New genetic data help explain the rapid adaptation of stickleback fish that invaded freshwater habitats in the 1960s.

In 1964, an earthquake shook the islands off the coast of Alaska, transforming the landscape as underwater terraces were thrust above the surface. From this cataclysmic event emerged a series of freshwater pools that became a natural laboratory in which to study evolution in action. A new report in GENETICS takes a closer look at how this sudden environmental shift influenced the adaptation of one particular inhabitant.

On the Alaskan islands, the newly-formed freshwater ponds were colonized by interlopers from the sea: marine stickleback fish. These ocean dwellers quickly adapted to the new environment, acquiring many traits not unlike those found in other, much older stickleback populations that are specialized for living in freshwater. Evolution at this dramatic scale is normally thought to take thousands of years rather than a half-dozen decades, which lead the authors to wonder how such rapid adaptation occurred. “It’s a great natural evolutionary experiment,” said Susan Bassham, one of the lead authors of the study.

Senior author William Cresko and his group have been studying sticklebacks (Gasterosteus aculeatus) for decades, and for good reason—the fish are an excellent model system for understanding adaptation and evolution.

“When our collaborator Frank von Hippel told us about his work surveying possible new stickleback habitats, including on these earthquake islands, we got excited. We immediately wanted to look at the phenotypic and genomic changes that might have happened after the island was uplifted and these new ponds were invaded by marine stickleback,” said Cresko. “This started a long and productive collaboration between our groups.”

Bassham explained that threespine stickleback have colonized a number of diverse environments over the millennia that the species has existed: as well as marine and freshwater stickleback varieties, there are sticklebacks that spend some time in both environments, much like salmon. Despite adapting to such varied habitats, all of these fish are still one species.

Marine (top) and freshwater (bottom) threespine stickleback fish. Photo by Emily Lescak.

To understand the genetics underlying the rapid adaptation of stickleback, the authors genotyped fish from three stickleback populations: those from the newly formed pools, those from other freshwater populations, and marine fish. They used restriction site-associated DNA sequencing, or RAD-seq, a technique that their lab has helped pioneer; this method allows for the rapid identification of genetic markers by sequencing regions of the genome adjacent to restriction sites. Cresko explained that RAD-seq’s focus on limited regions of the genome makes it more economical than other techniques, allowing for the acquisition of a complete genomic “snapshot” for thousands of individual fish. “This breadth of biological sampling was needed to answer some key population genomic questions about these fish,” said Cresko.

Using this approach and new computational tools developed in collaboration with second lead author Julian Catchen, the group identified several regions of the stickleback genome that vary significantly between the ancestral marine stickleback populations and those from the new freshwater pools.

Intriguingly, the changes that they found in the young freshwater populations on the Alaskan island were virtually identical to the changes seen in freshwater stickleback populations that have existed in other locations for thousands of years. They also found some of these same freshwater-adapted haplotypes scattered in the genomes of marine fish as far away as coastal Oregon—but at much lower frequencies.

These results suggest that the rapid adaptability of stickleback is largely attributable to standing genetic variation in the marine population. When environmental pressures change, the existing freshwater-adapted alleles face powerful selection and become prevalent. Although this idea was proposed a while ago, the current GENETICS study had the power to detect and accurately measure the frequency of these alleles in marine populations.

The similarities among different freshwater populations is also striking because those populations are otherwise genetically indistinguishable from marine stickleback. “When you look at the regions of the genome that are not divergent between ocean and freshwater and do a phylogeographic study, there’s no population structuring at all,” said Cresko. The genomes are so similar, he explains, that the only parts that differentiate them are the dramatic regions related to adaptation. “There’s very little  neutral divergence; it’s nearly all due to natural selection.”

Ironically, this fascinating finding has posed something of a technical stumbling block for learning more. Delving deeper into the precise genetic differences between freshwater and marine sticklebacks would usually be done with a genome-wide association study, but such studies require distinguishable variation between populations. In other words: these fish are evolving so quickly that it’s impossible to control for population structure.

That doesn’t mean these questions can’t be answered, though. Bassham, Cresko, and their colleagues are currently studying other wild stickleback populations to identify genes that might underpin their ability to rapidly adapt to freshwater conditions, and they are creating new models to experimentally validate those findings in the laboratory.

CITATION:

Repeated selection of alternatively adapted haplotypes creates sweeping genomic remodeling in stickleback

Susan Bassham, Julian Catchen, Emily Lescak, Frank A. von Hippel, William A. Cresko

Genetics July 2018 209: 921-939; https://doi.org/10.1534/genetics.117.300610
http://www.genetics.org/content/209/3/921

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For the first time in nearly 15 years, the rat genetic map has been updated.

Genetic maps help us navigate uncharted data, but to successfully use them to link genes to complex traits, their resolution must be high enough to yield a manageable list of candidate variants. That’s why genetic maps for mice and humans have been routinely updated in recent years as mapping technologies have improved.

However, one important map has lagged: the genetic map for rats had not been updated since 2004. As such, the resolution of that map was 100 times lower than the mouse genetic map. Since rats are such an important experimental organism for understanding disease, Littrell et al. set out to construct a new, high-resolution genetic map for lab rats, which they published in G3: Genes|Genomes|Genetics.

