Journal Club

2015-2016 Journal Club


Happy International Year of the Pulses! To celebrate these delicious legumes, please join us Monday, May 2 at noon in Moore 473, where Carlos Arbizu will lead a discussion on Andean bean diversity.

The United Nations, in collaboration with the FAO, declared 2016 the International Year of Pulses (IYP) to improve public awareness, encourage production, and increase dietary use of pulses. Pulses, which include beans, chickpeas, and lentils, are cultivated in many countries and are valued for their high amounts of protein, fiber, and micronutrients. Large-seeded dry beans (kidney and cranberry beans), also known as “Andean beans,” are an important source of food in the Americas and Africa. Despite their dietary importance, research on these crops is lagging behind their Mesoamerican counterparts. A study conducted by Cichy and collaborators (2015) genotyped and phenotyped a diversity panel, aiming to improve use of Andean bean germplasm in breeding efforts. What are the major challenges influencing pulse production and how are they being addressed? What efforts can we make to improve the utilization of pulses in the diet and in land management?

The article by Cichy et al (2015) can be accessed at

More information about the International Year of Pulses

In solidarity with the UN and FAO, JC will provide pulse-inspired treats and a traditional beverage made from coffee beans.


Please join us Monday, April 25 at noon in Moore 473, where Lynn Maher will discuss the regulation of organisms edited with CRISPR-Cas9.

The advent of novel DNA-editing technologies, such as zinc finger nucleases, TALENs, and CRISPR-Cas9, has raised questions regarding the existing regulatory framework for genetically modified organisms. Last week, USDA-APHIS informed Yinong Yang, a plant pathologist at Penn State, that a mushroom he developed using CRISPR-Cas9 would not be regulated, making it the first organism edited with CRISPR-Cas9 system to escape USDA oversight. The mushroom in question was engineered to resist browning by knocking out a polyphenol oxidase (PPO) gene, the same mechanism used to reduce browning in Arctic apples and Innate potatoes, which were subject to USDA scrutiny.

Is this a new era for GMOs? As scientists, how can we reframe the public discourse and stigmas surrounding gene-editing technology? What opportunities does this precedent offer, at the industry and academic level, for other products developed using CRISPR-Cas9?

Scientific American article: Gene-Edited CRISPR Mushroom Escapes U.S. Regulation

“Whether ’tis nobler in the mind to deliberate
The intricacies and bureaucracy of regulation
Or to eat cookies and drink a sea of coffee,
And by listening gain knowledge.”


Please join us Monday, April 18 at noon in Moore 473, where Guillaume Ramstein will lead a discussion on the business models of scientific publishing.

The industry of publishing is entering an interesting era! The “publishing giants” have typically applied a model based on subscriptions or one-article fees and, as the recent merger between Nature Publishing Group and major publisher Springer illustrates, they tend to get bigger! On the other hand, open-access journals (e.g. PLoS ONE) and repositories (e.g. arXiv) distribute articles for free, and are gaining importance in the game. Remarkably, strong and unlawful reactions to the traditional subscription model are also arising, through a science-paper equivalent of Napster: Sci-Hub. As a (future) scientist, what do you condone or condemn in these models? What evolution would like to see in the diffusion of (your) scientific knowledge? Come and share your opinion next Monday!

A Nature News article by van Noorden (2016) regarding open-access vs. subscription can be accessed at

New York Times article about Sci-Hub: Should all research papers be free?

Attend Journal Club to enjoy open access to coffee, cookies, and scientific dialogue.


Please join us Monday, April 11 at noon in Moore 473 for a discussion about germplasm conservation and seed industry consolidation.

Crop wild relatives are widely lauded as a valuable source of genetic diversity, but how well do conservation efforts truly capture ecological diversity? A recent study by Alvarez et al. quantified the global conservation and availability of wild accessions for 81 crops, highlighting collection gaps and the corresponding lack of diversity. The authors stress the need for a concerted effort to develop more comprehensive gene banks, which are constrained by lack of funding, political challenges, and biological limitations. The availability of genetic resources also stands to be impacted by recent consolidation within the seed industry (e.g. Dow & Dupont, Syngenta & Chem China). What are options for improving existing gene banks? Is there a trade-off between industry consolidation and conservation priorities (e.g. access to genetic resources and utilization of crop diversity)?

The article by Alvarez et al. (2016) and can be accessed at:

NPR article regarding seed industry consolidation:

Does coffee and cookie consumption increase the diversity of scientific discourse? Find out by enjoying complementary coffee and cookies at journal club.


Please join us Monday, April 4 at noon in Moore 473, where Brett Burdo will lead a discussion on the use of functional genomics to bridge the gap between quantitative genetics and molecular biology.

Large scale functional genomics projects, such as ENCODE, HapMap, and the 1000 Genomes Project, have revolutionized our understanding of elements underlying quantitative traits and genetic diseases in the human genome. Did you know that 80% of GWAS associations in humans lie outside of coding regions? Plant scientists and quantitative geneticists are now beginning to explore plant genomes on this scale and can learn from the work that has already been done on us! In this 2015 perspective piece, Tuuli Lappalainen discusses advances in molecular biology and quantitative genetics that have led to these projects, and how they have helped bridge the perceived gap between quantitative and molecular genetics in understanding human biology.

Coffee and cookies will be provided to help bridge the gap between your office and attendance at journal club.



Please join us on Monday, March 28 at noon in Moore 473 to discuss plant response to leaf vibrations.

In their 2014 paper, Appel & Cocroft describe systemic induction of plant defense compounds in Arabidopsis following exposure to the sound of insect chewing. That’s right, before any actual insect feeding has occurred! Their results suggest that plants have differential response to vibrational cues in nature (e.g. wind, insect chewing, insect songs) and that these responses may help prime plants for defense against herbivory as part of a vibration signaling pathway. How is plant response to sound measured? What are the ecological implications of these findings? Should we be singing to our research plots? Can we exploit plant by sound interaction for plant improvement?

Does sipping coffee and chewing cookies prime the brain for scientific discussion? Attend journal club to test this hypothesis!

Appel and Cocroft 2014


This is a reminder that there will be no journal club, coffee, or cookies on Monday, March 21, but there are still several openings for anyone interested in leading a discussion. Presenting at journal club is a great opportunity to share your research and/or experiences, critically analyze scientific articles, and promote discussion about current trends and developments in the plant sciences.


