
lndiana University
David D. Pollock
University of Colorado
School of Medicine
Julia E. Richards
University of Michigan
School of Public
Health
Jasper Rine
University of California,
Berkeley
Antonis Rokas
vanderbilt University
Fritz P. Roth
University of Toronto
Matthew S. Sachs
Texas A&M University
Helen K. Salz
Case Western Reserve
University
Michael J. Scanlon
Cornell University
David S. Schneider
Stanford University
Robert A. Sclafani
University of Colorado
School of Medicine
Marcus B. Smolka
Cornell University
Lars M. Steinmetz
European Molecular
Biology Laboratory &
Stanford University
Hidenori Tachida
Kyushu University
David W. Threadgill
Texas A&M University
Sarah A. Tishkoff
University of
Pennsylvania
Olga Troyanskaya
Princeton University
Mike Tyers
Universit de Montral
veronica J. vieland
Nationwide Children's
Hospital
Marian Walhout
University of
Massachusetts
Medical School
Jonathan F. Wendel
lowa State University
Brian S. Yandell
University of
Wisconsin-Madison
Zhenbiao Yang
University of California,
Riverside
Nevin D. Young
University of Minnesota
Dani Zamir
The Hebrew University
of Jerusalem
Monique Zetka
McGill University
2
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,()'*%+' 9':;'*<' %3 !"##$%&'( *+&(",-&& ./
Z|n|ng Wang, Dong Zhang, |y|n Wang, u Tan, Hu| Guo, and
Andrew H. Paterson
!"# !%&%' ( !%&)*%' ( !%&%+,-' October 2013 3:1759-1767
COTTON HARVEST One useful tool published in G3 was a whole genome
marker map for cotton that integrates information from DNA markers,
QTLs, and the reference genome sequence. Its density of one locus per 15.6 kb
is ve times higher than the most dense previously published map of cotton.
Te map will help advance molecular breeding and other studies of this
important crop.
Image credit: Cotton Harvest by Kimberly Vardeman
www.fickr.com/photos/kimberlykv/6288743600/
Available under a Creative Commons Attribution 2.0 Generic license.
3
S|nce |ts |aunch |n summer 2011, G3 has frm|y
estab||shed |tse|f as a forum for fnd|ngs and resources
usefu| to the genet|cs research commun|ty, regard|ess
of perce|ved |mpact or nove|ty. To ce|ebrate the
success and hard work of our authors, ed|tors, and
rev|ewers, we`re sh|n|ng a spot||ght on a se|ect|on of
exce||ent papers pub||shed |n G3 dur|ng 2013.
G3 f||s an |mportant n|che as a soc|ety-run, open-
access journa| w|th the same h|gh standards for
sc|ent|fc r|gor-and the same qua||ty of rev|ews-as |ts
s|ster journa| GENETlOS, p|us a t|me-to-frst-dec|s|on
of about a month. And because our journa|s are
ded|cated to genet|cs and genom|cs, G3 papers reach
your co||eagues and rece|ve the attent|on they deserve.
GENETlOS and G3 both feature ed|tor|a| boards
compr|sed of your peers, |eaders |n the|r fe|ds who
make the dec|s|ons on a|| papers. ||ke GENETlOS, G3
requ|res a|| pr|mary data assoc|ated w|th a paper to
be ava||ab|e. Both journa|s have art|c|e ||nks to mode|
organ|sm databases ||ke WormBase, SGD, and F|yBase.
So what`s the pr|mary d|st|nct|on between GSA`s
s|ster journa|s? To warrant pub||cat|on |n G3, the
research doesn`t have to be broad|y s|gn|fcant or
have a h|gh degree of nove|ty; rather, G3 requ|res
s|mp|y that the work |s h|gh-qua||ty and potent|a||y
usefu|. So even |f your paper |s |mportant to a narrow
group of researchers, |t`s |mportant to G3!
Work pub||shed |n G3 |s |ncred|b|y d|verse, spann|ng
d|sc|p||nes from agr|cu|ture to med|c|ne, projects from
|ab tra|n|ng too|s to v|ta| research resources ||ke the
He|a genome sequence, p|us the genet|cs of emerg|ng
mode| organ|sms. As we cont|nue to |nnovate, v|s|t G3
to read the |atest papers and subm|t your own work.
Brenda J. Andrews
Ed|tor-|n-Oh|ef,
G3: Genes Genomes Genet|cs
G3: Genes | Genomes | Genetics
gathers momentum in 2013
ON THE COVER Tis depiction of the genomic landscape of a HeLa Kyoto cell line
illustrates the multitude of structural variations compared to the human reference genome
(see p. 6). Image courtesy of Petra Riedinger, Paul Teodor Pyl, and Jonathan Landry.
4
=+/>?*' @%;0 A%01 %* 5$' 30%*5 <%B'0 %3 )C-CD=49 %0 )EF
GENETlOS and G3: Genes Genomes Genet|cs |nv|te you to subm|t or|g|na|
|mages for our frst ever Oover Art Oontest. One w|nn|ng |mage w||| be se|ected
for each journa| and featured on the cover of an upcom|ng |ssue, and w||| a|so
be repr|nted on postcards and other mater|a|s to be d|str|buted by GSA.
Our favor|te covers tend to use str|k|ng co|ors, shapes, textures, or
present a fam|||ar organ|sm |n a un|que way. You can a|so subm|t
or|g|na| art, draw|ngs, or just a c|ever photo! Browse past GENETlOS
and G3 covers at www.genet|cs.org/content/by/year/by/cover and
www.g3journa|.org/content/by/year/by/cover.
Subm|ss|ons w||| be judged by a pane| of journa| ed|tors and staff a|ong w|th
representat|ves from the Genet|cs Soc|ety of Amer|ca`s Pub||cat|ons Oomm|ttee
and Board of D|rectors. For contest ru|es, subm|ss|on gu|de||nes, and FAOs,
p|ease see www.genet|cs.org/s|te/m|sc/OoverOontest.xhtm| and ema|| any
quest|ons to genet|cs-gsa@thegsajourna|s.org. We |ook forward to see|ng
your best sc|ence |mages!
COvER ART CONTEST
5
l NvESTl GATl ONS
Extensive Transcript Diversity and Novel
Upstream Open Reading Frame Regulation
in Yeast
G/0& #/'0* /*8 .?<$/'& 9*@8'0
!"# !%&%' ( !%&)*%' ( !%&%+,-' February 2013 3:343-352
EDITORS NOTE Sequences |n the untrans|ated reg|on (TR} of a transcr|pt
can contro| trans|at|on, subce||u|ar |oca||zat|on, and transcr|pt stab|||ty. TRs
often change through the use of d|fferent|a| transcr|pt|on start s|tes and the
resu|t|ng d|fferent|a| transcr|pt ends. Th|s study exam|ned not on|y wh|ch
and how many transcr|pts have a|ternate forms, but a|so the ways |n wh|ch
d|fferent|a| ends vary across many cond|t|ons and affect gene express|on.