With a nearly 50-fold improvement, the new map has a much higher resolution than the previous one. Additionally, the authors created sex-specific gene maps, which had not previously been available for rats. They also examined some particular features of these new maps, finding that rates of recombination were higher on average in females than in males, which is a phenomenon that occurs in many mammal species.

To make it even more useful, the authors also added other data to the map, including the locations of tens of thousands of SNPs. The hope is that this new view of the rat genome will allow geneticists to more effectively explore genetic modifiers of common diseases.

CITATION:

A High-Resolution Genetic Map for the Laboratory Rat

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Watch presentations from the conference, including talks from Katie Peichel and Jonathan Pritchard.

Now that the dust has settled from the whirlwind of the first ever standalone GSA Population, Evolutionary, and Quantitative Genetics Conference (PEQG18), we’re delighted to be able to share the audio and synched slides from the Keynote and Crow Award sessions.

We’re gratified too that attendees got so much of value from the conference. Many have approached GSA staff and the conference organizers with rave reviews of their experience, and, despite the usual growing pains of a new conference, the results from the attendee survey have also been overwhelmingly positive.

We’re excited to incorporate some of the lessons we’ve learned into planning the next PEQG. It will be held April 22–26, 2020 in the metro Washington, DC, area at The Allied Genetics Conference (TAGC20). PEQG will join the C. elegans, Drosophila, mouse, Xenopus, yeast, and zebrafish research communities for a mix of community-specific and cross-community sessions.

Stay tuned for more announcements on the upcoming conference and for several more PEQG18 blog reports in the coming weeks. Enjoy the talks below!

PEQG18 Keynotes

Jonathan Pritchard Stanford University/HHMI

Omnigenic Architecture of Human Complex Traits

Catherine Peichel University of Bern

Genetics of Adaptation in Sticklebacks

Trudy Mackay North Carolina State University

Context-Dependent Effects of Alleles Affecting Genetic Variation of Quantitative Traits COMING SOON

Finalists for the 2018 Crow Award for Early Career Researchers

Amy Goldberg UC Berkeley

A mechanistic model of assortative mating in a hybrid population

Emily Josephs UC Davis

Detecting polygenic adaptation in maize

Jeremy Berg Columbia University 

Population genetic models for highly polygenic disease

Katherine Xue University of Washington 

Evolutionary dynamics of influenza across spatiotemporal scales

Alison Feder Stanford University 

Intra-patient evolutionary dynamics of HIV drug resistance evolution in time and space

Emily Moore North Carolina State University 

Genetic variation at a conserved non-coding element contributes to microhabitat-associated behavioral differentiation in Malawi African cichlid fishes

Videos

Jonathan Pritchard 

[youtube https://youtu.be/H18k55ruCOY&w=500&rel=0]

Catherine Peichel

[youtube https://youtu.be/QRCcLixjUtc&w=500&rel=0]

Amy Goldberg 

[youtube https://youtu.be/kccUNkF7SgY&w=500&rel=0]

Emily Josephs 

[youtube https://youtu.be/CxQOrK9h6D4&w=500&rel=0]

Jeremy Berg

[youtube https://youtu.be/HqA1H24LPZc&w=500&rel=0]

Katherine Xue

[youtube https://youtu.be/fTdaAwqdt0k&w=500&rel=0]

Alison Feder

[youtube https://youtu.be/ntM0448h2lA&w=500&rel=0]

Emily Moore

[youtube https://youtu.be/aX4_HS0K1kA&w=500&rel=0]

Attendees of the Population, Evolutionary, and Quantitative Genetics Conference are a creative bunch.  Inspired by one of the PEQG Bingo challenges, they bombarded Twitter with more than 50 #PEQG18 haikus (and one limerick), providing poetic snippets of the meeting to those who couldn’t make it. Joining the 17-syllable summaries were fantastic sketch notes of the meeting by scientist/artist April Wei.

Below are a couple of the haikus, including a few of the non-tweeted bingo entries. Enjoy and feel free to share your own science haikus using #sciku!

Rats in NYC
able to follow their dreams
with selective sweeps

—Markus Stetter on “How brown rats adapted to life in NYC’s concrete jungle“

Strange TE, new home.
Boy frog meets girl frog, hearts jump;
now let’s get hopping.

—Emily Baker on “Hostile genomic takeover by transposable elements in the Strawberry poison frog“

“Bet on sparsity”
vast labyrinth of haystacks
sifting for needles

—Kathie Sun

https://twitter.com/CristyGelling/status/996250105866084353

#PEQG18 #sciku
Sequenced genome, for
my genes. Sorry, I've found more
repeats. Sequenced ge-

— Monika Cechova Mich (@biomonika) May 16, 2018

the neutral theory
does not fit the data well
cherry blossoms fall#sciku #PEQG18

— Matthew Hahn (@3rdreviewer) May 16, 2018

Immortality?
That just means that we'll all die
In bike accidents#PEQG18 #sciku

— Silvan R. Urfer (@SilvanUrfer) May 16, 2018

#sciku #PEQG18
Detect selection, identify sweeps!
CNV mimics the signal,
Laugh in the corner!

