Genetics – Genes to Genomes https://genestogenomes.org A blog from the Genetics Society of America Mon, 24 Jun 2024 21:03:38 +0000 en-US hourly 1 https://wordpress.org/?v=6.6.2 https://genestogenomes.org/wp-content/uploads/2023/06/cropped-G2G_favicon-32x32.png Genetics – Genes to Genomes https://genestogenomes.org 32 32 A microbiologist’s quest to understand CRISPR in bacterial self-defense https://genestogenomes.org/a-microbiologists-quest-to-understand-crispr-in-bacterial-self-defense/ Mon, 20 May 2024 13:59:37 +0000 https://genestogenomes.org/?p=87150 Seldom do scientific breakthroughs penetrate daily public discourse and popular culture, shaping people’s understanding of science, as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing has. One of the biggest science stories of the decade, this technology undoubtedly captured both scientists’ and the public’s imaginations. Luciano Marraffini, who is Professor and Head of the Laboratory of Bacteriology at Rockefeller University and Investigator at Howard Hughes Medical Institute, was instrumental in determining how bacteria use CRISPR to develop immunity against foreign genetic elements. “My main interest is how CRISPR works for bacteria, less so on gene editing technology development,” says Marraffini, who was the first to show that bacterial CRISPR systems target DNA. This simple yet powerful observation led to the CRISPR toolbox development for gene editing. 

Falling in love with bacterial genetics

Marraffini was obsessed with space, astrophysics, and science fiction from a young age while growing up in Argentina. After reading about the advent and promise of recombinant DNA technology in a popular science magazine, his interest shifted toward biology. “During my undergraduate degree in biotechnology in Argentina, I did a lot of DNA manipulation and generated recombinant proteins. This experimental knowledge in molecular biology motivated me to follow a research path,” recollects Marraffini. Because the research opportunities were better in North America compared to Argentina, Marraffini uprooted his young family to pursue a PhD at the University of Chicago.

As part of the PhD curriculum, Marraffini recounts, “I took a class on bacterial pathogenesis and found molecular mechanisms by which bacteria cause diseases fascinating. I found bacteria a great experimental system because many tools were available to mutate and overexpress almost anything. There were also a lot of possibilities to purify proteins of interest using in vitro assays. This is why I fell in love with the bacterial experimental system and ended up joining the laboratory of the course teacher Olaf Schneewind for my PhD.” 

Dissecting CRISPR mechanisms in bacterial immunity

Bacteria are numerous but they are outnumbered by viruses that infect them. CRISPR-Cas is a major immune defense system that evolved in bacteria to fight viruses. Marraffini was interested in how bacteria employ CRISPR mechanisms to interact with and nullify infiltrating DNA and RNA. As a postdoc, Marraffini worked with Eric Sondheimer to experimentally demonstrate for the first time how CRISPR works against conjugative plasmids containing antibiotic resistance. “We showed that CRISPR can prevent the dissemination of antibiotic resistance among bacteria by directly targeting plasmid DNA,” explains Marraffini. This milestone in the CRISPR field was important later for gene editing technology development in mammalian cells. “I collaborated with Feng Zhang at the Massachusetts Institute of Technology. We transplanted a CRISPR-Cas9 system from Streptococcus pyogenes into human hepatocytes and showed that CRISPR cleaves DNA and can be repurposed for gene editing in cells,” shares Marraffini.

Over the years, Marraffini’s group gained mechanistic insights into how CRISPR systems contribute to bacterial immunity. When a phage or a plasmid invades bacteria, the CRISPR system captures a 30- to 40-nucleotides long sequence from the invader DNA called a spacer and incorporates it into the chromosome. This spacer DNA transcribed into the guide RNA gives Cas9—an enzyme that cuts DNA—the target specificity towards invading DNA. This is how bacteria acquire a memory of infection to then fight future infections.

Marraffini also discovered that phage DNA cleavage by Cas9 generates additional DNA fragments, resulting in the acquisition of new spacers for the CRISPR locus. More spacers and guide RNAs against the same-phage DNA are advantageous for bacteria as phages can escape Cas9 cleavage by mutating the target site, offering greater fitness to bacteria. According to Marraffini, “That’s one of our major contributions, showing how spacers acquisition determines infection memory. In addition, we also found that the CRISPR machinery uses free DNA ends, which is a way of diminishing autoimmunity since the bacterial chromosome is circular without a free end.”