Bes|des serv|ng as a va|uab|e resource, th|s study revea|ed that a|ternat|ve
TRs are pervas|ve |n yeast. Th|s work a|so revea|ed that sma|| upstream
open read|ng frames (uORFs}, wh|ch were known prev|ous|y to be negat|ve
regu|ators of gene express|on, can serve as pos|t|ve regu|ators of gene
express|on, |nd|cat|ng a d|verse ro|e for these e|ements |n gene regu|at|on.
ABSTRACT To understand the d|vers|ty of transcr|pts |n yeast (./--0/1)*2-%'
-%1%3,',/%} we ana|yzed the transcr|pt|ona| |andscapes for ce||s grown under
18 d|fferent env|ronmenta| cond|t|ons. Each samp|e was ana|yzed us|ng RNA-
sequenc|ng, and a tota| of 670,446,084 un|que|y mapped reads and 377,263
po|y-adeny|ated end tags were produced. Oons|stent w|th prev|ous stud|es,
we fnd that the major|ty of yeast genes are expressed under one or more
d|fferent cond|t|ons. By d|rect|y compar|ng the 5' and 3' ends of the transcr|bed
reg|ons, we fnd extens|ve d|fferences |n transcr|pt ends across many cond|t|ons,
espec|a||y those of stat|onary phase, growth |n grape ju|ce, and sa|t st|mu|at|on,
suggest|ng d|fferent|a| cho|ce of transcr|pt|on start and stop s|tes |s pervas|ve
|n yeast. Re|at|ve to the exponent|a| growth cond|t|on (,4%4, YPAD}, transcr|pts
d|ffer|ng at the 5' ends and 3' ends are pred|cted to d|ffer |n the|r annotated start
codon |n 21 genes and the|r annotated stop codon |n 63 genes. Many (431}
upstream open read|ng frames (uORFs} are found |n a|ternate 5' ends and are
s|gn|fcant|y enr|ched |n transcr|pts produced dur|ng the sa|t response. Mutat|ona|
ana|ys|s of fve genes w|th uORFs revea|ed that two sets of uORFs |ncrease
the express|on of a reporter construct, |nd|cat|ng a ro|e |n act|vat|on wh|ch had
not been reported prev|ous|y, whereas two other uORFs decreased express|on.
ln add|t|on, RNA b|nd|ng prote|n mot|fs are stat|st|ca||y enr|ched for a|ternate
ends under many cond|t|ons. Overa||, these resu|ts demonstrate enormous
d|vers|ty of transcr|pt ends, and that th|s heterogene|ty |s regu|ated under d|fferent
env|ronmenta| cond|t|ons. Moreover, transcr|pt end d|vers|ty has |mportant
b|o|og|ca| |mp||cat|ons for the regu|at|on of gene express|on. ln add|t|on, our
data a|so serve as a va|uab|e resource for the sc|ent|fc commun|ty.
6
l NvESTl GATl ONS
Te Genomic and Transcriptomic Landscape
of a HeLa Cell Line
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!"# !%&%' ( !%&)*%' ( !%&%+,-' August 2013 3:1213-1224
EDITORS NOTE He|a was the frst-and rema|ns the most w|de|y used-
ce|| ||ne for study|ng ce||u|ar and mo|ecu|ar human b|o|ogy. Yet unt|| 2013,
researchers re||ed on the human reference genome when des|gn|ng and
|nterpret|ng He|a exper|ments. Th|s study presented the frst comprehens|ve
genom|c dataset for He|a ce||s, prov|d|ng cruc|a| commun|ty resources and
revea||ng the ce||s` str|k|ng|y aberrant genom|c features.
||ke a|| research pub||shed |n G3, data from the study were or|g|na||y made free|y
ava||ab|e, wh|ch sparked a pub||c d|a|ogue on the hand||ng of human genom|cs
data. The fam||y of Henr|etta |acks, from whose tumor the or|g|na| He|a ce||s
were der|ved, vo|ced concerns about how the ava||ab|||ty of these data wou|d
affect the|r pr|vacy. ln response, the authors vo|untar||y w|thhe|d pub||c access
to the dataset and offered to work w|th the fam||y toward a mutua||y acceptab|e
so|ut|on. NlH offc|a|s and the |acks fam||y then came to an agreement to
a||ow b|omed|ca| researchers contro||ed access to the data v|a NOBl`s dbGaP.
To he|p foster open d|scuss|on about the broad |mpact of genom|cs research,
GSA comm|ss|oned three Perspect|ves wr|tten by b|oeth|c|sts and sc|ent|sts
prom|nent |n the eth|ca|, sc|ent|fc, and |ega| aspects of human genom|cs,
pr|vacy, consent, po||cy, and data access.
ABSTRACT He|a |s the most w|de|y used mode| ce|| ||ne for study|ng human
ce||u|ar and mo|ecu|ar b|o|ogy. To date, no genom|c reference for th|s ce|| ||ne has
been re|eased, and exper|ments have re||ed on the human reference genome.
Effect|ve des|gn and |nterpretat|on of mo|ecu|ar genet|c stud|es performed us|ng
He|a ce||s requ|re accurate genom|c |nformat|on. Here we present a deta||ed
genom|c and transcr|ptom|c character|zat|on of a He|a ce|| ||ne. We performed
DNA and RNA sequenc|ng of a He|a Kyoto ce|| ||ne and ana|yzed |ts mutat|ona|
portfo||o and gene express|on prof|e. Segmentat|on of the genome accord|ng to
copy number revea|ed a remarkab|y h|gh |eve| of aneup|o|dy and numerous |arge
structura| var|ants at unprecedented reso|ut|on. Some of the extens|ve genom|c
rearrangements are |nd|cat|ve of catastroph|c chromosome shatter|ng, known as
chromothr|ps|s. Our ana|ys|s of the He|a gene express|on prof|e revea|ed that
severa| pathways, |nc|ud|ng ce|| cyc|e and DNA repa|r, exh|b|t s|gn|fcant|y d|fferent
express|on patterns from those |n norma| human t|ssues. Our resu|ts prov|de the
frst deta||ed account of genom|c var|ants |n the He|a genome, y|e|d|ng |ns|ght
|nto the|r |mpact on gene express|on and ce||u|ar funct|on as we|| as the|r or|g|ns.
Th|s study underscores the |mportance of account|ng for the str|k|ng|y aberrant
character|st|cs of He|a ce||s when des|gn|ng and |nterpret|ng exper|ments, and
has |mp||cat|ons for the use of He|a as a mode| of human b|o|ogy.