— Wenbin Mei (@wbmei) May 16, 2018

Phenotypic plasticity*
Phenotypic plasticity*
Phenotypic plasticity*

*at 25degC, the phrase ‘phenotypic plasticity’ can have between 4-8 syllables. 5&7 most common. #sciku #peqg18

— Thom Nelson (@Genetreeclimber) May 16, 2018

My first attempt at a #sciku :
Grabbing DNA
Genes found in the fish schooling
Their wet past is known

— Martha Burford Reiskind #BLM (@MobReiskind) May 16, 2018

Talks are amazing
People are connecting
I am so delighted!#sciku #PEQG18 @GeneticsGSA

— Dmitri Petrov (@PetrovADmitri) May 16, 2018

connections we found
inspired, inspiring
plane’s brakes not yet fixed #sciku #PEQG18 #tarmacwoes

— tracey depellegrin (@editor_traceyd) May 17, 2018

Epilepsy is characterized by recurrent seizures, often with no immediately obvious cause. In the August issue of G3, Ferland et al. use a genome-wide association study in mice to show that after multiple seizures, the genetic basis of seizure variation shifts from previously identified genomic regions to new ones. This research shows that the genetic causes of initial seizures and the progression of epilepsy may be distinct.

Having a seizure changes brain physiology and alters its cellular environment, which can affect how genes are activated. To identify genetic regions that are involved in repeated seizures, the authors used fifty-eight genetically variable mouse strains. For eight consecutive days, they exposed these mice to a seizure-inducing chemical and measured how long it took the mice to have a generalized seizure. As expected, this time decreased as the days went on. They then let the mice rest for twenty-eight days before inducing a final seizure.

The team then identified variants associated with the time to seizure onset. Mice with the shortest time before seizure onset on the first day carried variants at Szs1 and Szs6 that had been previously associated with seizure susceptibility. However, on each passing day, these associations grew weaker. On day three, a new association with time to seizure began to appear, growing stronger until it reached statistical significance on day six. This locus was also associated with seizure susceptibility after twenty-eight days. Clearly, the genetic factors involved change along with brain physiology after repeated seizures.

They named the newly identified locus Epileptogenesis susceptibility factor 1, or Esf1. It may have a function related to calcium signaling in the brain, which is an important molecular mechanism in epilepsy progression. After repeated seizures, the brain tries to adjust itself to increase neuronal stability. Understanding this plastic response and the genes that control it may one day lead to novel epilepsy treatment and management options.

CITATION

Multidimensional Genetic Analysis of Repeated Seizures in the Hybrid Mouse Diversity Panel Reveals a Novel Epileptogenesis Susceptibility Locus

Russell J. Ferland, Jason Smith, Dominick Papandrea, Jessica Gracias, Leah Hains, Sridhar B. Kadiyala, Brittany O’Brien, Eun Yong Kang, Barbara S. Beyer and Bruce J. Herron

G3: Genes, Genomes, Genetics August 2017 7: 2545-2558

https://doi.org/10.1534/g3.117.042234

http://www.g3journal.org/content/7/8/2545

They rattle as warning, but during the hunt their strike is silent and sudden. Any rabbit or mouse targeted by a rattlesnake is doomed—the snake’s bite carries a paralyzing venom. The toxins in this venom are proteins encoded by a large gene family that arose by gene duplication. In the July issue of GENETICS, Margres et al. tackle two models of how gene family expansion gets started by analyzing individual variation in a rattlesnake toxin gene family. They find that the most important factor in gene family growth via duplication was selection pressure to increase protein expression level.

Gene families are groups of similar genes born through duplication and are extremely common in eukaryote genomes. The different genes in a family often have sequence changes that allow them to carry out distinct functions, but additional gene copies also mean a higher overall expression level. Theoretically, both of these consequences of gene family expansion can be adaptive, but it’s unclear which is more important during the initial stages of gene family evolution. To clarify this question, Margres et al. use the rattlesnake gene family that encodes myotoxin, a component of venom.

Venom is a useful model because the connection between protein expression and phenotype is clear: the more protein is expressed, the more potent the effect. And importantly, there is still variation in the size of the myotoxin gene family among rattlesnakes. For this study, the authors collected venom and blood samples from over a hundred live-caught, wild rattlesnakes from across the Southeastern US. The number of myotoxin gene copies in these snakes ranged from zero to nearly 50, with a corresponding increase in myotoxin protein expression in venom. However, only four individuals carried gene copies with a nucleotide polymorphism within the key exons, indicating that the duplicate copies are essentially identical.

Clearly, these carbon-copy myotoxin genes aren’t carrying out different functions. The direct relationship between venom protein level and the number of myotoxin gene copies shows that the expansion of this gene family is likely driven by selection for increased expression and thus stronger venom. Animals as diverse as platypuses and cone snails use venom for hunting and defense. This study not only shows how this fascinating and frightening adaptation evolves, but it also provides a glimpse of the forces that can trigger a gene to start down the road of expansion—and ultimately—diversification.

CITATION

Selection To Increase Expression, Not Sequence Diversity, Precedes Gene Family Origin and Expansion in Rattlesnake Venom

Mark J. Margres, Alyssa T. Bigelow, Emily Moriarty Lemmon, Alan R. Lemmon and Darin R. Rokyta

GENETICS July 1, 2017 vol. 206 no. 3 1569-1580; https://doi.org/10.1534/genetics.117.202655

http://www.genetics.org/content/206/3/1569

Whether a thunderclap drives your dog to cower behind the couch or leaves it unfazed may be determined in part by genetics. In the June issue of GENETICS, Ilska et al. analyze genetic contributors to canine personality traits—such as fear of loud noises—using owners’ reports of their pets’ behavior.