Please join us in Moore 473 on Monday, March 14 at noon to discuss the role of scientists in reducing food waste.

The need to feed a growing population is a common discussion point in the plant sciences. We often focus on the genetic gain aspect of food security, but this is just one piece of a large, complex puzzle, discussed in depth by Foley et al. (2011). Recent news has focused extensively on efforts to combat food waste, which comprises an estimated 30% of total agricultural production. In February, the French senate unanimously passed a law requiring supermarkets to donate unsold food to charities or food banks, with plans to extend this law to the rest of the EU. Food waste was also the cover story in the latest issue of National Geographic, titled “Eat me: How ugly food can help feed the planet.” Is the precedent in France a good model for other countries? How much do crop yields really need to improve by 2050? As plant scientists, how can we contribute to the fight against food waste and the larger goal of agricultural sustainability?

More about the French law forbidding food waste:

Foley et al 2011


Please join us Monday, March 7 at noon in Moore 473, where Alex Marand will lead a discussion about the genetics of circadian clocks in tomatoes.

Circadian clock genes play a central role in plant physiology and key developmental transitions in plants. It has been demonstrated that natural genetic variation in these loci is crucial to local adaptation. A recent study by Muller et al. demonstrates that artificial selection by humans has led to drastic modulations in circadian clock rhythm in cultivated tomato species. By utilizing a classic genetic mapping approach coupled with contemporary evolutionary and population genetic methods, Muller et al. mapped the causal domestication polymorphism by investigating signatures of selection concomitant with significant quantitative trait loci for quantitative variation in circadian rhythm modulation.

Muller et al 2016


Please join us for a special debate edition of journal club next Monday, Feb. 29 in Moore 473 at noon!

In the public debate on government budgets, scientific funding is often scrutinized. Journal Club next week will cover an essay series titled,”Who Pays for Science?” in which arguments for and against public funding of research are examined. This essay series has a keynote essay ( as well as three response essays ( by prominent scientists/economists. Regardless of the position one takes on this, these arguments are sure to shape funding allocations for plant science research in the future. This discussion will be moderated by Curtis Frederick in a debate style format. The conversation will be directed by a set of questions and responses will be regulated by the moderator so all parties have a chance to voice their position.


Are you interested in conservation biology and/or crowdfunding for research? Please join us Monday, February 22 at noon in Moore 473, where Chris D’Angelo will lead a discussion about parrot conservation and the pursuit of public funding.

What if you could sequence every individual in a species? Andrew Digby is doing just that as part of a conservation effort for the kakapo, an unusual, flightless parrot endemic to New Zealand. Because they are a ground-dwelling species, kakapos are particularly susceptible to predation and only an estimated 125 individuals remain. While it’s easy to support conservation efforts in spirit, securing funding is a constant challenge. As an alternative to grants, Digby’s group has started a crowdfunding campaign to support their research and encourage public interest. Can crowdfunding provide a viable substitute for grants and bridge the gap between scientists and the public?

More about the kakapo research effort and fundraising:

Press article about the effort to sequence all known kakapo:

“The Crowdfunding Phenomenon: Can it Work for Biomedical Research?”


Computational thinking is a widely applicable analytical skill with potential to improve the way we approach scientific inquiries. Jeannette Wing (2006, 2008) presents a case for actively developing this ability, which combines abstract thought processes from mathematics, engineering, and the sciences. Please join us Monday, Feb. 15 at noon in Moore 473, where Schuyler Smith will lead a discussion on the what, how and why of computational thinking.

The forecast is intellectually stimulating with a 100% chance of coffee and cookies

Wing 2006

Wing 2008


Ever wonder how things work on the animal side? Many of the techniques we use in plant genetics have origins in animal science. Following up on our previous dialogue about MAGIC populations, Matthew Murray will lead a discussion about the mouse Collaborative Cross (Collaborative Cross Consortium, 2012) and Diverse Outbred Populations (Svenson et al., 2012). Please join us Monday, Feb. 8 at noon in Moore 473 for a thought-provoking conversation about the development of genetic resource populations, analytical methods, and how these techniques can be adapted for the plant sciences.




Please join us for the first journal club of the Spring 2016 semester on Monday, Feb. 1 @ noon in Moore Hall 473.

Do you believe in MAGIC? Multi-parent Advanced Generation Inter-Cross populations are a unique approach to fine mapping, novel QTL identification, and applied breeding. In their 2013 paper, Bandillo et al. describe the development and use of MAGIC populations in rice. These populations offer plant scientists a valuable new tool with advantages over traditional QTL mapping and GWAS, as well as an opportunity to justify your results with “magic.” The article can be accessed at Keeping with tradition, coffee and cookies will be provided.


Please join us next Monday at noon in Moore 473 as we will talk about the impact of climate change on U.S. soybean production.

Increases in crop yields over time are often attributed to genetic and management advances, but the impact of climate change on yield gain is often confounded with these advances or simply overlooked. Efforts led by the Conley lab here at the UW examined how temperature and precipitation changes have solely influenced soybean yield in the U.S. over the past 20 years. The work by Mourtzinis et al. (2015) shows that climate change has benefited growers in some states while negatively impacting others.

David Marburger will lead this discussion describing the positive and negative impacts of climate change on soybean production throughout the U.S. and share ways soybean growers can adapt their management strategies in order to mitigate the negative impacts.

You can access the article (and supplementary files) through the following link:


Please join us next Monday at noon in Moore 473 to talk about the origins of modern tomato.

We all know modern crops went through a process of domestication, which is considered the first stage in plant breeding. Even though tomato is one of the most studied vegetables worldwide and is considered a high value crop, little is known about how human selection altered its genome to make it 100 bigger than its wild ancestor! Lin et al. (2014) used genome sequences to provide evidence for the changes in the tomato genome due to domestication and improvement.

Carlos Arbizu will lead the discussion around this impressive study which provided key insights into the (beneficial as well detrimental) effects of human selection on the world most-valued vegetable.

Lin et al. 2014


Please join us next Monday at noon in Moore 473 to talk about genotyping in polyploid species.

