Yaniv Brandvain
Associate Editor, Empirical Population Genetics section

Yaniv Brandvain is an Associate Professor of Plant and Microbial Biology at the University of Minnesota working in theoretical and empirical population genomics. He received a BA in Human Ecology from the College of the Atlantic and a PhD in Biology from Indiana University, working on the robe of conflict, cooperation, and co-adaptation in plant evolution and speciation. During his postdoc at the University of California, Davis, he developed evolutionary theory concerning meiotic drive, and he developed population genomic approaches to study the evolutionary origins of self-fertilizing plant species. He is interested in understanding how new plant species arise with a particular interest in how mating systems and genomic conflicts shape plant diversity. His lab combines empirical and theoretical population genomic analyses with collaborative work in empirical systems to study the evolutionary forces shaping flowering plant diversity. He was also named McKnight Land-Grant Professor from the University of Minnesota (2017-2019) for his research efforts and received the Stanley Dagley-Samuel Kirkwood Undergraduate Education Award for his efforts in undergraduate instruction in biostatistics. 

Justin Borevitz
Associate Editor

Justin Borevitz is a researcher and professor at The Australian National University. The Borevitz lab works on evolutionary plant genomics, moving from model organisms to foundation species of agriculture and ecosystems. They are interested in the identification and prediction of climate adaptation alleles, the traits they control, and the environments they are filtered in. Borevitz’s lab takes a landscape genomic approach, using long read sequencing, assembly and (structural) variant calling of individuals across large, diverse populations. They also take a phenomic approach to dissect adaptive traits among offspring in selected families, grown across common gardens (seedlings to saplings to satellite).

Why Publish in G3?

A formidable invader of freshwater bodies, duckweed’s ability to thrive in diverse environments is a remarkable display of resilience, especially considering its small genome size and lack of sexual reproduction. Duckweed—the common name for members of the Lemnaceae family of monocots—defies conventional reproductive norms through clonal propagation. New individuals sprout from a single parent, bypassing the need for sexual reproduction and allowing for the fast reproduction that underlies their invasiveness.

Research recently published in G3: Genes|Genomes|Genetics delves into DNA methylation in the duckweed Spirodela polyrhiza, exploring its implications for clonal propagation and shedding light on the intricacies of plant biology.

Duckweed’s resilience hints at the intricate role epigenetic variation plays in shaping the plant kingdom’s evolution. Epigenetic modifications, particularly DNA marks like 5-methylcytosine (5mC), play pivotal roles in regulating gene expression and genome stability in plants. But duckweed deviates from the norm for plants, exhibiting notably low levels of 5mC.

Prompted by this intriguing anomaly, Harkess, Bewick, et al., set out to better understand the genetic and epigenetic impact that clonal propagation has on duckweed.

In plants, DNA methylation occurs in three sequence contexts: CG, CHG, and CHH (where H = A, C, T). It is initiated by the highly conserved RNA-directed DNA methylation (RdDM) pathway, which generates 24-nucleotide heterochromatic siRNAs via processing of double-stranded RNAs by DICER-LIKE 3 (DCL3). Subsequently, maintenance methyltransferases like MET1, CMT2, and CMT3 ensure the preservation of methylation during DNA replication.

However, key players of the RdDM pathway are notably absent in duckweed, as is the CMT2 maintenance methlytransferase. These absences have profound implications, particularly at CHH sites, where methylation is significantly reduced.

Interestingly, this phenomenon extends beyond duckweed, with related species Landoltia punctata, Lemna minor, and the aquatic seagrass Zostera marina exhibiting a similar absence of methylation machinery. The loss of these methylation players may represent a shared evolutionary adaptation among aquatic plants, potentially conferring advantages in varied climates and stresses.