The researchers chose this survey-based method in place of standardized behavior testing both to create a large body of data and to eliminate any influence of a foreign testing environment on the dogs’ behavior. They measured 12 different traits, from trainability to tendency to bark, using a 101-item questionnaire called the Canine Behavioral Assessment and Research Questionnaire (C-BARQ) that was originally designed to screen potential guide dogs. Then they looked for relationships between these traits and aspects of the dogs’ pedigrees and genotypes.

Of these traits, the most heritable were fear of noises and ability to play fetch. Perhaps surprisingly, many of the genetic factors linked to fetching ability were not related to other aspects of trainability. Aggression toward strangers and other dogs was also heritable, but aggression toward owners was not, likely because humans have placed strong selective pressure on dogs to be loyal and gentle toward their owners, leading to low genetic variance. Some traits were also related to each other—trainability had an inverse relationship with “unusual behavior,” a finding that probably wouldn’t shock most dog owners.

Some of the variants associated with the personality traits were located near genes with known neurological functions. For example, dogs that were prone to agitation often carried a variant near the gene for tyrosine hydroxylase, which is involved in the synthesis of the neurotransmitter dopamine. In humans, dopamine dysfunction is implicated in psychological conditions such as attention deficit-hyperactivity disorder, and some variants of the tyrosine hydroxylase gene are associated with the tendency to experience negative emotions and excitability—both traits related to impulsivity.

Because the study was conducted only on Labrador Retrievers in the United Kingdom, the authors caution that other dog breeds may differ in how heritable different personality traits are. But in any case, just like human personalities, it seems that dog personalities have a strong genetic component. So if your dog stares at you blankly next time you throw it a ball, don’t succumb to frustration—fetching just may not be in its genes.

CITATION:

Ilska, J.; Haskell, M.; Blott, S.; Sánchez-Molano, E.; Polgar, Z.; Lofgren, S.; Clements, D.; Wiener, P. Genetic Characterisation of Dog Personality Traits.
GENETICS, 206(2), 1101-1111.
DOI: 10.1534/genetics.116.192674
http://www.genetics.org/content/206/2/1101

Fascinating discoveries sometimes emerge from the most daunting of experimental roadblocks. Designed to generate over 1,000 recombinant inbred mice lines for genetic mapping, the Collaborative Cross (CC) project unearthed astounding variation in male fertility when nearly 95% of the highly inbred CC lines went extinct. As part of the Multiparental Populations series in the June issue of GENETICS, Shorter et al. use these fortuitous results to map the genetic variation underlying differences in male fertility and other reproductive traits. Their findings suggest the infertility in these lines is caused by genetic variants distributed across the genome, revealing incompatibilities between subspecies.

The CC project was designed as a powerful genetic mapping population consisting of thousands of highly inbred lines that are extremely genetically different from each other. The population founders came from several common varieties of lab mice, as well as wild-derived animals representing the three mouse subspecies. All of these lines were crossed to incorporate as much genetic variation in the population as possible. The hybrid offspring were then inbred to create high homozygosity within a line. As the lines became more and more inbred, something unexpected began to happen.

From the start, the collaborating research teams agreed they would not undertake “heroic” efforts to save lines that were struggling to persist due to high mortality or low reproduction. This policy changed as the CC lines began to go extinct at an alarming rate. In the end, 95% of the CC lines were lost despite the efforts of researchers to maintain them through between-line crosses and male fertility testing. Although some extinctions are expected as the hidden phenotypes of deleterious alleles are progressively revealed by inbreeding, the number observed far exceeded these expectations.

The culprit behind this perplexing mouse mass extinction was male infertility; nearly half of the failed lines included males that were unable to sire offspring. This gave the authors an opportunity to turn lemons into lemonade: they decided to map male reproductive traits to identify the underlying genetic basis of the problems in the extinct CC lines. They found that the contribution of the X-chromosome and the autosomes to the genomes of the extinct lines was different, with the extinct lines showing a deficit in X-linked haplotypes from the wild-derived founders. This suggests selection against retaining wild alleles at X-linked genes during the inbreeding process. Looking more closely at the extinct lines, they found very high variability in sperm count, sperm motility, and reproductive organ weights. They performed QTL mapping on fertility and reproductive traits using the extinct CC lines and identified several loci across the genome associated with variation in reproductive phenotypes. One identified locus on the X-chromosome contained a region previously identified as affecting hybrid incompatibility and speciation.

They also found that the majority of haplotypes associated with infertility and poor reproductive traits came from the wild-derived founders of different subspecies than common lab mice. It seems that genetic incompatibility between these distinct subspecies causes male infertility and reproductive isolation. Indeed, the surviving CC strains were found to have a deficit of genetic contributions from these founders across their entire genome.

The wild-derived mice were meant to provide as much genetic variation as possible to the CC lines, but this variation has turned out to be a double-edged sword. The crossing scheme between these diverged subspecies created new genetic combinations that disrupted male reproduction—often one of the first processes to be affected during speciation. Although the line extinction was unplanned and unwanted, it also provided a unique opportunity to dissect the genetics of male reproduction and the early stages of species isolation in mammals.