In contrast to the ready usability of SNP chip in diploid organisms, tetraploid crops have lagged in entering the age of big data in molecular genetics. At any given marker, the high number of possible genotype classes (allelic dosages) makes automation of genotype scoring from maker chip intensity data challenging! Voorrips et al. (2011) offered a solution using mixture models, and research is underway in the Endelman lab at the UW to implement alternatives, using hierarchical clustering.

Cari Schmitz Carley will lead a discussion of the Voorrips paper and share some additional methods for tackling this fundamental problem in polyploid genetics, based on the work of other labs, including her own.

Voorrips et al. 2011


Please join us next Monday at noon in Moore 473 to talk about big data in molecular genetics.

As we are acquiring more and more diverse and massive data (genomics, transcriptomics, metabolomics, shovelomics,…), we now get to peek at the stunning complexity of processes underlying the elaboration of a particular trait. Ritchie et al. (2015) recently published a review about the leading-edge methods addressing the issue of integrating different types of data to provide a realistic picture of genotype-phenotype relationships. After our last discussion in Journal club about components of traits, let’s take a step further back and contemplate an even bigger picture…

Scott Stelpflug will lead this discussion around the ambitious path of deciphering genotype-to-phenotype processes using big data!

Ritchie et al. 2015


Please join us next Monday at noon in Moore 473 to talk about root architecture and precision phenotyping.

We are all well aware that high-quality, high-throughput phenotyping now lags behind genotyping. The review article by Kuijken et al. (2015) discusses current semi- and fully-automated root system architecture (RSA) phenotyping platforms and determines how well they have been able to increase genetic gain for crop genetic improvement. In addition to discussing the article, we hope to have an open conversation about what phenotyping hardware and software others have used and how successful these various systems were at capturing – or resolving – traits of interest.

Shelby Ellison will lead a discussion around the pros and cons of various root architecture phenotyping platforms, but also discuss the opportunities offered by precision phenotyping for plant breeding in general!

Kuijken et al. 2015


Please join us next Monday at noon in Moore 473 as we will talk about (self-)deception in science!

As scientists, we are always on the hunt for new, interesting, and profound results. Most journals are heavily focused on positive, rather than negative, results, and we design and conduct experiments in the hopes of finding something new. The downside of our search for meaning amongst noise is that we sometimes see patterns where they do not really exist. This article from a recent issue of Nature highlights the ways in which scientists can introduce bias into their research, as well as some ways to avoid doing so.

Whatever your field, come and talk about your own experience and share your opinions with us next week in this discussion, which will be led by Joe Gage.

You can access the article through the following link:


Please join us next Monday at noon in Moore 473 to talk about the domestication and diffusion of maize landraces.

Earlier this semester, we talked about the effect of breeding on genetic diversity in maize. Now Manfred Mayer will go further back in time and present the findings of Hufford et al. (2013), who shed light upon the domestication and spread of maize from its wild ancestor, teosinte.

A single event of maize domestication from teosinte was dated back to about 9,000 years ago. However, there remained one interesting paradox: maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where Balsas teosinte does not grow! The paradox was resolved by showing that the surpassing relationship between maize populations of the Mexican highlands and Balsas teosinte was caused by introgression from another subspecies of Zea mays, Mexicana teosinte (van Heerwaarden et al. 2011). Hufford et al. (2013) describe the gene flows that still occur between Mexicana teosinte and domesticated maize.

Manfred will guide us through this great example of investigation, built up over the years, on maize history.

Hufford et al. 2013

van Heerwaarden et al. 2011


Please join us next Monday at noon in Moore 473 as we will talk about the scent of roses…

Would a rose with any other biosynthesis pathway smell as sweet? Roses are prized for their fragrant flowers, but many cultivars have lost their aromatic appeal due to preferential breeding for appearance and longevity. Hundreds of volatile compounds, most notably monoterpenes, contribute to the special scent of roses.

Although monoterpene synthase is the canonical enzyme for monoterpene production, Magnard et al. recently reported an alternative pathway, which utilizes a Nudix hydrolase. Their findings have identified a potential marker for breeders to fortify flowers with fragrance and raised many new and exciting research questions: Why did this unusual pathway evolve? When did it originate? Is it specific to roses? Did it evolve independently in other species? What are the implications for Shakespeare’s classic metaphor? Let’s discuss!

Sarah Turner will lead the discussion around the recent research article of Magnard et al. (2015) but also the perspective piece from Tholl & Gershenzon (2015).

Magnard et al. 2015

Tholl & Gershenzon 2015


Please join us next Monday at noon in Moore 473 as we will talk about the ecology of mosquitoes (yes we will!).

Brett Burdo will present a news article by Janet Fang titled “A World Without Mosquitoes”, published in Nature in 2010, which explores the potential outcomes if humanity was able to completely eradicate the mosquito from the face of the planet.

You can’t just get rid of an entire species, right? Extinctions of species by humans have generally been a cause for lament, not celebration, but what if that species sucked your blood and was the most significant animal vector of disease our species has ever known? Janet interviews several ecologists about the ecological significance of this major pest, the benefits to worldwide health should the mosquito be eradicated, as well as the ways we might accomplish such a task.

Brett will lead the discussion around those questions which, at one time or another, had to cross our minds!

Fang 2010


Please join us next Monday at noon in Moore 473 to talk about the use of NIRS in prediction of sugar content in potatoes.

Plant scientists want to rapidly evaluate their material in a cost effective manner. There exist wet chemistry protocols that are used to reliably measure particular chemical compounds, but they are usually time consuming and expensive. So researchers are attempting to replace such assays with Near Infrared Reflectance Spectroscopy (NIRS) based models that use the properties of light to estimate the quantity of the compounds under study. However, there are multiple ways to evaluate material with the light source and multiple ways to analyze the reflectance data. In the paper that we’ll talk about next week, Rady and Guyer (2015) evaluate potatoes for sugar content and compare a variety of NIRS techniques and analysis tools.

Are you interesting in using NIRS in your research? Curtis Frederick will lead a discussion that relates the topics of Rady and Guyer (2015) to his own work! He will also cover some aspects of Partial Least Squares Regression, an important technique used for analyzing NIRS data.

Tobias 1995

Rady & Guyer 2015


Please join us next Monday at noon in Moore 473 to talk about the erosion of genetic diversity in plant breeding programs.