The authors also report the absence of transposon proliferation in the S. polyrhiza genome, despite the loss of highly conserved genes involved in CHH methylation, prompting them to speculate on the role of CHH methylation in silencing transposons in asexual species. They suggest that clonally propagated species may rely more heavily on maintenance methylation mechanisms, rendering CHH methylation unnecessary for transposon suppression. Based on the research, it appears that losing CHH-type methylation and heterochromatic siRNAs may benefit duckweed by facilitating rapid asexual reproduction. The authors suggest that duckweed’s reproductive efficiency through quick clonal propagation might be enhanced by foregoing the RdDM and CMT2 pathway. Duckweed serves as a captivating case study in plant biology, offering invaluable insights into the intricate interplay between epigenetics, evolution, and environmental adaptation. As researchers continue to unravel its mysteries, the implications for agriculture, ecology, and beyond are boundless.

Yao-Wu Yuan
Associate Editor, Complex Traits

Yao-Wu Yuan is an Associate Professor at the University of Connecticut, Storrs. He is interested in understanding how and why organisms evolve so many beautiful forms in nature. His lab primarily studies floral trait diversification in the wildflower genus Mimulus (monkeyflowers) and aims to uncover the genes, pathways, and principles that explain the tremendous diversity of flowers by integrating genetics, genomics, development, mathematical modeling, and pollination ecology.

Why Publish in GENETICS?

Pears are big business in the United States’ Pacific Northwest. But did you know that traditional pear breeding has remained largely unchanged for centuries? This slow process is difficult and costly, requiring the long-term commitment of labor, materials, and land-space resources. However, traditional pear breeding might get some help from genomics, thanks to a unique collaboration between students, scientists, and the pear industry fostered through an initiative called the American Campus Tree Genomes (ACTG) Project.

ACTG was born from two professors’ desire to memorialize Auburn University’s iconic Toomer’s Oak trees that were poisoned during the 2010 Auburn University football season. Their plan: sequence the oak’s DNA and create the first-ever live-oak reference genome. To sweeten the pot, they decided to create a semester-long course so that actual Auburn students could take part in sequencing the Auburn oak trees.

“ACTG leverages iconic and economically valuable trees to bridge the gap between students and cutting-edge genomics,” says ACTG co-founder Alex Harkess, PhD. “Students collaboratively assemble, analyze, and publish tree genomes in prestigious journals, gaining invaluable experience.”

The first semester was a success despite most of the students having never written a manuscript, performed command line bioinformatics, or engaged in plant genomics molecular work. It sparked a nationwide initiative, which was officially founded in 2021 by Alex Harkess, PhD, Faculty Investigator at HudsonAlpha Institute for Biotechnology, and Les Goertzen, PhD, Director of the John D. Freeman Herbarium at Auburn University. Other institutions can replicate the experience using their own campus trees as a springboard for scientific and educational endeavors.

ACTG is disrupting traditional academic models, offering students a unique entry point into the world of genomic research. The initiative transcends textbook learning, immersing participants in the actual process of assembling, analyzing, and publishing tree genomes in esteemed scientific journals. Students in this course have access to cutting-edge genome sequencing techniques and bioinformatic skills through experts at HudsonAlpha. By working on genuine research projects with tangible outcomes, students gain confidence and experience, shaping their trajectories toward successful careers in the ever-evolving field of genomics.

“This course is a welcoming opportunity for students and trainees to not just interact with a completely new idea but become proficient in it no matter their skill level. I had no previous experience with bioinformatics, and I came out with an entirely new, highly marketable skill set,” says Harrison Estes, an Auburn University ‘23 grad who participated in the pear genome class. He is currently a graduate student at the University of Wisconsin and credits the ACTG class as helping him achieve this goal.

The emphasis on student participation extends beyond technical training. ACTG actively addresses barriers to STEM entry and persistence, providing valuable opportunities for individuals without access to advanced technologies. The ACTG team seeks out participation from small universities and colleges, community and junior colleges, and HBCUs that lack mature genetics and bioinformatics training pipelines.

The transformative power of ACTG goes beyond equipping students with invaluable skills and experience. By delving into real-world research projects, ACTG participants translate their knowledge into tangible applications that directly benefit the scientific community and economically important industries.