7
l NvESTl GATl ONS
Imputation-Based Genomic Coverage
Assessments of Current Human
Genotyping Arrays
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!"# !%&%' ( !%&)*%' ( !%&%+,-' October 2013 3:1795-1807
EDITORS NOTE Th|s study est|mated the coverage of e|ght ava||ab|e human
SNP m|croarrays us|ng genome-w|de |mputat|on and phase 1 of the 1000
Genomes Project. The resu|ts w||| he|p researchers choose from among the
many ava||ab|e arrays, based on the|r genotyp|ng budget, number of ava||ab|e
samp|es, and overa|| research goa|s.
ABSTRACT M|croarray s|ng|e-nuc|eot|de po|ymorph|sm genotyp|ng, comb|ned
w|th |mputat|on of untyped var|ants, has been w|de|y adopted as an effc|ent
means to |nterrogate var|at|on across the human genome. 'Genom|c coverage"
|s the tota| proport|on of genom|c var|at|on captured by an array, e|ther by
d|rect observat|on or through an |nd|rect means such as ||nkage d|sequ|||br|um
or |mputat|on. We have performed |mputat|on-based genom|c coverage
assessments of e|ght current genotyp|ng arrays that assay from ~0.3 to
~5 m||||on var|ants. Ooverage was determ|ned separate|y |n each of the four
cont|nenta| ancestry groups |n the 1000 Genomes Project phase 1 re|ease.
We used the subset of 1000 Genomes var|ants present on each array to |mpute
the rema|n|ng var|ants and assessed coverage based on corre|at|on between
|mputed and observed a||e||c dosages. More than 75% of common var|ants
(m|nor a||e|e frequency > 0.05} are covered by a|| arrays |n a|| groups except
for Afr|can ancestry, and up to ~90% |n a|| ancestr|es for the h|ghest dens|ty
arrays. ln contrast, |ess than 40% of |ess common var|ants (0.01 < m|nor
a||e|e frequency < 0.05} are covered by |ow dens|ty arrays |n a|| ancestr|es and
50-80% |n h|gh dens|ty arrays, depend|ng on ancestry. We a|so ca|cu|ated
genome-w|de power to detect var|ant-tra|t assoc|at|on |n a case-contro| des|gn,
across vary|ng samp|e s|zes, effect s|zes, and m|nor a||e|e frequency ranges,
and compare these array-based power est|mates w|th a hypothet|ca| array that
wou|d type a|| var|ants |n 1000 Genomes. These |mputat|on-based genom|c
coverage and power ana|yses are |ntended as a pract|ca| gu|de to researchers
p|ann|ng genet|c stud|es.
8
l NvESTl GATl ONS
Comparative Genomics of a Plant-Pathogenic
Fungus, Pyrenophora tritici-repentis,
Reveals Transduplication and the Impact
of Repeat Elements on Pathogenicity and
Population Divergence
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!"# !%&%' ( !%&)*%' ( !%&%+,-' January 2013 3:41-63
EDITORS NOTE Over the past ha|f century, tan spot has become one of
the most cost|y and rap|d|y-spread|ng d|seases |n certa|n wheat-grow|ng
reg|ons wor|dw|de. The |ncrease |n d|sease |nc|dence has been b|amed on
chang|ng agr|cu|tura| pract|ces favor|ng the propagat|on of the causat|ve
funga| agent 521%&)60)1/ +1,+,-,71%6%&+,' and the acqu|s|t|on of a v|ru|ence
factor v|a hor|zonta| gene transfer. These authors used comparat|ve genome
ana|yses to better understand the d|fferences between pathogen|c and
non-pathogen|c |so|ates. They conc|uded that pathogen|c|ty |n th|s system
||ke|y started w|th structura| changes to the genome fac|||tated by an |nfux of
transposab|e e|ements.
ABRIDGED ABSTRACT 521%&)60)1/ +1,+,-,71%6%&+,' |s a necrotroph|c fungus
causa| to the d|sease tan spot of wheat, whose contr|but|on to crop |oss has
|ncreased s|gn|fcant|y dur|ng the |ast few decades. Pathogen|c|ty by th|s
fungus |s attr|buted to the product|on of host-se|ect|ve tox|ns (HST}, wh|ch are
recogn|zed by the|r host |n a genotype-spec|fc manner. To better understand
the mechan|sms that have |ed to the |ncrease |n d|sease |nc|dence re|ated to
th|s pathogen, we sequenced the genomes of three 54 +1,+,-,71%6%&+,' |so|ates.
Exam|nat|on of gene-cod|ng reg|ons has prov|ded cand|date pathogen-spec|fc
prote|ns and revea|ed gene fam|||es that may p|ay a ro|e |n a necrotroph|c
||festy|e. Ana|ys|s of transposab|e e|ements suggests that the|r presence |n
the genome of pathogen|c |so|ates contr|butes to the creat|on of nove| genes,
effector d|vers|fcat|on, poss|b|e hor|zonta| gene transfer events, |dent|fed
copy number var|at|on, and the frst examp|e of transdup||cat|on by DNA
transposab|e e|ements |n fung|. Overa||, comparat|ve ana|ys|s of these genomes
prov|des ev|dence that pathogen|c|ty |n th|s spec|es arose through an |nfux
of transposab|e e|ements, wh|ch created a genet|ca||y fex|b|e |andscape that
can eas||y respond to env|ronmenta| changes.
9
l NvESTl GATl ONS
A High Fidelity Cell Lineage Tracing Method
for Obtaining Systematic Spatiotemporal Gene
Expression Patterns in Caenorhabditis elegans
,/*?'& JI ./<'K L'5'0 #'?78'22K J%;?7 )'B?05Q+/*K D$%+/7 6%@&'K /*8
N%M'05 SI #/5'075%*
!"# !%&%' ( !%&)*%' ( !%&%+,-' May 2013 3:851-863
EDITORS NOTE nderstand|ng where and when genes are turned on
and off |s a fundamenta| cha||enge |n deve|opmenta| b|o|ogy, w|th profound
|mp||cat|ons for human d|seases and cond|t|ons. Here the authors presented
a probab|||st|c computat|ona| method that creates h|gh-fde||ty express|on
maps from m|croscopy |mage data of deve|op|ng worms.
ABSTRACT Advances |n m|croscopy and fuorescent reporters have
a||owed us to detect the onset of gene express|on on a ce||-by-ce|| bas|s |n
a systemat|c fash|on. Th|s |nformat|on, however, |s often encoded |n |arge
repos|tor|es of |mages, and deve|op|ng ways to extract th|s spat|otempora|
express|on data |s a d|ffcu|t prob|em that often uses comp|ex doma|n-
spec|fc methods for each |nd|v|dua| data set. We present a more un|fed
approach that |ncorporates genera| prev|ous |nformat|on |nto a h|erarch|ca|
probab|||st|c mode| to extract spat|otempora| gene express|on from 4D
confoca| m|croscopy |mages of deve|op|ng 8/%&)10/9:,+,' %;%</&' embryos.