Plant breeders, in an effort to improve existing germplasm, must also combat the specter of decreased diversity. In a study of two recurrently selected maize populations, Gerke et al. (2015) showed that while the observed decrease in genetic diversity is mostly due to drift, the selected populations still show greater reduction in heterozygosity than expected according to models of the same populations without any selection. In addition, the authors could infer the breeding history of cultivars, by tracing the ancestry of certain haplotypes back to individual founding inbred lines.

Joe Gage will lead the discussion around this elegant and conclusive study on the long-term breeding history of corn!

Gerke et al. 2015


Please join us next Monday at noon in Moore 473 to talk about the characterization of microbial communities for plant disease resistance.

Soil communities have the potential to contribute to important agronomic traits. As we saw last semester, enrichment of soil communities for specific genera may explain improvement for traits such as flowering time or biomass yield. However, in the case of disease resistance, it is critical to characterize communities more precisely and identify the particular species that may serve as biocontrol agents. Next week, Marian Lund will present the work of Duan et al. (2003) on the characterization of Pasteuria species that can be useful against plant-parasitic nematodes. With input from her own research, Marian will talk about the usefulness and limits of using 16S rRNA sequences to discriminate Pasteuria species.

Meet with us next week to learn more about the very promising field of community genetics in plants!

Duan et al. 2003


Please join us next Monday at noon in Moore 473 to talk about the genetics around beer!

This summer, the wild yeast genetics lab at the UW published the genome sequence of the yeast species S. eubayanus, which is used commercially in fermented beverages. Matt Murray will talk about the paper from Baker et al. (2015), which deals with the effect of domestication on this much appreciated species! Matt will also provide a short introduction to general yeast genetics to make sure everyone has a working knowledge of the genetics of that model species. So we included a review paper in case you want to get some background.

I hope everyone is excited to leave their comfort zone of plants!

Baker et al. 2015

Dujon 2010


Please join us next Monday at noon in Moore 473 to talk about next-generation sequencing in plant genetics: opportunities, challenges… and limitations.

Guillaume Ramstein will be talking about the use of exome-sequencing and genotyping-by-sequencing technologies for better understanding and utilizing genetic variation in crops. The paper from Voss-Fels and Snowdon (2015) provides a concise yet extensive review of possibilities offered by next-generation sequencing in plant breeding and plant genetics. Next week, particular attention will be devoted to applications in genome-wide association studies and genomic prediction in perennial grasses for forage and biofuel, while discussing concrete issues encountered in such situations.

Voss-Fels & Snowdon 2015

2014-2015 Journal Club


Next Monday, we’ll meet at noon in room 473 (Moore hall) to talk about an intriguing piece of news concerning genetically modified crops…

Despite the fact that GMOs were introduced commercially in the mid-1990s and have 2000+ peer-reviewed studies confirming their safety, they are still an especially “touchy” political subject today in terms of safety, labeling, patents, etc.

Scott Stelpflug will present a recent publication by Kyndt et al. 2015 (PNAS), who revealed that signatures of genetic transformation (two foreign T-DNA sequences containing 9 different genes from Agrobacterium – used to create “lab-made GMOs”) are naturally found in modern sweet potato, and may have been associated with domestication.

The authors, rather optimistically, suggest that “[their] finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops”. What do you think? Come to journal club to weigh in!

See also the popular press article:

This will be our last Journal club this semester! Thank you all for participating! But don’t be too sad, we’ll meet again in Fall!

Kyndt et al. 2015


Next week, there will be no journal club; we invite you to attend the special seminar given by Greg Heck (lead scientist in Monsanto):

RNA-based Technologies for Agricultural Applications: Examples, Potential and Considerations

The seminar will take place on April 27th at noon in room 1420 (Microbial Sciences building).

Also, graduate students and postdocs interested in talking to Greg Heck more informally can meet with him after the seminar, at 1:15 PM in room 473 (Moore Hall).


Please join us next Monday at noon in room 473 (Moore hall) to talk about a component of crop production systems that is still poorly understood: the soil microbiome.

Matt Murray will present the paper of Panke-Buisse et al. (2014) published in ISMEJ, in which the authors showed that flowering time – but also biomass – in A. Thaliana could be manipulated in a reproducible way only from different soil microbiomes. After several cycles of selection for soil microbiomes (not plant genotypes!), significant differences in composition and nitrogen-mineralization activity of microbiomes were observed, which may explain the observed effects.

Panke-Buisse et al. 2014


Originally present in eukaryotes as a defense mechanism against extraneous genetic material, RNA interference (RNAi) has proved extremely useful as a tool for artificially knocking out genes. Interfering RNA was later considered to target genes in insects, acting as a highly-specific and environmentally sound insecticide. This strategy has encountered important practical constraints, but thanks to the clever trick presented by Zhang et al. (2015) in Science, RNAi for protection against insects now seems feasible!

Please join us next Monday at noon in room 473 (Moore hall) to learn more about this new breakthrough in RNAi technology!

Zhang et al. 2015


Please join us next Monday at noon in room 473 (Moore hall) to talk about resilience, a topic we are all familiar with as we cope with the many challenges of graduate school.

The ability to change and adapt to both predictable and unexpected changes is essential for agricultural systems. Sarah Turner will present the article by Milestad and Darnhofer, which discusses the socio-ecological resilience of organic systems using the International Federation of Organic Agriculture Movements (IFOAM) standard. What is the relationship between sustainability and resilience? Is organic agriculture sustainable? Will it remain sustainable as it becomes more commercialized? What is the optimal balance among regulation, market forces, and the underlying principles of the organic movement?

Milestad & Darnhofer 2003


Next week is spring break! As a result, there will be no journal club on Monday March 30th. Journal club will resume on Monday April 6th, and we hope to see you then!


Growing up is part of life, both for humans and for plants. Although growing up isn’t always fun, finding out how it happens certainly is! Join us on Monday as we discuss how plants make the leap from juvenile leafy greens to the mature flowering wonders that keep us in business. We’ll spend the hour having a nice adult discussion on Hong & Jackson’s paper Floral induction and flower formation—the role and potential applications of miRNAs , drinking coffee (a classic adult beverage made from adult plants), and doing lots of other adult things because grad students are grown ups, right?