CITATION

Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross  

John R. Shorter, Fanny Odet, David L. Aylor, Wenqi Pan, Chia-Yu Kao, Chen-Ping Fu, Andrew P. Morgan, Seth Greenstein, Timothy A. Bell, Alicia M. Stevans, Ryan W. Feathers, Sunny Patel, Sarah E. Cates, Ginger D. Shaw, Darla R. Miller, Elissa J. Chesler, Leonard McMillian, Deborah A. O’Brien, and Fernando Pardo-Manuel de Villena

Genetics June 2017 206: 557-572

http://www.genetics.org/content/206/2/557

https://doi.org/10.1534/genetics.116.199596

Multiparental populations (MPPs) have brought a new era in mapping complex traits, as well as new analytical challenges. To face these challenges and encourage innovation, the GSA journals launched the ongoing Multiparental Populations series in 2014. This month’s issues of GENETICS and G3 feature a bumper 16 MPP articles, timed to celebrate a new easy-to-use site for browsing the series. In line with our goal of encouraging communication across disciplinary boundaries, the “MPP People” profiles aim to introduce series authors working in a wide range of systems.

Not all sand field crickets can fly. The “short wing” morph of this species is grounded by its stumpy wings and feeble flight muscles. But because female short-wings don’t need to sink their limited resources into the costly trappings of flight, they are champion reproducers. In contrast, the “long wing” morphs can fly to new and better habitats, but produce substantially fewer eggs than their Earth-bound peers.

Libby King has long been fascinated by such dramatic tradeoffs in how organisms allocate their limited pool of energy to key traits, particularly in how they coordinate their allocation strategy with the nutritional environment.

“If they have a lot of resources and a big pool of energy, then there might be one optimal way to divvy up that pie, but if they’re really resource limited, then there might be another, better way,” says King.

During her PhD research with Daphne Fairbairn and Derek Roff at the University of California, Riverside, King investigated how the proportion of long-wing to short-wing morphs in a cricket population is influenced by variation in resource availability across the landscape. From this ecological and evolutionary perspective, King was drawn to thinking about the mechanisms behind these patterns. What are the genes involved in strategy variation? There were no easy answers.

“That’s how I got pulled into the very hard problem of how to dissect a very complex phenotype,” says King. To work on such problems, she shifted focus in her postdoc research to fruit fly genomics.

Elizabeth G. King, University of Missouri–Columbia

“Libby is really talented and has already made big contributions to the field,” says her former postdoc mentor Anthony Long at the University of California, Irvine. “She is one of the rare people with a really deep appreciation for both classical quantitative genetics and more modern molecular approaches to the dissection of complex traits.”

Working with Long and Stuart Macdonald (University of Kansas), she played a key role in the development and testing of the Drosophila Synthetic Population Resource (DSPR), a pair of multiparental populations with high power and resolution for complex trait mapping.

The DSPR is derived from 15 founder inbred lines capturing fruit fly genetic diversity from around the world. Each of the two replicate DSPR populations was created by crossing eight founder lines (seven unique, one shared by both replicates) for 50 generations and then establishing more than 800 recombinant inbred lines (RILs) per population.

Some of the main advantages of the DSPR, says King, include the very high mapping resolution and the fact that initial trait mapping requires only phenotyping of the RILs because the genome sequence of each can be imputed. During her postdoc, King developed a Hidden Markov Model method to infer the RIL sequences using dense genotyping with RAD markers and the known genome sequences of the founders.

Inbred lines also enable testing multiple phenotypes across the same genotypes. This last feature is particularly important for King now that she has established her own lab and is using the DSPR to investigate resource allocation in Drosophila.

“These are pretty complex traits that encompass all sorts of other traits, so it’s really useful to be able to measure phenotypes at those multiple levels of organization,” she says.

In a paper published in the MPP series in the June issue of GENETICS, King’s group, led by graduate student Patrick Stanley, examined a widespread resource allocation pattern: in many eukaryotes, individuals tend to live longer and reproduce less when nutrients are scarce. This is hypothesized to help conserve resources for survival while the individual waits for conditions to improve.

One potential avenue for the evolution of this pattern is the highly conserved insulin/insulin-like growth factor/Target of Rapamycin (IIS/TOR) pathway. In many models, knockouts for genes in this pathway live longer than wild-type, and there is substantial evidence that the pathway is involved in coordinating growth and metabolism with nutritional conditions. Changing expression of these IIS/TOR genes is often hypothesized to drive the lifespan/reproduction shift seen in low nutrient conditions.

Stanley et al. used the DSPR to investigate the link between this pathway and the nutrient-induced lifespan shift by focusing on 56 core IIS/TOR genes. They assayed how expression of these genes changed on three different diets, mapped genetic variation influencing these responses, and then measured lifespan of a subset of flies under these conditions.

As expected, most genes in the pathway changed expression between diet conditions. The team successfully mapped the genetic basis for these changes, including two trans QTLs that likely represent transcription factors that respond to diet.

But, consistent with mixed results emerging elsewhere in the literature, the results do not provide strong evidence that IIS/TOR gene expression changes drive the lifespan response to diet. They observed relatively small expression changes in most genes, rather than strong changes at a few key genes, and these were not in the direction you would predict based on knockout mutant phenotypes. “There is a change in global gene expression in response to diet, and this may well be partially driving what’s going on, but it’s clearly not the whole story,” says King.