Th|s approach reduces the overa|| error rate of our automated ||neage trac|ng
p|pe||ne by 3.8-fo|d, a||ow|ng us to rout|ne|y fo||ow the 84 %;%</&' ||neage
to |ater stages of deve|opment, where |nd|v|dua| neurona| subspec|fcat|on
becomes apparent. n||ke prev|ous methods that often use custom
approaches that are organ|sm spec|fc, our method uses genera||zed ||near
mode|s and extens|ons of standard revers|b|e jump Markov cha|n Monte Oar|o
methods that can be read||y extended to other organ|sms for a var|ety of
b|o|og|ca| |nference prob|ems re|at|ng to ce|| fate spec|fcat|on. Th|s mode||ng
approach |s fex|b|e and prov|des tractab|e avenues for |ncorporat|ng
add|t|ona| prev|ous |nformat|on |nto the mode| for s|m||ar d|ffcu|t h|gh-fde||ty/
|ow error to|erance |mage ana|ys|s prob|ems for systemat|ca||y app||ed
genom|c exper|ments.
10
l NvESTl GATl ONS
EDITORS NOTE ln th|s pa|r of stud|es, m|cron-|eve| s|ze and shape tra|ts
were extracted from |mages of thousands of seed and seed||ng root samp|es
from =1/9,:)6',' recomb|nant |nbred ||nes. ln the G3 art|c|e, the authors
|dent|fed new seed morpho|ogy |oc| us|ng prec|se|y measured tra|ts from the
automated |mage ana|ys|s. ln the GENETlOS art|c|e, the authors used h|gh-
throughput comput|ng to |ncorporate the t|me ax|s |nto a OT| map of a p|ant
growth response to grav|ty.
Mapping Quantitative Trait Loci Afecting
Arabidopsis thaliana Seed Morphology Features
Extracted Computationally From Images
4/*8/<' NI .%%0'K ,/B?8 9I )0%*A/&&K -/5$/* ,I .?&&'0K /*8 C8>/0 LI 92/&8?*>
!"# !%&%' ( !%&)*%' ( !%&%+,-' January 2013 3:109-118
ABSTRACT Seeds are stud|ed to understand d|spersa| and estab||shment
of the next generat|on, as un|ts of agr|cu|tura| y|e|d, and for other |mportant
reasons. Thus, e|uc|dat|ng the genet|c arch|tecture of seed s|ze and shape
tra|ts w||| beneft bas|c and app||ed p|ant b|o|ogy research. Th|s study sought
quant|tat|ve tra|t |oc| (OT|} contro|||ng the s|ze and shape of =1/9,:)6',' +0/;,/&/
seeds by computat|ona| ana|ys|s of seed phenotypes |n recomb|nant |nbred
||nes der|ved from the sma||-seeded |andsberg %1%-+/ |arge-seeded Oape
verde ls|ands access|ons. On the order of 10
3
seeds from each recomb|nant
|nbred ||ne were automat|ca||y measured w|th fatbed photo scanners and
custom |mage ana|ys|s software. The e|ght s|gn|fcant OT| affect|ng seed area
exp|a|ned 63% of the var|at|on, and over|apped w|th fve of the s|x major-ax|s
(|ength} OT| and three of the fve m|nor-ax|s (w|dth} OT|, wh|ch accounted
for 57% and 38% of the var|at|on |n those tra|ts, respect|ve|y. Because the
Arab|dops|s seed |s exa|bum|nous, |ack|ng an endosperm at matur|ty, the
resu|ts are re|atab|e to embryo |ength and w|dth. The Ov| a||e|e genera||y
had a pos|t|ve effect of 2.6-4.0%. Ana|ys|s of var|ance showed her|tab|||ty
of the three tra|ts ranged between 60% and 73%. Repeat|ng the exper|ment
w|th 2.2 m||||on seeds from a separate harvest of the Rl| popu|at|on and
approx|mate|y 0.5 m||||on seeds from 92 near-|sogen|c ||nes confrmed the
aforement|oned resu|ts. Structured for down|oad are f|es conta|n|ng phenotype
measurements, a|| sets of seed |mages, and the seed tra|t measur|ng too|.
11
High-Troughput Computer Vision Introduces the
Time Axis to a Quantitative Trait Map of a
Plant Growth Response
4/*8/<' NI .%%0'K J%>/* 9I H%$*7%*K =&(@%;2 GA/1K .?0%* J?B*@K G/0& #I 60%+/*K
/*8 C8>/0 LI 92/&8?*>
!%&%+,-' November 2013 195:1077-1086
ABSTRACT Automated |mage acqu|s|t|on, a custom ana|ys|s a|gor|thm, and
a d|str|buted comput|ng resource were used to add t|me as a th|rd d|mens|on
to a quant|tat|ve tra|t |ocus (OT|} map for p|ant root grav|trop|sm, a mode|
growth response to an env|ronmenta| cue. D|g|ta| |mages of =1/9,:)6',' +0/;,/&/
seed||ng roots from two |ndependent|y reared sets of 162 recomb|nant |nbred
||nes (Rl|s} and one set of 92 near |sogen|c ||nes (Nl|s} der|ved from a Oape
verde ls|ands (Ov|} |andsberg %1%-+/ (|er} cross were co||ected automat|ca||y
every 2 m|n for 8 hr fo||ow|ng |nduct|on of grav|trop|sm by 90 reor|entat|on of the
samp|e. H|gh-throughput comput|ng (HTO} was used to measure root t|p ang|e
|n each of the 1.1 m||||on |mages acqu|red and perform stat|st|ca| regress|on of
t|p ang|e aga|nst the genotype at each of the 234 Rl| or 102 Nl| DNA markers
|ndependent|y at each t|me po|nt us|ng a standard stepw|se procedure. T|me-
dependent OT| were detected on chromosomes 1, 3, and 4 by th|s mapp|ng
method and by an approach deve|oped to treat the phenotype t|me course
as a funct|on-va|ued tra|t. The OT| on chromosome 4 was ear||est, appear|ng
at 0.5 hr and rema|n|ng s|gn|fcant for 5 hr, wh||e the OT| on chromosome 1
appeared at 3 hr and thereafter rema|ned s|gn|fcant. The Ov| a||e|e genera||y had
a negat|ve effect of 2.6-4.0%. Her|tab|||ty due to the OT| approached 25%. Th|s
study shows how computer v|s|on and stat|st|ca| genet|c ana|ys|s by HTO can
character|ze the deve|opmenta| t|m|ng of genet|c arch|tectures.