Chris D’Angelo will lead this discussion. Please join us next Monday at noon in room 473 (Moore hall) to learn more about the importance of microRNAs for reproductive development!

Hong & Jackson 2015


Next Monday, a special journal club will be held! Please join us at noon in Room 473 (Moore hall) to meet Beth Werner, an intellectual property manager for WARF.

Lynn Maher asked her to cover a variety of topics including:
– WARF’s history and how it functions,
– how WARF protects and commercializes plant technologies, and
– disclosing procedures for researchers and graduate students.

There will be ample time for questions, especially for those curious about previous journal club discussions around CRISPR technology and patenting new varieties.
If you have questions in advance, please send them to


Please join us next Monday at noon in Room 473 (Moore hall) to talk about the the functional basis of causal variants for complex traits. Since the advent of genome-wide association studies (GWAS), it has been deceptively hard to relate causal genes to complex traits of interest. In fact, “genes” are just the beginning of the story.

Scott Stelpflug will present a very recent paper published in Nature, titled “Genetic and epigenetic fine mapping of causal autoimmune disease variants”. Their authors developed a fine-mapping algorithm to identify candidate causal variants for 21 diseases from genotypic data and integrate these predictions with cell-type specific transcription, cis-regulatory elements and “open chromatin” epigenetic marks and found that most associations lie in enhancer regions of the genome. In the context of plant breeding and plant improvement in the future, this paper highlights the need to integrate genotypic data with other genomic data related to the regulation of gene expression to identify causal variants.

Farh et al. 2015


Please join us next Monday at noon in Room 473 (Moore hall) to talk about the implications of spatial soil sampling on modern field designs and its effect on phenotyping.

Curtis Frederick will present a paper titled “Soil mapping for improved phenotyping of drought resistance in lowland rice fields” by S. Klassen et al from the International Rice Research Institute. This is an initial investigation of using electromagnetic induction technologies to estimate soil electrical conductivity (EC) and account for that important source of variation in rice drought stress experiments.

Klassen et al. 2014


Next Monday we will meet at noon in Room 473 and follow on a discussion started this week to talk about seed patents and their significance in the plant breeding industry. Brett Burdo will present a paper titled “What if Seeds were not Patentable?” by Elizabeth I. Winston, which explores the consequences of allowing seeds to be patentable subject matter, other protections put forth by the U.S. government to spur growth in research and investment in the seed industry, and the licenses developed by private companies to expand on the protections put forth by the federal government, as well as circumvent them.

Winston 2008


Next Monday we will meet at noon in Room 473 to talk about biological and regulatory aspects of the last ground-breaking invention in (plant) biotechnologies: targeted genome editing, with two short articles:

Jones (2015) briefly describes the genome-editing technologies – which include the very famous CRISPR/Cas9 system – and present the regulatory challenges for such indefinite technologies, still poorly understood by the public. Wang et al. (2014) provides a good example of the potentialities of genome editing for plant breeding, that is engineering recessive disease resistance in a species with a very complex genome (wheat).

Jones 2015

Wang et al. 2014


Next Monday the first Journal Club of the year will be held! As usual from now on, we will meet on Monday at noon in Room 473 to discuss – more or less broadly and informally – around a paper that one volunteer chose to present.

Next week (February 9th), Matt Murray will present a paper about patterns of genetic ancestry in African Americans, Latinos, and European Americans across the United States (attached).

Many authors of this paper work with the company 23andMe, the personal genotyping company that has become very common in the US. In this paper they use some of their consumer data as well as some well-known data sets, for example, the 1000 genomes project, to look at ancestry of different sub-populations of humans in the US. The authors pick apart present day admixture with the help of self-reported genealogies and historical human geography.

Bryc et al. 2015


Please join us for the final Engaged Scholarship Roundtable of the Fall Semester on  Friday, December 12, 1-3pm, in the On Wisconsin Room (1st  floor Red Gym): Incorporating Engaged Scholarship into the Tenure Dossier.

A panel of 3 recently tenured faculty will discuss how they purposefully integrated Engaged Scholarship into their tenure dossier, including developing a long-term plan for utilizing Engaged Scholarship, assessing community impacts, and documenting their scholarship. They will also address issues they encountered along the way and how those impediments were successfully resolved. The panel includes Professors Young Mie Kim in Journalism and Mass Communication, Sam Dennis in Landscape Architecture and Brian Christens in Civil Society and Community Studies. Learn more!

Engaged Scholarship Roundtable 12 12 14_FINAL


We hope you enjoyed the last two weeks of special seminars. Since they will no longer conflict with the usual time, journal club is back!

With the recent rapid innovations in genotyping technology, it is becoming easier and cheaper than ever to collect large amounts of genotypic data. Phenotypic data, however, is inherently much more difficult to quantify and unfortunately lags behind.

Carlos Arbizu has selected a very interesting paper for us to discuss this week in which the authors have developed a high-throughput facility to measure rice phenotypes and use that information for a subsequent GWAS study. Please take a look and join us next week to discuss gene discovery, genome-wide associations, high-throughput techniques, or anything else you would like to talk about!

Yang et al. 2014


In lieu of Journal Club next week, we encourage you to attend the special seminar to be given by Dr. Tony Studer at usual journal club time (noon to 1) in the DeLuca Biochemical Sciences Bldg, Room 1211. See the attached flyer for more information.


11-3-14 Moore Hall 473

With advancing technology, it’s amazing how much science can be down nowadays without the need to step into a lab (or a field). Bioinformatics, big data, and computer models are a very interesting branch of research, and the paper for next week explores how simulated predictions can be used in plant breeding.

Matt Murray has selected a very interesting paper for us to discuss this week exploring those topics in biparental crosses in corn. In it, the author simulates the crossing outcome of double haploids based on which favorable alleles are contained in the parents. Please take a look and join us next week to discuss predictive models, computer simulations, and their practicality in plant breeding, or anything else you would like to talk about!

Genomewide selection of parental inbreds_Bernardo_13


10-27-14 Moore Hall 473

With domesticated crop species in many places of the world growing alongside their wild counterparts, an interesting question to explore is if and to what extent our cultivation affects these wild species. A study of their genetic diversity can also tell us where the crop was likely domesticated and what changes occurred along that process.