Fostering curiosity and boldness

Joshua Modell, Assistant Professor of Molecular Biology and Genetics at Johns Hopkins University School of Medicine, describes his former postdoctoral mentor as “a rare scientist and an intellectual heavyweight who makes the laboratory a stimulating and fun place to do science.” Modell adds, “His ability to interact with and inspire scientists at any career stage, from the greenest summer intern to a long-tenured professor, is what makes him truly special. When I started my postdoc, he explained how much we still had to learn about CRISPR biology and how the work we do could end up in the textbooks. I still try to use that textbook standard with my trainees.”

“My mentors were extremely supportive of my interest in CRISPR despite CRISPR being unknown when I started my academic career,” says Marraffini. He champions the same generosity in his mentorship style, supporting projects his trainees want to pursue. 

“I wanted to investigate a new type of CRISPR that targeted RNA exclusively. No one understood how it worked. While everyone in the laboratory worked on Staphylococcus, I worked on a Listeria strain that naturally carried this RNA-targeting CRISPR system and developed it into a model system,” says Alex Meeske, Assistant Professor in the Department of Microbiology at the University of Washington, who did his postdoctoral training with Marraffini. “He encouraged me to be bold and try new methodologies, even if they were outside his expertise. He taught me to focus, keep my eyes on the prize, and investigate the most significant and testable questions.”

Join us in congratulating Luciano Marraffini, who received the Genetics Society of America Medal at The Allied Genetics Conference 2024 in Metro Washington, DC.


2024 GSA Awards Seminar Series

On September 9, at 1:00 p.m. EDT, Luciano Marraffini will join us to discuss CRISPR-CARF immunity and sacrificing the host for the benefit of the population. Save the date and register here!


Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

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Unlocking mysteries of trait and disease heritability in dogs https://genestogenomes.org/unlocking-mysteries-of-trait-and-disease-heritability-in-dogs/ Mon, 13 May 2024 14:36:00 +0000 https://genestogenomes.org/?p=87129 2024 Edward Novitski Prize recipient Elaine Ostrander, a pioneer of the domestic dog model, discovered numerous genes affecting dog size, morphology, behavior, and disease susceptibility—many of which have relevance in humans.]]>

“How do genes control physical, behavioral, and disease traits?” is a perennial question for geneticist Elaine Ostrander, Chief and Distinguished Senior Investigator of the Cancer Genetics and Comparative Genomics Branch at the National Human Genome Research Institute of the National Institutes of Health and Section Head of Comparative Genetics. Ostrander, who is known for her seminal discoveries in trait heritability in dogs and humans, tracked the history of dog breeds to address questions in morphology, behavior, and disease variation. She also mapped important cancer genes in canines and humans, advancing the knowledge of how complex diseases are inherited. 

Developing a canine genetic model from scratch

Ostrander started her scientific journey by investigating the relationship between the DNA structure and transcription in yeast during her PhD and postdoctoral years. Learning about the discovery of microsatellites steered her into mammalian research. “It became immediately clear that microsatellites were polymorphic in a population that they were useful for studying variation, but they were also stable enough to track inheritance of sections of DNA within a family. Suddenly, it became possible to make a genetic map of any mammal you cared about,” she recalls.

For Ostrander and Jasper Rine, that choice of mammal was a dog. While other scientists studying genetics were mapping genes in flies, worms, yeast, and humans, Ostrander, working in Jasper Rine’s research group at the University of California, Berkeley, began to construct a genetic map of the dog genome, with a long-term goal of using the map to find genes that distinguish breed appearance and behavior as well as genes associated with disease susceptibility. Continuing this work in her own research group at Fred Hutchinson Cancer Center, Ostrander created the first linkage maps in dogs in the early 90s. A decade later, her foundational work snowballed into a modern canine genetics project establishing dogs as a genetic model system. “Ostrander’s work built the stage and collected, in collaboration with several institutions, the first whole genome sequence of a domestic dog, the Boxer, in 2005. The subsequent decade was populated by an explosion of publications and genome developments led by her research group and collaborators,” says Bridgett vonHoldt, Associate Professor of Ecology and Evolutionary Biology at Princeton University and a long-time collaborator of Ostrander.