12
l NvESTl GATl ONS
MAPfastR: Quantitative Trait Loci Mapping
in Outbred Line Crosses
N%*/&8 .I -'&7%*K 4/0& -'55'&M&/8K ./57 CI L'55'077%*K X?/ 9$'*K J;<@ 40%%17K
T0/*<%?7 6'7*?'0K H%7Y .I Z&B/0'Q(4/750%K J/07 N[**'>\08K #'0%*?</ C1K
O$'@/ 9$'*>K ./0<?* G?'0<Q/1K 9B'01'0 S%&+>0'*K /*8 ]0^/* 4/0&M%0>
!"# !%&%' ( !%&)*%' ( !%&%+,-' December 2013 3:2147-2149
EDITORS NOTE Most software packages for detect|ng OT| from marker
data were deve|oped to ana|yze crosses between |nbred ||nes. Software
des|gned for outbred crosses |s typ|ca||y unab|e to hand|e the |arge amount of
data generated by SNP ch|p techno|ogy. These authors presented a software
package that hand|es |arge datasets and ana|yzes OT| data from both |nbred
and outbred ||ne crosses, resu|t|ng |n fast and accurate ana|yses.
ABSTRACT MAPfastR |s a software package deve|oped to ana|yze
quant|tat|ve tra|t |oc| data from |nbred and outbred ||ne-crosses. The
package |nc|udes a number of modu|es for fast and accurate quant|tat|ve
tra|t |oc| ana|yses. lt has been deve|oped |n the R |anguage for fast and
comprehens|ve ana|yses of |arge datasets. MAPfastR |s free|y ava||ab|e at:
http://www.computat|ona|genet|cs.se/?page_|d=7
13
l NvESTl GATl ONS
Genetic Variants Tat Confer Resistance to
Malaria Are Associated with Red Blood Cell
Traits in African-Americans: An Electronic
Medical Record-based Genome-Wide
Association Study
G'@;' ,?*>K ./0?Q/ 8' !*80/8'K D'0? !I ./*%&?%K ,/*/ 4I 40/A3%08K
J/;0/ HI N/7+;77'*(D%0B?1K ./0@&@* ,I N?5<$?'K H%7$;/ 4I ,'**@K ,/*?'& NI ./7@7K
S/@/* H%;*?K H'**?3'0 !I L/<$'<$%K !M'& -I G$%K ,/* .I N%8'*K N'_ 4$?7$%&+K /*8
=35?1$/0 HI G;&&%
!"# !%&%' ( !%&)*%' ( !%&%+,-' Ju|y 2013 3:1061-1068
EDITORS NOTES s|ng over 2,300 e|ectron|c med|ca| records, these authors
conducted a genome-w|de assoc|at|on study of red b|ood ce|| (RBO} tra|ts
|n Afr|can-Amer|cans. The|r fnd|ngs revea|ed that genet|c var|ants conferr|ng
res|stance to ma|ar|a are assoc|ated w|th RBO tra|ts |n Afr|can-Amer|cans, and
suggest that the genet|c arch|tecture of RBO tra|ts d|ffers by ethn|c group.
ABSTRACT To |dent|fy nove| genet|c |oc| |nfuenc|ng |nter|nd|v|dua| var|at|on |n
red b|ood ce|| (RBO} tra|ts |n Afr|can-Amer|cans, we conducted a genome-w|de
assoc|at|on study (GWAS} |n 2315 |nd|v|dua|s, d|v|ded |nto d|scovery (& = 1904}
and rep||cat|on (& = 411} cohorts. The tra|ts |nc|uded hemog|ob|n concentrat|on
(HGB}, hematocr|t (HOT}, RBO count, mean corpuscu|ar vo|ume (MOv},
mean corpuscu|ar hemog|ob|n (MOH}, and mean corpuscu|ar hemog|ob|n
concentrat|on (MOHO}. Pat|ents were part|c|pants |n the e|ectron|c MEd|ca|
Records and GEnom|cs (eMERGE} network and underwent genotyp|ng of
~1.2 m||||on s|ng|e-nuc|eot|de po|ymorph|sms on the l||um|na Human1M-Duo
array. Assoc|at|on ana|yses were performed adjust|ng for age, sex, s|te, and
popu|at|on strat|fcat|on. Three |oc| prev|ous|y assoc|ated w|th res|stance
to ma|ar|a->?? (11p15.4}, >?=@A>?=B (16p13.3}, and !C5D (q28}-were
assoc|ated (5 1 10
-6
} w|th RBO tra|ts |n the d|scovery cohort. The |oc|
rep||cated |n the rep||cat|on cohort (5 0.02}, and were s|gn|fcant at a genome-
w|de s|gn|fcance |eve| (5 < 5 10
-8
} |n the comb|ned cohort. The proport|ons
of var|ance |n RBO tra|ts exp|a|ned by s|gn|fcant var|ants at these |oc| were as
fo||ows: rs7120391 (near >??} 1.3% of MOHO, rs9924561 (near >?=@A=B} 5.5%
of MOv, 6.9% of MOH and 2.9% of MOHO, and rs1050828 (|n !C5D} 2.4% of
RBO count, 2.9% of MOv, and 1.4% of MOH, respect|ve|y. We were not ab|e
to rep||cate |oc| |dent|fed by a prev|ous GWAS of RBO tra|ts |n a European
ancestry cohort of s|m||ar samp|e s|ze, suggest|ng that the genet|c arch|tecture
of RBO tra|ts d|ffers by race. ln conc|us|on, genet|c var|ants that confer
res|stance to ma|ar|a are assoc|ated w|th RBO tra|ts |n Afr|can-Amer|cans.
14
l NvESTl GATl ONS
PRICE: Software for the Targeted Assembly of
Components of (Meta) Genomic Sequence Data
HI )0/$/+ N;M@K L0?@/ 6'&&/0'K /*8 H%7'2$ JI ,'N?7?
!"# !%&%' ( !%&)*%' ( !%&%+,-' May 2013 3:865-880
EDITORS NOTE D% &)3) assemb|y of metagenomes-the tota| genome
comp|ement of an ent|re ecosystem or env|ronmenta| samp|e-|s cha||eng|ng,
and has been much |ess thorough|y deve|oped than standard s|ng|e-genome
assemb|y. Th|s paper descr|bed :% &)3) genome assemb|y software created
w|th an eye toward u|tra-h|gh-throughput DNA sequenc|ng techno|og|es and
the needs of metagenom|c ana|ys|s. lts seeded-assemb|y strategy a||ows
researchers to focus computat|ona| effort on the re|evant components
of comp|ex env|ronmenta| datasets, wh||e |gnor|ng the |arge amounts of
|rre|evant sequence.