Claire Luby has selected a very interesting paper for us to discuss this week exploring those topics in cotton. Please take a look and join us next week to discuss crop domestication, gene flow, speciation, plant evolution, or anything else you would like to talk about!



10-20-14  Moore Hall 473

There is much debate in both the academic and public sector question whether or not organic produce is any different than conventionally-produced vegetables. This recent meta-analysis explores this question by looking at composition differences between organic and non-organic food, and we hope that you will be intrigued by the results!

Chris D’Angelo has selected a very interesting paper for us to discuss this week, so please look it and join us next week to discuss organic production, human health, or anything else you would like to talk about.

Baranski British Journal of Nutrition 2014

10-13-14  Moore Hall 473

Hello plant scientists!

Firstly we would like to thank you all of you who attended or viewed the Plant Science Symposium! Thank you for helping us make it a successful event.

Now, what better way to resume our regularly scheduled Journal Clubs than a paper that was published in Science just two days ago? The coffee genome has been sequenced, so come help us celebrate our favorite alkaloid on Monday, September 13th at noon in Moore 473! There will be coffee and chocolate-covered coffee beans.

So please look over the attached paper and join us next week to discuss how such sequencing projects can help plant breeding, future research directions, convergent evolution, interesting phytochemicals, or anything else you would like to talk about!

See you there,


P.S. Thank you to Dr. Goldman for the paper suggestion!



10-6-14  Moore Hall 473

Hello plant scientists!

In lieu of Journal Club next week, we will be gathering to talk about and reflect upon this year’s Plant Science Symposium.

So please attend the symposium tomorrow for as little or as much time as you can. It will be from 8:00 AM to 5:00 PM at the Union South Varsity Room. Then join us next Monday, October 6th at noon in Moore 473. Bring your thoughts on integrating each speakers’ talk into the broader theme of plants and society as well as suggestions for next year. We would love to hear them!

We hope to see you there,



9-29-14  Moore Hall 473

In anticipation of the 2014 Plant Sciences Symposium, entitled Plants and Society: Integrating Food and Science in Today’s Culture (find more information and register HERE) our first few journal clubs will be featuring papers authored by professors who will be presenting at the symposium.

We hope that this will get everyone excited about the Symposium as well as open a dialogue about plant breeding in the larger context of society.

The paper we will be discussing next Monday is written from the perspective of a sociologist, something we don’t see much around this journal club! Our last visiting speaker, Gilbert Gillespie, writes about what farmers in New York think about alternative energy sources and how it affects adoption. Please look it over and come to Journal Club next Monday, September 29th at noon in Moore 473 ready to discuss this research as well as the broader topic of sustainability.

Gillespie 2010 Renew Agr Food Syst


9-22-14  Moore Hall 473

In anticipation of the 2014 Plant Sciences Symposium, entitled Plants and Society: Integrating Food and Science in Today’s Culture (find more information and register HERE) our first few journal clubs will be featuring papers authored by professors who will be presenting at the symposium.

We hope that this will get everyone excited about the Symposium as well as open a dialogue about plant breeding in the larger context of society.

The paper we will be discussing next Monday  is attached. Dr. Robin Buell et al. elucidate the metabolic pathways surrounding the formation of plant phytochemicals that are important for medicinal use. Please look it over and come to Journal Club next Monday, September 22nd at noon in Moore 473 ready to discuss this research as well as the broader topic of Genomics and Bioinformatics in plant breeding.

Buell journal.pone.0052506


9-15-14  Moore Hall 473

Hello plant scientists! Welcome to the start of a new semester and the beginning of Journal Club!

In anticipation of the 2014 Plant Sciences Symposium, entitled Plants and Society: Integrating Food and Science in Today’s Culture (find more information and register HERE) our first few journal clubs will be featuring papers authored by professors who will be presenting at the symposium.

We hope that this will get everyone excited about the Symposium as well as open a dialogue about plant breeding in the larger context of society.

The paper we will be discussing next Monday at the first Journal Club is attached. Dr. Ivan Ingelbrecht et al. explore the genetic diversity of Striga-resistant maize. Please look it over and come to Journal Club next Monday, September 15th at noon in Moore 473 ready to discuss his research as well as biotechnology’s place in improving crops, both in the developing and developed world.

See you there,


Intgelbrecht – Striga-resistant maize



2013-2014 Journal Club

This Fall 2013, Journal club is back on its original schedule and will meet every MONDAY @ NOON in Room 473. Please bring your lunch, prepare for some excellent conversation, and share your thoughts and/or opinions.

If you come across some cool papers that you think should be discussed in journal club, we highly encourage you to please let us know.  Also, if you want to lead journal club send us your name and the date you want to lead. The schedule for 2014:

April 28th – 473 Moore Hall

This week in our last journal club of the semester, Carlos Arbizu will be leading discussion about nutrition and plant breeders’ roles in improving it.

Nutritional quality of food delivered to the consumer is often a product of many factors, including storage, processing, and preparation once it reaches its destination. How much can a plant breeder do, then, to increase nutrition when many of the sources of variation are out of their control?

In this paper by Hennig et al., they explore breeding efforts to increase the levels of glucosinolates in the brassicas, and how a collaboration between plant breeders and food scientists is possible to increase the quality of foods that reach the consumer. It will be interesting to hear your opinions on the feasibility and practicality of this approach!

Hennig et al 2014

April 14th – 473 Moore Hall

Lynn Maher will lead journal club discussion next week. Below is a short summary of what we will be discussing!

In partial continuation of the conversation started last week, we will look at “dry lab biology”. With the multitudes of large databases now publicly available, many scientists can make basic fundamental discoveries without getting their hands “wet” in a lab or field capacity. The article attached is a focus piece looking at this trend in science. What does this mean for funding, lab structure and education as plant breeders? This piece provides a broader look at where breeding is going and could provide framework to discuss what others in the think are important skills to have going into a profession post graduation.

Biology’s Dry Future

April 7th – 473 Moore Hall

Scott Stelpflug will be leading journal club on Monday, April 7th. Below is a summary of the topic:

We all know that biological systems underlying observed phenotypes are impossibly complex, and as plant breeders, we use quantitative genetics and statistics to model and approximate these phenomena to make selections and improve varieties. However, quantitative genetics traces its roots back through more than a century of theory, largely formed in the absence of directly observable genotypic data, and has remained essentially unchanged for decades. By contrast, molecular genetics arose from direct observations, and it is advancing at an unprecedented rate thanks to modern technology and ginormous data sets.