In the case of the pear industry, a cohort of Auburn students in the ACTG initiative worked with pear experts at Washington State University and the USDA Agricultural Research Service to create a high-quality pear genome. The meticulous work of the ACTG students yielded a fully phased, chromosome-scale assembly, a significant advancement over previous efforts.

The d’anjou genome assembly, recently published as a featured article in G3: Genes|Genomes|Genetics, reveals thousands of genomic variants which are of great importance to pear breeding efforts. This high-quality resource unlocks a treasure trove of information for pear breeders. The new genome assembly is also an important tool for studies on the evolution, domestication, and molecular breeding of pear.

“The ACTG: American Campus Tree Genomes program not only built high-quality genomic resources for a valuable pear cultivar that will ultimately benefit growers and consumers alike, but it educated nearly 20 students and scientists in the needs of the apple and pear industry,” said Ines Hanrahan, PhD, Executive Director, Washington Tree Fruit Research Commission.

The pear is only one of many important tree species in the ACTG pipeline. Learn more about the American Campus Tree Genomes project here.

We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates.

Divya Mishra
Career Development Subcommittee
National Institute of Plant Genome Research, India

Research Interest

I have always been deeply curious about various aspects of life. This curiosity has continued to drive me along my scientific journey. I am fascinated by the dynamic interplay among various signaling pathways under stressful conditions. My research interest involves unraveling the intricate molecular mechanisms behind plants’ responses to harsh environments. I aspire to significantly contribute to an in-depth understanding of plant stress biology to generate climate-resilient crops with better yields. Stress-resilient crops are more likely to adapt to climate change, decrease food security, and be farmed sustainably. Collaborating with the scientific community, I hope to minimize global challenges, including food security and sustainability.

As a PhD-trained scientist, you have many career options. What interests you the most?

I recall the beginning of my PhD journey, a time when alternative career paths were not widely explored or considered mainstream. Nevertheless, the landscape has evolved, and individuals now leverage their PhD training to embark on different career trajectories. It’s crucial to acquire transferable skills during the PhD, skills that guide researchers in defining their future paths. I think career options are subjective to each individual because everyone has a different personality and capabilities. It is not easy to navigate the scientific journey to both understand what exactly we want and find a path for it in a competitive world.

I feel immense satisfaction from conducting experiments in the lab, feeling almost therapeutic. Throughout the scientific journey, it has been clear to me that I am a lifelong researcher, whether in academia, industry, or even pursuing my start-up ideas. The exploration in science keeps me engaged. Every day brings something new, often pushing the boundaries of how experiments are approached and sometimes uncovering cool things about them.

Equally, I love effectively communicating and presenting science to a wider audience, as I aim to enhance its accessibility and broader impact.

In addition to your research, how do you want to advance the scientific enterprise?

I believe in effectively communicating science to audiences beyond my research arena to bridge the gap between scientists, policymakers, and the rest of the public. I value providing people with the overview of what we are doing in the lab. I enjoy spreading knowledge and resources among my peers, as well as younger generations. I strongly encourage thinking outside of the box. It is so important to develop a scientific mindset that helps younger generations create hypotheses about science and life in general. Incorporating a course within the PhD curriculum that involves effective writing, hypothesis testing, scientific illustration, and data representation would benefit their PhD work and overall scientific journey.

I want to mentor and support aspiring scientists through my experiences. We are often unaware of the career choices in science; therefore, we need a support group for sharing knowledge. By doing this, we can surely make a better scientific community.

Another goal is to make the research workplace more inclusive so that we get opinions from a more diverse scientific community. I always feel that individuals from different backgrounds and experiences come with unique problem-solving approaches that could lead to effective, meaningful solutions. Inclusivity might help to reduce bias and stereotyping towards specific individuals in a working team. An amalgamation of diversity in the scientific community enhances the research quality and contributes to the development of a better society as a whole.

As a leader within the Genetics Society of America, what do you hope to accomplish?