ABSTRACT |ow-cost DNA sequenc|ng techno|og|es have expanded
the ro|e for d|rect nuc|e|c ac|d sequenc|ng |n the ana|ys|s of genomes,
transcr|ptomes, and the metagenomes of who|e ecosystems. Human
and mach|ne comprehens|on of such |arge datasets can be s|mp||fed
v|a synthes|s of sequence fragments |nto |ong, cont|guous b|ocks of
sequence (cont|gs}, but most of the progress |n the fe|d of assemb|y
has focused on genomes |n |so|at|on rather than metagenomes. Here,
we present software for pa|red-read |terat|ve cont|g extens|on (PRlOE},
a strategy for focused assemb|y of part|cu|ar nuc|e|c ac|d spec|es us|ng
comp|ex metagenom|c data as |nput. We descr|be the assemb|y strategy
|mp|emented by PRlOE and prov|de examp|es of |ts app||cat|on to the
sequence of part|cu|ar genes, transcr|pts, and v|rus genomes from comp|ex
mu|t|component datasets, |nc|ud|ng an assemb|y of the BOB|-1 stra|n of
Kapos|`s sarcoma-assoc|ated herpesv|rus. PRlOE |s open-source and
ava||ab|e for free down|oad (http://der|s||ab.ucsf.edu/software/pr|ce/ or
http://sourceforge.net/projects/pr|cedenovo/}.
15
l NvESTl GATl ONS
FlyPrimerBank: An Online Database for
Drosophila melanogaster Gene Expression
Analysis and Knockdown Evaluation of
RNAi Reagents
V/*$;? S;K N?<$'&&' 9%21%K ./0?/**/ T%%7K 4%&&''* G'&&'@K =/* T&%<1$/05K
-%'+?' !++';_K X?/%A'? #/*>K J?Q/M'5$ L'01?*7K -%0M'05 L'00?+%*K /*8
95'2$/*?' CI .%$0
!"# !%&%' ( !%&)*%' ( !%&%+,-' September 2013 3:1607-1616
EDITORS NOTE Des|gn|ng h|gh-qua||ty qPOR pr|mers |s not tr|v|a|. These
authors deve|oped and exper|menta||y va||dated a genome-w|de qPOR pr|mer
resource for D1)')60,;/. F|yPr|merBank a||ows researchers to |dent|fy and
v|ew pr|mer sets, eva|uat|on data and more. To further |mprove and contr|bute
to th|s commun|ty resource, sc|ent|sts may a|so subm|t the|r own va||dated
pr|mers and data.
ABSTRACT The eva|uat|on of spec|fc endogenous transcr|pt |eve|s |s
|mportant for understand|ng transcr|pt|ona| regu|at|on. More spec|fca||y, |t |s
usefu| for |ndependent confrmat|on of resu|ts obta|ned by the use of m|croarray
ana|ys|s or RNA-seq and for eva|uat|ng RNA |nterference (RNA|}-med|ated
gene knockdown. Des|gn|ng spec|fc and effect|ve pr|mers for h|gh-qua||ty,
moderate-throughput eva|uat|on of transcr|pt |eve|s, ,4%4, quant|tat|ve, rea|-
t|me POR (qPOR}, |s nontr|v|a|. To meet commun|ty needs, predefned qPOR
pr|mer pa|rs for mamma||an genes have been des|gned and sequences
made ava||ab|e, %4<4, v|a Pr|merBank. ln th|s work, we adapted and refned the
a|gor|thms used for the mamma||an Pr|merBank to des|gn 45,417 pr|mer pa|rs
for 13,860 D1)')60,;/ *%;/&)</'+%1 genes, w|th three or more pr|mer pa|rs
per gene. We exper|menta||y va||dated pr|mer pa|rs for ~300 random|y se|ected
genes expressed |n ear|y D1)')60,;/ embryos, us|ng SYBR Green-based
qPOR and sequence ana|ys|s of products der|ved from convent|ona| POR. A||
re|evant |nformat|on, |nc|ud|ng pr|mer sequences, |soform spec|fc|ty, spat|a|
transcr|pt target|ng, and any ava||ab|e va||dat|on resu|ts and/or user feedback,
|s ava||ab|e from an on||ne database (http://www.fyrna|.org/fypr|merbank}. At
F|yPr|merBank, researchers can retr|eve pr|mer |nformat|on for fy genes e|ther
one gene at a t|me or |n batch mode. lmportant|y, we |nc|uded the over|ap of
each pred|cted amp||fed sequence w|th RNA| reagents from severa| pub||c
resources, mak|ng |t poss|b|e for researchers to choose pr|mers su|tab|e for
knockdown eva|uat|on of RNA| reagents (,4%4, to avo|d amp||fcat|on of the
RNA| reagent |tse|f}. We demonstrate the ut|||ty of th|s resource for va||dat|on
of RNA| reagents ,& 3,3).
16
MUTANT SCREEN REPORTS
ln 2013, G3 |ntroduced Mutant Screen Reports, wh|ch prov|de a c|ear format
for descr|b|ng the resu|ts of mutant screens. The reports are succ|nct and
fo||ow a structured temp|ate des|gned to make |t fast and easy for authors to
subm|t, for rev|ewers to rap|d|y assess, and for readers to eas||y understand
the screen. Or|ter|a for acceptance |nc|udes usefu|ness of the screen, qua||ty
and comp|eteness of the resu|ts, and the authors` |nterpretat|on of the resu|ts.
The Reports fu|f|| one of G3`s goa|s: to make usefu| data and |nformat|on
pub||c|y ava||ab|e to the commun|ty w|thout de|ay.
0+112+*"($13# 13*34&#&+3 )'*'7 =*B%&B'8 ?* 9;0B?B/& %3 S'/5 9$%<1
Stefan|e Jaro||m, An|ta Ayer, Bethany P|||ay, A|||son O. Gee, A|ex Phrakaysone,
Gabr|e| G. Perrone, M|chae| Bre|tenbach, and lan W. Dawes
!"# !%&%' ( !%&)*%' ( !%&%+,-' December 2013 3:2321-2333
012&5"#+112+*"($13# 6+%",&1'# V'/75 L%?7'8 5% 6'<%+' / T/B%0?5' C_2'0?+'*5/&
R0>/*?7+ 3%0 C;1/0@%5?< N'7'/0<$
Amar J. S. K|ar
!"# !%&%' ( !%&)*%' ( !%&%+,-' October 2013 3:1869-1873
7*"#"%2&8+ C+M0@%*?< 4'&&(4@<&' .;5/*57
Y|ngdee nhava|thaya, Eugen|a A. Park, lrena Royzman, and Terry |. Orr-Weaver
!"# !%&%' ( !%&)*%' ( !%&%+,-' October 2013 3:1875-1880
C33'<57 %3 6%8@(4%&%0 .;5/5?%*7 %* U?5/&?5@` !* !55'+25 5% C75/M&?7$ C/7@(5%(
60''8 9''(D$0%;>$ .'8/1/ 950/?*7 M@ R;5<0%77?*>
Ayaka Ohsh|ma, Nor|ko Mor|mura, Oh|zuru Matsumoto, Am| H|raga, R|tsuko Kom|ne,
Tetsuak| K|mura, K|yosh| Naruse, and Shoj| Fukamach|
!"# !%&%' ( !%&)*%' ( !%&%+,-' September 2013 3:1577-1585
! )'*'5?< 9<0''* 3%0 S?>$ 4%2@ -;+M'0 9;220'77%07 %3 5$' 9@*5$'5?< J'5$/&?5@
6'5A''* 389: /*8 #*#; ?* V'/75
lnba| Gazy, Bat|a ||efsh|tz, A|ex Bronste|n, Oren Parnas, N|r At|as, Roded Sharan,
and Mart|n Kup|ec
!"# !%&%' ( !%&)*%' ( !%&%+,-' May 2013 3:917-926
17
MOSAIC SCREEN Drosophila ovarioles screened for early oogenesis defects
with various markers, including for polarity, membranes, meiosis, and cell
cycles. Image courtesy of Jean-Ren Huynh.