These two disciplines are disparate both in their origins and their current states, yet they address the same fundamental question: how does genotype affect phenotype?

The topic we will be discussing is: how can we as next generation plant breeders intregrate these seemingly disparate schools of thought to make genetic gain more efficient? We will examine this by discussing two papers: Nelson et al. 2013 explores possible ways we can explore a paradigm shift in quantitative genetics that reflects more of the underlying molecular biology in organisms. Additionally, we will highlight examples from Grishkevich et al. 2013, who discusses how certain molecular features of the genome contribute more to GxE variance in gene expression than others.

March 31st – 473 Moore Hall

Backcrossing has been around for many years as a way to introduce a gene of interest to your favorite line. However, it requires many generations and screenings to be successful, and can only be used in a limited number of situations. Today, a quicker and easier way to introduce a single gene is through a transformation, or inserting your gene of interest through genetic modification. Theoretically, the result is the same: your favorite line is maintained, but now has a new gene. But are these two methods really equivalent? The attached paper by Gao et al. explores this question by comparing two strains of rice that contain a disease resistance gene, one obtained through backcrossing and the other by transforming. You may find their results interesting!

March 24th – 473 Moore Hall

Claire Luby has something new and exciting planned! Next week we will discuss intellectual property rights for plants. We will have a guest, IP manager Victoria Sutton from WARF (Wisconsin Alumni Research Foundation that manages IP for UW), there to answer questions about IP in general and also IP related to research you might be working on.

To get the conversation started, we have attached 3 documents for you to take a look at before hand: a plant patent for a cranberry released at UW, a PVP on a UW potato, and a utility patent on a hybrid carrot from Seminis. Take a look specifically at the claims sections of the different documents. We will go over the differences between these three types of IP on Monday so bring your questions and ideas! Also, don’t be too concerned with understanding the papers as much as you normally would for a scientific publication. Just get a general idea of what they are, and remember that Victoria Sutton will be around to answer your questions.

March 10th

Continuing our trend of discussing the larger issues of plant breeding and the scientific community, next week we will be discussing how we view statistical significance as well as replication and validation of experiments. The two attached short papers critique the p-values’ ubiquity as a measure of significance, and the other compares the scientific rigor of basic biology versus clinical studies, and questions why other scientific work is not as rigorous or prone to replication. These topics are certainly applicable to journal club as we read more papers throughout the semester, but should hopefully get you thinking about your own research as well.

Shelby Ellison will lead this interesting discussion about the validity of publications. Attached are the articles; we hope to see you there!

Also, feel free to email us at with comments or suggestions about Journal Club. Do you have a suggestion for a paper? Would you like to recommend a topic? Let us know!


March 3rd

Global food production is important, especially when considering our ability to feed the world’s growing population. This paper by Grassini et al. asserts that our prior models of food production are too optimistic. They warn that extrapolating current data on crop production is dangerous, because past trends were largely determined by “one-time innovations” of the green revolution, and the further yield gains will be increasingly difficult to attain and linear at best. This clearly has implications for land use and plans for the future of agriculture. We look forward to discussing this paper and the assumptions they make, and hearing your opinions on weather or not their arguments are convincing.

Ashley Schneider will lead this interesting discussion about future crop production. Attached is the paper; we hope to see you there!

Nature Communications


February 24th

Next Week’s Journal Club will be held on Monday February 24 in Moore 462, just down the hall from 473.

The paper we will be discussing next week reports the most recently sequenced crop genome: that of the hot pepper. With decreasing costs of whole-genome sequencing, it is very exciting that breeding of horticultural crops are beginning to benefit from increased genetic information. The pepper is an interesting crop in that it is closely related to the tomato, but contains the famous capsaicinoids that give the Capsicum species their name. This paper explores the evolution of this unique metabolite, as well as changes in genome size, gene expression, and ripening regulators.

Irwin Goldman will lead this interesting discussion about reference genomes and peppers. Attached is the paper; we hope to see you there!

Pepper Genome


February 17th

We will take a look at a review of crop domestication. It has a good review of domestication theory as well as snippets of lots of current literature. In many species we are now starting to understand many of the specific genes associated with domestication. We are also continually learning that due to our past selection methods we have left behind many valuable traits we are now looking for today.

Evolution of Crop Species


February 10th

Josh Parsons will lead the discussion this week. Our topic will be disease resistance, facilitated by the article titled ‘Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354.’ Major disease resistance genes are often NBS-LRR genes, but what is under many disease resistance QTL is a mystery. This group did fine mapping and identification of candidate genes controlling the resistance to southern root knot nematodes in soybeans and has a great hypothesis of what is under one of the QTL.

Fine mapping and identification of candidate genes

Matt Murray will lead this interesting discussion about crop domestication. Attached is the paper; we hope to see you there!



Sept 16

Have you ever wondered what is the future of phenotyping in plant research especially in plant breeding?  In the attached paper, Fiorani and Schurr (2013)  provided an overview of the future scenarios of plant phenotyping. We heard that some scientists believe that there will come a time when phenotyping will no longer be necessary and all we need is genotypic data. What do you think? We would love to hear your ideas. Bring your lunch and join us for an excellent discussion. See you there.

Click here for the paper Fiorani and Schurr (2013) – Future Scenarios of Plant Phenotyping; the abstract is provided below:

With increasing demand to support and accelerate progress in breeding for novel traits, the plant research community faces the need to accurately measure increasingly large numbers of plants and plant parameters. The goal is to provide quantitative analyses of plant structure and function relevant for traits that help plants better adapt to low input agriculture and resource-limited environments. We provide an overview of the inherently multidisciplinary research in plant  phenotyping, focusing on traits that will assist in selecting genotypes with increased resource use efficiency. We highlight opportunities and challenges for integrating noninvasive or minimally invasive technologies into screening protocols to characterize plant responses to environmental challenges for both controlled and field experimentation. Although technology evolves rapidly, parallel efforts are still required because large-scale phenotyping demands accurate reporting of at least a minimum set of information concerning experimental protocols, data management schemas, and integration with modeling. The journey toward systematic plant phenotyping has only just begun.