As a leader in GSA, my aspirations align with enhancing the professional development program of the Career Development Subcommittee. The ECLP holds significance both for my own professional growth and for the empowerment of other early career researchers. Therefore, I am committed to raising awareness about this wonderful program among peers.

My main objective is to provide resources on career paths and trajectories. These resources are made up of workshops and written materials where field experts shed light on their experiences and accomplishments. The workshops and seminars could provide a platform for researchers to communicate, network, and collaborate with field experts.

For broader reach, I am determined to enhance the visibility of the ECLP and various events of the GSA by reaching out to interested individuals who can benefit from seminars organized by the Career Development Subcommittee. By harnessing the power of social media platforms, I will make the information from seminars and workshops available for global access and engagement. Knowledge becomes more valuable when shared with different people. That’s why it is essential to make the information available to everyone.

Previous leadership experience:

• Early Career Representative, Education Committee in American Society of Plant Biologist (2023-present)
• Social Media Editor, Crop Science Journal (January 2023-June 2023)
• Spotlight Editor, Physiologia Plantarum (2022-2023)
• Assistant Feature Editor, Plant Physiology (2021-2023)

In a changing climate, corn growers need to be ready for anything, including new and shifting disease dynamics. Because it’s impossible to predict which damaging disease will pop up in a given year, corn with resistance to multiple diseases would be a huge win for growers. Now, University of Illinois Urbana-Champaign researchers are moving the industry closer to that goal. 

Goss’s wilt, a bacterial disease, and fungal diseases gray leaf spot, northern corn leaf blight, and southern corn leaf blight are important to growers across the Midwestern US and, in some cases, globally. The study, published in G3 Genes|Genomes|Genetics, reveals genomic regions associated with resistance to all four diseases.

“We not only found regions of the genome conferring resistance to each disease, but also identified a handful of experimental corn lines that were resistant to all of them. These findings should help the industry develop materials with resistance to multiple diseases at once,” said Tiffany Jamann, senior author of the new study and associate professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences at the University of Illinois, Urbana-Champaign.

The team made several strategic crosses between disease-resistant and susceptible corn lines that let them map resistance traits to specific locations in the genome. For now, those regions are fairly large, comprising hundreds of individual genes. If there are specific genes with outsized effects, they haven’t been identified yet. 

Still, identifying important regions is helpful, as disease resistance rarely comes down to a single gene. In fact, the additive or quantitative power of multiple genes working together can mean more durable resistance. There’s a backup if a pathogen finds a way around a given resistance mechanism. Interestingly, this durability may even work against different groups of pathogens. 

“We found 19 regions associated with resistance to the bacterial disease Goss’s wilt. Several of those regions are also involved with resistance to fungal pathogens,” Jamann said. “Thus, it is possible to breed for resistance to several diseases at one time using the same genetic regions.”

Fungi and bacteria are very different biologically, but both have to find ways to get into the plant, travel throughout, and reproduce. Jamann says it’s possible that resistance genes trigger changes in the plant’s vasculature to make it harder for both kinds of pathogens to move around, but she still can’t say exactly how the genes help plants protect themselves. She’s working on it, though, thanks to a 2022 grant from the National Science Foundation.  

Although the team identified three corn lines with resistance to all four diseases, it will be a while before growers can purchase seed for multiple-resistant corn as a result of this work. First, Jamann’s team will fine-map the regions highlighted in this study to find any major-effect genes, then pass that information off to breeders who can develop hardy new hybrids. Still, Jamann says, multiple resistance is on its way.

This post has been republished with permission of the author.

We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates.

Aishwarya Kothari

Community and Membership Engagement Subcommittee

Montana State University

Research interest

I am a fourth-year PhD student at Montana State University studying plant genetics. My interests are in the fields of epigenetics and molecular biology as I work toward improving human health and nutrition through increased access to quality food.