Detail from the cover of the July 2012 issue of GENETICS, which included an article describing the properties of the Drosophila Synthetic Population Resource (DSPR). The center image represents the 15 inbred founder lines used to create the DSPR (blue = A population, red = B population, center purple fly representing the founder line shared between the populations). The background shows a sample of 100 RILs with the colors representing the founder ancestry across the genome. White areas represent an uncertain founder assignment.

A second MPP paper by King and Long in the June issue of G3 uses simulation to explore how an important bias affecting QTL mapping applies to large panels like the DSPR. This bias, known as the Beavis effect, is the tendency of significant QTLs to have overestimated effect sizes. This is because a test with an overestimated effect size is more likely to be found significant than one with an underestimated effect.

This phenomenon is one reason that, even for a true hit, validating a significant locus in a second population can fail if the experimental design lacks the power to detect the QTL at its true effect size. Although the Beavis effect is well established for traditional two-way QTL mapping, its importance is unknown for multiparental designs and association mapping, which can involve millions of tests.

The study revealed that the most important factor affecting the strength of the Beavis effect is the sample size, with the detail of the mapping design mattering much less. In essence, the more lines that are phenotyped, the weaker the Beavis effect becomes and the more accurate the QTL effects estimates become. Using only a few lines from the DSPR would make it is highly likely that the effect sizes of significant QTL are overestimated, and they may be difficult to validate in replicate experiments or cross-validate between different mapping designs. King and Long use their results to provide guidelines on the sample sizes needed to accurately estimate the percent effect variance of an identified QTL and the conditions under which a mapped QTL is likely to be successfully replicated.

King’s work with the DSPR has not only provided her the means to pursue her interest in the evolution of resource allocation strategies. It has also enriched the field as a whole, providing a powerful new component to the Drosophila toolkit for unraveling the molecular mechanisms of complex traits.

Read other MPP People profiles.

Browse the GSA Journals MPP series.

MPP AUTHOR:

Elizabeth G. King, University of Missouri–Columbia

MPP ARTICLES:

The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster

Elizabeth G. King and Anthony D. Long

Genetic Dissection of Nutrition-Induced Plasticity in Insulin/Insulin-Like Growth Factor Signaling and Median Life Span in a Drosophila Multiparent Population

Patrick D. Stanley, Enoch Ng’oma, Siri O’Day, and Elizabeth G. King

The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans

Galina Kislukhin, Elizabeth G. King, Kelli N. Walters, Stuart J. Macdonald, and Anthony D. Long

Fine-Mapping Nicotine Resistance Loci in Drosophila Using a Multiparent Advanced Generation Inter-Cross Population

Tara N. Marriage, Elizabeth G. King, Anthony D. Long, and Stuart J. Macdonald

Using Drosophila melanogaster to identify chemotherapy toxicity genes

Elizabeth G. King, Galina Kislukhin, Kelli N. Walters, and Anthony D. Long

Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits

Elizabeth G. King, Stuart J. Macdonald, and Anthony D. Long

The GSA Journals are proud to announce a brand new site for our Multiparental Populations (MPP) series. We’re celebrating this redesigned, easy-to-browse site with the addition of sixteen new papers from both journals to the series.

As the field of genetics has grown, the rapid development of genomic technologies has given researchers the ability to dissect genetic variation and complex trait inheritance in sophisticated ways. Now, the challenge is often analysis.

A growing community of plant and animal researchers have established multiparental populations as a way to more accurately capture genetic variation and its contribution to phenotypes of interest. Analysis of these populations is complex, and the clear communication of experimental design and methodology bolsters the community, paving the way for continuing advances.

The GSA Journals began the MPP series in 2014 to collect emerging data and transparent methods and to stimulate discussion. We have published work across a broad range of species—including mouse, maize, Drosophila, wheat, yeast, and others. We hope to foster a cross-disciplinary flow of information and to provide a rich resource of experimental and methodological data to the community. We welcome submissions to the MPP series on a continuous basis, and we accept presubmission inquiries.

Check out the new site and see how simple it is to browse and search the collection. Stay up to date with community news through the “Multiparental Populations in the News” sidebar. In line with our goal of encouraging communication across disciplinary boundaries, the “MPP People” profiles aim to introduce series authors working in a wide range of systems.

Geoffrey Morris

Andrew Morgan

Elizabeth King

The newest papers added to the series are summarized below.

GENETICS

Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits

Dirk-Jan de Koning, Lauren M. McIntyre

Epistasis: Searching for Interacting Genetic Variants Using Crosses

Ian M. Ehrenreich

Epistasis refers to situations in which combinations of genetic variants have nonadditive phenotypic effects. Epistasis between two variants is more commonly explored, but higher-order interactions involving multiple variants also occur. In this editorial, Ehrenreich makes the case for exploring epistasis in quantitative genetic crosses.