Sept 23

On Monday, 23Sept13, we will discuss a review article paper entitled “Site-Directed Nucleases (SDNs):  a Paradigm Shift in Predictable, Knowledge-Based Plant Breeding” written by Podevin (2013).  The authors talked about the modes of action, types, and use of SDNs in developing commercial crops. Like many other new technologies, safety is a concern. At the last part of the paper, the authors discussed regulatory considerations and potential safety issues associated with SDNs. As plant breeders/plant scientists, think about the potential uses of SDNs in your current/future research. Bring your lunch and ideas and let us have a great discussion in room 473. We hope to see you there.

PSGSC will provide cookies and coffee; you can view the article here.

Sept 30

We will discuss a review article paper entitled “Family-based association mapping (FBAM) in crops” by Guo et al. (2013). Please click here for the article; Sarah Turner will lead the discussion. The paper discusses FBAM technique which adapts human family-based association tests for plant species and can be used to identify and study the alleles involved in complex traits. PSGSC will provide cookies and coffee; we hope to see you there.

Oct 7

Scott Stelpflug will be leading discussion in journal club for Monday, October 7th, discussing a recent paper published by Uga et al. 2013 in Nature Genetics titled, “Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.” It is a very elegant example of progressing from identifying a large-effect QTL to cloning and functionally characterizing the effect of an agronomically relevant gene. While this paper will serve as the main topic of discussion, we will also be discussing the relevance and merit of cloning genes from QTLs, and possible ways to improve this process. A second excellent review by Salvi and Tuberosa is attached to provide background and enhance discussion of this topic. The papers are  DRO1_gene_2013_7Oct13 and Cloning QTLs_Salvi_Tuberosa 2005_7Oct13.

Oct 14

Josh Parsons will lead journal club’s discussion on Monday, 14Oct13 @ noon in Room 473.

Biparental QTL mapping is still a useful tool for plant breeders even in the age of association mapping and genomic selection, and balancing limited resources is always an issue in any program. Michael Stange et al. (2013) discuss the necessary marker density for QTL detection and characterization in the attached paper.  We invite you to join us and let us discuss the attached paper, any experiences we have, and applications.

You can access the article here Genotyping Overkill_14Oct13;  PSGSC will provide cookies and coffee.

Oct 21

Austin Meier will lead journal club’s discussion on Monday, 21Oct13 @ noon in Room 473.

The long generation time of some crops can be a serious constraint in plant breeding. Thus, any technology that can shorten generation time is a valuable breeding tool. In the attached article, Yamagashi et al. (2013) discuss their findings on reducing the generation time of apple seedlings by simultaneously expressing the FLOWERING LOCUS T and silencing the apple TERMINAL FLOWER 1 gene. We invite everyone to join our discussion and share their thoughts on the subject.  PSGSC will provide cookies and coffee.  You can access the article here Yamagashi et al 2013.

Oct 28

Drought tolerance in wheat is a complex trait that is controlled by many genes. In the attached paper, Edae et al. (2013) talked about characterizing five wheat drought tolerance genes using association mapping and nucleotide sequence variation. We look forward to seeing you on Monday, 28Oct13 @ Room 473 and discuss the mentioned paper.  Edae et al 2013 – Asso Mapping and NSV in wheat_28Oct13

Nov 4

Tondelli et al-2013-Structural and Temporal Variation in Barley and AM_4Nov13

Nov 11

In the attached paper, Korte and Farlow (2013) discuss how Genome Wide Association Studies (GWAS) have become an incredibly powerful tool for connecting the phenome to the genome. More importantly the author’s dicuss biological and statistical considerations that must be implemented for GWAS to be successful and meaningful. Another GWAS review by McCarthy et al. (2008) is provided for additional reading.

GWAS Review 2008-11Nov13

GWAS Review 2013-11Nov13

Nov 18

Stella Salvo will lead journal club discussion on Monday, November 18th at noon in Rm 473.

There are only 37 more years until we reach a world population of over 9 billion people in 2050, how do we produce enough for a growing population in the midst of climate change?  What are the the most innovative tools and techniques we can tap into to increase the breeding cycle?  Murray et al propose a new approach: the cycling of gametes in vitro (COGIV).



Nov 25

In plant breeding, the microorganisms living in the field are easily overlooked, and thier interactions with the plant are generally not considered a target of selection. However, in this week’s journal club article, Peiffer and colleagues have found a small component of heritable variability in the diversity of microbes colonizing maize inbred’s rhizosphere. This paper should provide interesting discussion on the feasibility of selection for novel traits such as this, and the importance (or lack thereof) of microbial interaction with non-legume crops. See you on Monday!


The abstract is below:


The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly understood. Here, we characterized the rhizosphere bacterial diversity of 27 modern maize inbreds possessing exceptional genetic diversity grown under field conditions. Randomized and replicated plots of the inbreds were planted in five field environments in three states, each with unique soils and management conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial richness, diversity, and relative abundances of taxa between bulk soil and the maize rhizosphere, as well as between fields. The rhizospheres from maize inbreds exhibited both a small but significant proportion of heritable variation in total bacterial diversity across fields, and substantially more heritable variation between replicates of the inbreds within each field. The results of this study should facilitate expanded studies to identify robust heritable plant–microbe interactions at the level of individual polymorphisms by genome wide association, so that plant-microbiome interactions can ultimately be incorporated into plant breeding.


Dec 2

This group looked at using a modifier of flowering locus T to get tobacco plants to flower more quickly and thereby speed up the breeding cycle, and demonstrated it with a single seed descent procedure.   Flowering Locus T and Inbreeding

 December 9th

Selection theory, GWAS, Genomic selection… These methods have in common the fact that they rely on additive models, whereas biological models generally see additive effects as the exception rather than the rule. In this very interesting paper, Nelson, Pettersson & Carlborg comment on the pitfalls of current quantitative genetics methods and address the question of possible alternatives to GWAS for deciphering the relation between genome and phenotype. Please join us next Monday if you’d like to discuss these challenges and (humbly!) talk about possible solutions.  Nelson et al 2013 – new paradigm in quantitative genetics

By the way, Journal club is also a great place to meet new people and discuss your research with other plant scientists.

Happy Journal Clubbing everyone!

For questions and/or more information, contact