As a small step to this ambitious goal, I study the effects of heat stress in wheat at the molecular level. My current research objective is to use functional genomics—specifically ChIP, ATAC-Seq, and RNA-Seq—to identify molecular mechanisms of wheat grain development in response to heat stress. The complexity of the wheat genome makes it difficult to identify stress-tolerant genes and incorporate them into breeding. However, determining the effects of heat stress on transcriptome and chromatin accessibility in developing wheat spikes will potentially enhance cereal breeding. My research also involves the use of a class of plant growth regulators, brassinosteroids, to improve stress tolerance by altering plant response to stress during development. Brassinosteroids have a significant role in plant growth and development and in stress-response regulation. In the future, I want to study the effects of these plant hormones in conjunction with whole genome sequencing to better understand chromatin dynamics and the internal mechanisms of hormonal action in plant systems towards stress-tolerance.

As a PhD-trained scientist, you have many career options. What interests you the most?

After graduating, I am interested in doing research in industry—preferably related to sustainability and environmental effects. To protect our planet, we must take steps to slow down and control climate change.

I am specifically interested in sustainably growing crops with high nutritional quality that can cope with climate change without loss in yield. As the population increases, so does the demand for more food and better health; these increases then cause food prices to skyrocket, making healthy-eating and better-quality food very expensive.

My main goal is to provide research support to agriculture industries by establishing various methods to develop new, tolerant plant varieties without impacting the environment. Growing up in India, an agriculture-based country where nearly 50 percent of the farmers face issues pertaining to crop health and yield losses, greatly influenced this goal. The farmers struggle each year to get their crops to the market and suffer huge losses due to natural disasters. Additionally, the agriculture sector in India is not fully equipped with highly sophisticated techniques in molecular breeding, and I wish to fill that gap.

My undergraduate degree in biotechnology cultivated my passion for research. As an undergraduate student, I worked on diverse projects involving plant tissue culture, food quality, and genetics. Being a plant scientist will help me hone my skills in sophisticated molecular techniques and in visualizing agronomic characteristics of vigorous plants, which will guide me on proper management, breeding, and engineering practices.

In addition to your research, how do you want to advance the scientific enterprise?

I am a strong advocate for promoting science communication, especially to the general public. There have been many instances where information was poorly communicated and misconstrued, causing a lot of panic. Effectively sharing scientific findings with the public will promote scientific advancements at a faster pace. Additionally, instilling scientific knowledge in children at an early age may encourage them to pursue science in the future.

My personal ambition is to help international students and scientists. Being one myself, I know the hardships we must face to fit into the scientific community outside of our home countries. Also, not all countries have the resources required to enhance the abilities of their early career scientists, limiting their potential. Having forums like the Early Career Leadership Program makes it easier to connect with scientists all over the world and share our experiences. Making such forums more widespread and accessible to everyone is the next step.

Along with that, promoting mental well-being among students is one of my recent goals. Research has shown that almost 40 percent of graduate students deal with depression and anxiety. This was especially prevalent during the pandemic. The uncertainty during these times—mixed with the competitive nature of the scientific enterprise—takes a toll on the mental well-being of students, affecting their performance, academically and beyond. Therefore, supervisors, faculty, and higher management need to recognize their influence on the overall well-being of graduate students and postdocs. They can help enhance the graduate student experience by promoting a healthy work-life balance.

As a leader within the Genetics Society of America, what do you hope to accomplish?

I have wanted to engage in professional career development activities since I was an undergrad. Now as a graduate student, I feel strongly that we need to invest in career development workshops and events for early career scientists. Being an Early Career Leader at GSA will expand my network and knowledge; everything I learn here I can bring back to my institution and work toward implementing it. The demand for professional development workshops for scientists is increasing. Hence, it is imperative that we bring this much-needed content to early career scientists.

Ultimately, through my efforts to engage early career scientists in various opportunities of professional and personal development, I want to foster a healthy and inclusive culture of welfare in scientific communities.

Previous leadership experience

• Graduate Wellness Champion, Montana State University, 2020–2022
• International Peer Advisor, Montana State University, 2017–2018
• Student Engagement Global Ambassador, Montana State University, 2017–2018
• Orientation Leader, Montana State University, 2016–2018