! .%7/?< )'*'5?< 9<0''* 3%0 )'*'7 =*B%&B'8 ?* 5$' C/0&@ 95'27 %3
7*"#"%2&8+ R%>'*'7?7
Mar|ene Jagut, |ud|v|ne M|ha||a-Bodart, Anah| Mo||a-Herman,
Mar|e-Frano|se A||n, Jean-Anto|ne |epesant, and Jean-Rene Huynh
!"# !%&%' ( !%&)*%' ( !%&%+,-' March 2013 3:409-425
18
THEMATl C COLLECTl ONS
One way G3 and |ts s|ster journa| GENETlOS comp|ement each other |s through
co||ect|ons of art|c|es cover|ng re|ated themes and top|cs. By br|ng|ng together
work from d|fferent groups |nto one corpus, the GSA journa|s a|m to st|mu|ate
d|scourse, to e|uc|date ex|st|ng debates, and to shed ||ght on emerg|ng research
areas. Art|c|es |n a co||ect|on are bund|ed and easy to fnd on||ne, and they`re
||sted |n both journa|s` tab|es of contents. Most co||ect|ons are ongo|ng; we
we|come cont|nued subm|ss|ons from authors |ook|ng to ensure the greatest
|ong-term |mpact and reach for the|r work.
These cross-journa| co||ect|ons have |nc|uded the fo||ow|ng:
)'*'5?<7 %3 =++;*?5@
Defense aga|nst |nfect|on |s |ncreas|ng|y recogn|zed to have a comp|ex
determ|nat|on. Hosts may res|st |nfect|on through act|ons of the |mmune system,
or they may to|erate |nfect|on by m|t|gat|ng pathogen|c processes. Res|stance and
to|erance are both |nfuenced by host cond|t|on pr|or to |nfect|on, and by changes
|n behav|or or env|ronment after |nfect|on. The genet|cs of th|s comp|ex v|ew of
|mmun|ty |s be|ng stud|ed us|ng a w|de var|ety of approaches and organ|sms, from
agr|cu|tura||y re|evant p|ants, to genet|c mode|s such as D1)')60,;/, to humans.
)'*'5?<7 %3 9'_
Sex determ|nat|on |s among the most |nterest|ng areas of study |n modern
genet|cs, w|th research spann|ng a w|de range of top|cs, |nc|ud|ng deve|opmenta|
mechan|sms, behav|or, sex chromosome b|o|ogy and evo|ut|on. Modern too|s
prov|de opportun|t|es to comb|ne genet|c and mo|ecu|ar approaches to study
such processes |n mode| and non-mode| systems. Th|s co||ect|on features
art|c|es on the |arger theme of sex, |nc|ud|ng for examp|e: the me|ot|c process
and recomb|nat|on, sex chromosomes, mat|ng and |ncompat|b|||ty systems.
WDJ ./22?*> ?* .;&5?2/0'*5/& L%2;&/5?%*7
A|though Mu|t|parenta| Popu|at|ons (MPPs} may take many forms, two pr|mary
types ex|st. The frst cons|sts of a number of b|-parenta| offspr|ng popu|at|ons
that share parents. The crosses that produce the offspr|ng popu|at|ons may
fo||ow a regu|ar structure such as d|a||e|s and nested assoc|at|on mapp|ng
popu|at|ons, but more |rregu|ar structures can a|so be formed w|th popu|at|ons
that are part|a||y connected by common parents, or parents connected v|a
a ped|gree. A further var|at|on on th|s theme |nc|udes offspr|ng popu|at|ons
of d|fferent types (F2, DH, Rl|, etc.}. The second major category of MPP |s
the Mu|t|p|e Advanced Generat|on lnterOross, or MAGlO popu|at|on. MAGlO
popu|at|ons are constructed from a poo| of |ntermat|ng parenta| ||nes whose
offspr|ng are subsequent|y |nbred. The GSA Journa|s` MPP focus encompasses
exper|menta| and methodo|og|ca| contr|but|ons |n both p|ants and an|ma|s.
19
GENOMl C SELECTl ON
Resource Allocation for Maximizing Prediction
Accuracy and Genetic Gain of Genomic Selection
in Plant Breeding: A Simulation Experiment
!/0%* HI J%0'*Q
!"# !%&%' ( !%&)*%' ( !%&%+,-' March 2013 3:481-491
EDITORS NOTE Th|s art|c|e |s part of the ongo|ng GENETlOS and G3
Genom|c Se|ect|on Oo||ect|on, wh|ch a|ms to encourage d|scourse on th|s
|mportant top|c |n crop and ||vestock breed|ng research. Genom|c se|ect|on
(or genome-w|de pred|ct|on} uses genotyp|c |nformat|on to pred|ct breed|ng
va|ues for part|cu|ar phenotypes, but w|thout spec|fc know|edge of the
|nd|v|dua| genes contr|but|ng to that tra|t.
ln marker-ass|sted se|ect|on, ba|anc|ng resources between popu|at|on s|ze
and rep||cat|on |s cr|t|ca| to max|m|z|ng OT| detect|on power and pred|ct|on
accuracy. |orenz showed that th|s ba|ance d|ffers between genom|c se|ect|on
and marker-ass|sted se|ect|on because genom|c se|ect|on can ach|eve h|gh
pred|ct|on accuracy when popu|at|on s|zes are sma||.