Genomes of the Mouse Collaborative Cross

Anuj Srivastava, Andrew P. Morgan, Maya L. Najarian, Vishal Kumar Sarsani, J. Sebastian Sigmon, John R. Shorter, Anwica Kashfeen, Rachel C. McMullan, Lucy H. Williams, Paola Giusti-Rodríguez, Martin T. Ferris, Patrick Sullivan, Pablo Hock, Darla R. Miller, Timothy A. Bell, Leonard McMillan, Gary A. Churchill, and Fernando Pardo-Manuel de Villena

The Collaborative Cross (CC) is a panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here, Srivastava et al. present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. This study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection.

Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross

John R. Shorter, Fanny Odet, David L. Aylor, Wenqi Pan, Chia-Yu Kao, Chen-Ping Fu, Andrew P. Morgan, Seth Greenstein, Timothy A. Bell, Alicia M. Stevans, Ryan W. Feathers, Sunny Patel, Sarah E. Cates, Ginger D. Shaw, Darla R. Miller, Elissa J. Chesler, Leonard McMillian, Deborah A. O’Brien, and Fernando Pardo-Manuel de Villena

The extinction rate in the Collaborative Cross (CC) population is estimated at 95%. Shorter et al. analyzed fertility and reproductive phenotypes on the last unproductive males from 347 independent CC lines and performed the largest trait mapping experiment in the CC to date. Extinction in the CC is largely due to male infertility. The results from several experiments suggest that poor fertility and hybrid incompatibilities between subspecies contribute to breeding difficulties and strain extinction.

Increased Power to Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

Sophie Bouchet, Marcus O. Olatoye, Sandeep R. Marla, Ramasamy Perumal, Tesfaye Tesso, Jianming Yu, Mitch Tuinstra, and Geoffrey P. Morris

In crop species, adaptation to different agroclimatic regions creates useful variation, but also leads to genetic correlations that confound trait dissection. To address this challenge in sorghum, a widely adapted cereal crop, Bouchet et al. have developed and characterized a Nested Association Mapping (NAM) population, which reshuffles global genetic diversity for trait mapping. This manuscript describes the sorghum NAM resource, a population of 2214 recombinant inbred lines genotyped at 90,000 markers. The authors validated the NAM resource by mapping flowering time and plant height and used simulated traits to demonstrate that NAM is generally more powerful for dissection of traits under strong selection.

Genetic Dissection of Nutrition-Induced Plasticity in Insulin/Insulin-Like Growth Factor Signaling and Median Life Span in a Drosophila Multiparent Population

Patrick D. Stanley, Enoch Ng’oma, Siri O’Day, and Elizabeth G. King

The insulin/insulin-like growth factor signaling (IIS) and target of rapamycin (TOR) pathways have long been thought to be involved in how organisms respond to their nutritional environment; however, little is known about the genetic basis of naturally-occurring variation in these pathways. Stanley et al. use a multiparent population to genetically dissect diet-dependent IIS/TOR expression and connect it to diet-dependent changes in lifespan.

Structural Variation Shapes the Landscape of Recombination in Mouse

Andrew P. Morgan, Daniel M. Gatti,  Maya L. Najarian, Thomas M. Keane, Raymond J. Galante, Allan I. Pack, Richard Mott, Gary A. Churchill, and Fernando Pardo-Manuel de Villena

To study local variation in recombination rates and the impact of genetic diversity on the pattern and distribution of crossover events, Morgan et al. analyzed genotype data from 6,886 Diversity Outbred mice. They find that approximately three-quarters of crossover events occur within putative recombination hotspots. They further show that crossovers are suppressed in regions with copy number variation. They hypothesize that the epigenetic features of these regions may reflect altered chromatin structure in meiosis that results in a failure of pairing between chromosomes carrying different structural alleles.

Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice

Anna L. Tyler, Bo Ji, Daniel M. Gatti, Steven C. Munger, Gary A. Churchill, Karen L. Svenson, and Gregory W. Carter

Tyler et al. analyzed the complex genetic architecture of traits related to metabolic disease using the Diversity Outbred (DO) mouse population. By jointly analyzing epistasis across multiple phenotypes, the authors inferred a multi-scale network of quantitative trait loci (QTL) involving QTL-QTL, QTL-sex, and QTL-diet interactions that jointly influence body composition, serum markers, and transcriptome expression. They found that genetic contributions from different founder ancestries often combine to drive more extreme phenotypes, leading to the broad phenotypic diversity observed in the DO population.

G3

Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders

Daniel Oreper, Yanwei Cai, Lisa M. Tarantino, Fernando Pardo- Manuel de Villena, William Valdar

The Collaborative Cross (CC) is a large panel of recently established multiparental recombinant inbred mouse strains. CC experimental design and analysis are facilitated by Oreper et al.’s newly developed Inbred Strain Variant Database (ISVdb), which provides easy-to-access CC sequence-based information. In particular, the ISVdb provides haplotype-imputed exonic variant data—an alternative and complement to direct sequencing of the CC, which is also not yet easily accessible. Additionally, the ISVdb 1) provides exonic variant consequences, 2) rapidly simulates F1 populations, and 3) maintains imputation uncertainty, allowing imputed CC data to be refined by upcoming sequencing. The ISVdb is accessible at http://isvdb.unc.edu/.

Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster

Michael A. Najarro, Jennifer L. Hackett, Stuart J. Macdonald

Boric acid is a widely-used household insecticide, but we do not fully understand how it leads to mortality. In this study, Najarro et al. assayed the genetic background for Boric Acid resistance by measuring resistance to the compound in a diverse set of Drosophila melanogaster strains and uncovered substantial trait variation. Several short genomic regions impact the phenotype, in one case implicating a member of a known family of detoxification enzymes. While the authors were unable to confidently identify DNA sequence changes leading to variation in toxicity, their work provides a platform for future genetic exploration of the mechanism of action of boric acid on metabolism and physiology in Drosophila.

The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster

Elizabeth G. King, Anthony D. Long

Two critical components of characterizing the genetic loci underlying complex traits are 1) to accurately estimate the relative contribution of mapped loci to the overall genetic variance of the trait and 2) to validate the mapped loci. Estimations of the contribution of mapped loci to the genetic variance are known to be upwardly biased. Here, King and Long quantify this effect for modern mapping techniques and shows how this bias can lead to false expectations for validating loci.

Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice

Lisa E. Gralinski, Vineet D. Menachery, Andrew P. Morgan, Allison L. Totura, Anne Beall, Jacob Kocher, Jessica Plante, D. Corinne Harrison-Shostak, Alexandra Schäfer, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Ralph S. Baric

SARS-Coronavirus (CoV) caused a wide range of disease during the global outbreak, from mild respiratory illness to significant morbidity and mortality. Gralinksi et al. performed an F2 cross of two Collaborative Cross (CC) recombinant inbred lines to search for host genes that contribute to SARS-CoV resistance and susceptibility. They identified five QTL with contributions from seven of eight CC founders. One QTL was associated with multiple phenotypes including weight loss, virus titer, and lung pathology. Ticam2-/- mice confirmed the role of that gene in contributing to SARS-CoV-induced weight loss and pulmonary hemorrhage, demonstrating the importance of Toll Like Receptor signaling in protecting from coronavirus-induced disease.

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross

Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Renee C. Ireton, Michael Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Shannon McWeeney, Michael Gale

The oligoadenylate-synthetase (OAS) gene family includes Oas1b, a non-canonical OAS that lacks enzymatic activity. Full-length Oas1b is essential for protection against West Nile virus neuroinvasion and disease in inbred mouse models of infection, but how it programs innate immune defense across distinct genetic backgrounds is not defined. Green et al. examined Oas1b genetics, in vivo transcriptomics, and WNV infection among genetically distinct Collaborative Cross (CC) mouse strains. Their results reveal that Oas1b genotype and gene dosage link with novel innate immune gene expression signatures that impact specific biological pathways for WNV infection control and immunity.

Identification of Ganoderma Disease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population

Sébastien Tisné, Virginie Pomiès, Virginie Riou, Indra Syahputra, Benoît Cochard, Marie Denis

Stem rot caused by Ganoderma boninense is a devastating disease for oil palm, but information on the genetic architecture of Ganoderma resistance has not yet been reported. Tisné et al. implemented an original statistical modeling approach to analyze data based on 25 years of field monitoring the natural infection of an oil palm multiparental population. They identified four resistance loci in a broad genetic diversity that are relevant for breeding programs, showing that resistance is quantitative and that favorable alleles can be selected using the current reciprocal recurrent selection scheme.

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

Francisco A. Cubillos, Claire Brice, Jennifer Molinet, Sébastien Tisné, Valentina Abarca, Sebastián M. Tapia, Christian Oporto, Verónica García, Gianni Liti, Claudio Martínez

Nitrogen is an essential nutrient for yeast, and natural fermentation musts across the world differ in their nitrogen content. In this manuscript, Cubillos et al. studied nitrogen consumption differences under oenological conditions in the SGRP-4X, a recombinant population derived from the intercross of four parental strains. The results provided evidence of six allelic variants responsible for minor differences in consumption levels for arginine and aromatic amino acids, demonstrating the power of complex populations to unveil a larger number of small effect allelic variants.

Pedigree-Based Analysis in a Multiparental Population of Octoploid Strawberry Reveals QTL Alleles Conferring Resistance to Phytophthora cactorum

Jozer Mangandi, Sujeet Verma, Luis Osorio, Natalia A. Peres, Eric van de Weg, Vance M. Whitaker

Mangandi et al. describe the genetic locus in cultivated strawberry (Fragaria ×ananassa) that controls resistance to Phytophthora cactorum, which causes crown rots in the major strawberry production regions of the world. This locus, named FaRPc2, was discovered and analyzed in a complex breeding population arising from 139 crosses among 61 parents. The authors performed a pedigree-based analysis across families simultaneously, giving strong evidence for the presence of two different resistance alleles. The FaRPc2 locus has robust effects across a wide array of genetic backgrounds, making it an excellent target for genetic improvement of resistance.   

Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population

Chitra Raghavan, Ramil Mauleon, Vanica Lacorte, Monalisa Jubay, Hein Zaw, Justine Bonifacio, Rakesh Kumar Singh, B. Emma Huang, Hei Leung

Raghavan et al. explore the genetic structure of a rice MAGIC population consisting of 1316 lines derived from eight parents. To determine the impact of missing data and errors on recombination levels and mapping resolution, they filtered the genotyping-by-sequencing data on all lines and imputed the data at varying levels of stringency. They map QTL for agronomic, biotic, and abiotic stress traits, and provide guidelines on best approaches to overall analysis pipelines, including quality control. These findings will serve as a guideline to researchers developing crop multiparent populations.