ABSTRACT A||ocat|ng resources between popu|at|on s|ze and rep||cat|on
affects both genet|c ga|n through phenotyp|c se|ect|on and quant|tat|ve tra|t |oc|
detect|on power and effect est|mat|on accuracy for marker-ass|sted se|ect|on
(MAS}. lt |s we|| known that because a||e|es are rep||cated across |nd|v|dua|s |n
quant|tat|ve tra|t |oc| mapp|ng and MAS, more resources shou|d be a||ocated
to |ncreas|ng popu|at|on s|ze compared w|th phenotyp|c se|ect|on. Genom|c
se|ect|on |s a form of MAS us|ng a|| marker |nformat|on s|mu|taneous|y to
pred|ct |nd|v|dua| genet|c va|ues for comp|ex tra|ts and has w|de|y been found
super|or to MAS. No stud|es have exp||c|t|y |nvest|gated how resource a||ocat|on
dec|s|ons affect success of genom|c se|ect|on. My object|ve was to study
the effect of resource a||ocat|on on response to MAS and genom|c se|ect|on
|n a s|ng|e b|parenta| popu|at|on of doub|ed hap|o|d ||nes by us|ng computer
s|mu|at|on. S|mu|at|on resu|ts were compared w|th prev|ous|y der|ved formu|as
for the ca|cu|at|on of pred|ct|on accuracy under d|fferent |eve|s of her|tab|||ty
and popu|at|on s|ze. Response of pred|ct|on accuracy to resource a||ocat|on
strateg|es d|ffered between genom|c se|ect|on mode|s (r|dge regress|on best
||near unb|ased pred|ct|on [RR-B|P|, BayesO} and mu|t|p|e ||near regress|on
us|ng ord|nary |east-squares est|mat|on (O|S}, |ead|ng to d|fferent opt|ma|
resource a||ocat|on cho|ces between O|S and RR-B|P. For O|S, |t was
a|ways advantageous to max|m|ze popu|at|on s|ze at the expense of rep||cat|on,
but a h|gh degree of fex|b|||ty was observed for RR-B|P. Pred|ct|on accuracy
of doub|ed hap|o|d ||nes |nc|uded |n the tra|n|ng set was much greater than of
those exc|uded from the tra|n|ng set, so there was ||tt|e beneft to phenotyp|ng
on|y a subset of the ||nes genotyped. F|na||y, observed pred|ct|on accurac|es
|n the s|mu|at|on compared we|| to ca|cu|ated pred|ct|on accurac|es, |nd|cat|ng
these theoret|ca| formu|as are usefu| for mak|ng resource a||ocat|on dec|s|ons.
20
Efcient Sing|e-Ce|| Transgene Induction in <+3,"*2+=-&>&# 3839+,#
a7?*> / L;&7'8 =*30/0'8 J/7'0
Matthew A. Ohurg|n, ||p|ng He, John l. Murray, and Ohr|stopher Fang-Yen
!"# !%&%' ( !%&)*%' ( !%&%+,-' October 2013 3:1827-1832
LASER POINTING Heat shock promoters can be used to regulate
transgenes with pin-point precision. Tese images from Churgin et al. show
GFP expression (left) after previous infrared laser heat shock of individual
cells during the 4-cell stage. GFP is only expressed in the descendants of each
illuminated cell. Each pair represents the result of targeting a diferent cell
at the 4-cell stage, with the expected positions of the descendants simulated
by AceTree (right). Pulsed laser illumination enables a much higher degree of
spatial selectivity than previously-reported continuous-wave methods because
heat difuses between pulses.
GENETl CS SOCl ETY OF AMERl CA
The Genet|cs Soc|ety of Amer|ca (GSA}, founded |n 1931, |s the profess|ona|
membersh|p organ|zat|on for sc|ent|fc researchers and educators |n the fe|d of
genet|cs and genom|cs. Our members work to advance know|edge |n the bas|c
mechan|sms of |nher|tance, from the mo|ecu|ar to the popu|at|on |eve|.
GSA |s ded|cated to promot|ng research and educat|on |n genet|cs and to
encourag|ng commun|cat|on among genet|c|sts wor|dw|de. GSA pub||shes the peer-
rev|ewed journa|s GENETlOS and G3: Genes Genomes Genet|cs and organ|zes
profess|ona| conferences-such as those that focus on the genet|cs of key mode|
organ|sms, |nc|ud|ng 84 %;%</&', D1)')60,;/, fung|, m|ce, yeast, and zebrafsh.
GSA has approx|mate|y 5,000 members from a|| 50 states and near|y 50 countr|es
around the wor|d. They work at co||eges and un|vers|t|es, government and pr|vate
research |nst|tutes, med|ca| schoo|s, corporate and |ndustr|a| sett|ngs, and other
|nst|tut|ons. More than ha|f of our members are postdoctora| scho|ars, graduate
students, and undergraduates, wh|ch refects our comm|tment to foster|ng the next
generat|on of genet|c|sts.
GSA represents the co||ect|ve |nterests of the genet|cs and mode| organ|sm
commun|t|es, serv|ng as the vo|ce of our membersh|p to po||cymakers and
government |eaders. The Soc|ety |s a strong supporter of educat|on and outreach,
he|p|ng to exp|a|n the tenets and va|ue of genet|cs to K-12 and undergraduate
students and the genera| pub||c.
2014 BOARD OF DIRECTORS
vicki Chandler,
President (2015j
Gordon and Betty Moore
Foundation
Jasper Rine,
vice-President (2016j
University of California,
Berkeley
Michael Lynch,
Past President (2014j
lndiana University
Sue Jinks-Robertson,
Treasurer (2016j
Duke University Medical
School
Anne M. villeneuve,
Secretary (2015j
Stanford University School of
Medicine
Angelika Amon (2016j
Howard Hughes Medical
lnstitute & Massachusetts
lnstitute of Technology
Brenda J. Andrews,
Editor-in-Chief (2015j
G3: Genes | Genomes | Genetics
University of Toronto
Lynn Cooley (2015j
Yale University
Anna Di Rienzo (2015j
University of Chicago
Sarah C. R. Elgin (2015j
Washington University in
St. Louis
Marnie E. Halpern (2014j
Carnegie lnstitution for
Science
Mark Johnston,
Editor-in-Chief (2018j
GENETlCS
University of Colorado School
of Medicine
Lauren M. Mclntyre (2016j
University of Florida
Mohamed A. F. Noor (2014j
Duke University
Dmitri A. Petrov (2016j
Stanford University
John C. Schimenti (2014j
Cornell University
Deborah A. Siegele (2015j
Texas A&M University
EXECUTIVE DIRECTOR
Adam P. Fagen
Genetics Society of America
TRAINEE ADVISORY
REPRESENTATIVES
Andrew Adrian (2015j
University of lowa
Kathleen Dumas (2014j
Buck lnstitute for Research
on Aging
Krista Dobi (2014j
Memorial Sloan-Kettering
Cancer Center