According to Leonid Kruglyak, Professor of Human Genetics and Biological Chemistry at the University of California, Los Angeles and Howard Hughes Medical Institute Investigator who nominated Ostrander for this honor, “Ostrander is without a doubt the leader in the field of canine genetics and genomics.” Leading an international consortium, Ostrander helped generate a global public repository consisting of genomes from 2,000 individual canids—including 1,611 dogs of known breeds (321 breeds), 309 village dogs, 63 wolves, and 4 coyotes—to address questions surrounding domestication, behavior, morphology, and disease susceptibility.

“Dogs were an obvious choice because the dog breed structure makes it easier to find genes responsible for traits. To be a member of a breed, parents and grandparents must be members of the same breed, making each breed a closed population,” explains Ostrander. Tapping into breed structure, where breed appearance and behavior remain intact generation after generation, Ostrander’s group identified genes responsible for the remarkable differences in size and shape between breeds. Her work showed that a single allele of IGF-1 is a major determinant of size in small breeds and that coat variation is determined by variants in just three genes. By identifying the time when variants first showed up in ancient DNA, her work takes a holistic view of morphology and behavior across different canid species.

Studying man’s best friend to understand humans

In addition to genes in dogs, Ostrander extensively studied human cancer genes in her laboratory at the Fred Hutchinson Cancer Research Center, focusing on human breast and prostate cancer. Her group was one of the first to describe a role for BRCA1 and BRCA2 mutations in women from the general population at risk for breast and ovarian cancer. Her expertise in dog genetics dovetailed well with this work, as she ended up discovering cancer-causing DNA variants in both humans and dogs. “Most things that dogs get, humans also get—they get the same cancers and diabetes; they also get many of the same neuromuscular, kidney and heart diseases. Some breeds are at an extraordinary risk for certain types of cancer. For instance, a Scottish Terrier is at 20-fold higher risk of getting bladder cancer than any mixed breed dog. Therefore, the underlying genetics must be really strong and profound,” explains Ostrander.

In an effort to explore the history between the dog and cancer genomes, her group used a multi-omics approach that was largely unexplored in the canine model to create the largest catalog of canine whole-genome, transcriptome, and chromatin immunoprecipitation sequencing. Such resources allow scientists today to identify common cancer-causing alleles in dog breeds and link them to human malignancies. For example, Ostrander identified two regions in the canine genome that explain a risk for developing a lethal histiocytic sarcoma, which also occurs in humans. By understanding genes in these risk regions in cancer-related pathways, her work empowered new diagnostics and therapeutic strategies for human cancers.

Ostrander’s group also studies aging and survival-related genes. “Big dogs do not live as long as little dogs. We would like to know why that happens,” she says. To solve this puzzle, Ostrander collaborated with international researchers looking for dog samples in the most unlikely places. “We are studying DNA samples from over 400 dogs, sampled by collaborators, from the exclusion zone around the Chernobyl nuclear power plant. We are looking for changes in DNA that dogs have accumulated over 15 generations which allows them to survive in this radioactive environment,” says Ostrander.  

A champion in all walks of life

Ostrander has contributed greatly to the scientific community through making her cutting-edge research in dog genetics accessible to the general public. A big proponent of community outreach, she takes pride in regularly engaging with dog groups, breed clubs, professional dog trainers’ associations, and families to help answer questions about behavior and diseases.

In addition to being a pioneer in science, Ostrander is also at the top of her game in powerlifting. She is a nationally ranked powerlifter, competing as a Masters lifter for five years. With a growing accumulation of first- and second-place medals, Ostrander looks forward to a time when she trains Masters lifters herself.  

Join us in congratulating Elaine Ostrander, who received the Edward Novitski Prize at The Allied Genetics Conference 2024 in Metro Washington, DC.


2024 GSA Awards Seminar Series

In a recent seminar, Elaine Ostrander discussed how domestic dogs are among the most variable mammalian land-based species on earth and the genetic underpinnings of that variation, including breed-associated morphology, behavior, and disease susceptibility. Watch the recording here.


Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

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Build-a-Genome course: Recruiting an army of undergraduates to synthesize yeast genome https://genestogenomes.org/build-a-genome-course-recruiting-an-army-of-undergraduates-to-synthesize-yeast-genome/ Thu, 09 May 2024 13:51:52 +0000 https://genestogenomes.org/?p=87101 Professors in colleges and universities strive to promptly bring new techniques to undergraduate classrooms. While the theory and concepts readily become part of the curriculum, the practical laboratory classes do not get much focus beyond a few protocol-based exercises. Only undergraduate students who are lucky enough to obtain internships in a research laboratory can learn and master different techniques. Jef Boeke, who is Professor in the Department of Biochemistry and Molecular Pharmacology and Director of the Institute of Systems Genetics at New York University, developed an undergraduate-level intensive laboratory course to teach practical aspects of molecular biology, synthetic biology, and bioinformatics, allowing students to perform extensive research in a class setting.

Build-a-Genome (BAG) course 

Boeke studied transposable elements in yeast and mammalian cells. Along the way, he decided to synthesize transposon DNA from scratch. “I was impressed with the power of being able to do that, which led me to synthesize first a synthetic chromosome arm and eventually the entire yeast genome with people around the world,” he describes. Using this first synthetic eukaryotic genome project, Boeke developed a unique laboratory component for his class that allowed students to contribute to this mammoth research endeavor.

“We built the genome from scratch, starting with oligonucleotides to entire genomes worth of synthetic chromosomes, piece by piece. In the early phases, we involved a lot of undergraduate students,” he explains. For Boeke, the course had two essential components. “One was to use the manpower needed to build such an enormous genome. The other was that it’s a fantastic way to teach molecular biology and genetics to undergraduate students, for whom it was new. They were doing original research as part of a course, learning about how to do a PCR reaction,” he shares. Because students were synthesizing genome fragments that were never created before, they faced several setbacks and performed extensive troubleshooting. This integral component of the course provided an authentic research experience to students.

Eventually, the course evolved as the technologies advanced. In the early years, students would generate 750 base pairs (bp) of synthetic fragments using PCR reactions on overlapping oligos. They would run gels to get clean bands and regularly present their observations in lab meetings. However, as the cost of synthesizing synthetic DNA fragments rapidly decreased, the course shifted from fundamental molecular biology in E. coli to yeast genetics. “The students started assembling medium-sized DNA pieces into bigger pieces using homologous recombination in yeast. After successfully running the course for 20 years and using work from undergraduate students, they are now helping combine sixteen fully man-made synthetic chromosomes and put them into a single strain,” says Boeke.

“Running the course wasn’t always easy,” describes Patrick Cai, Professor of Synthetic Genomics at the Manchester Institute of Biotechnology and former course instructor. “Boeke was running the course on a very limited budget, so we did a lot of work ourselves. One night, he drove his pickup truck and two of us moved all the chairs across the campus to a new course location. He was that dedicated and serious about the course,” says Cai.

With Boeke’s steadfast commitment and exceptional planning, the course eventually culminated in a global research and teaching consortium. Researchers from across the globe came to Boeke’s laboratory and learned teaching modules to build their parallel courses. “For example, Yingjin Yuan, Professor of Biochemical Engineering at Tianjin University, came to us and we helped him set up this course in China. He and colleagues focused on turning the course into a production machine and developed a landmark project by finishing one whole synthetic yeast chromosome in just a year,” says Boeke.

Teaching how to teach

Boeke involved his graduate students and postdoctoral researchers in teaching the course. According to Lisa Scheifele, Associate Professor in the Department of Biology at Loyola University Maryland, “The number of postdoctoral fellows and graduate students who have been empowered to learn the art of teaching, mentoring students, and developing course structure and content is notable and impressive.” She adds, “Boeke has been incredibly supportive of trainees who wanted to include a significant teaching aspect in their future careers. The Build-a-Genome course was my first teaching experience that ‘lit the fire’ for a future career where I’ve been able to blend teaching and cutting-edge research as we have done in Build-a-Genome.” Plus, the fact that this course inspired several of Boeke’s trainees in pivoting to a teaching career is something he’s quite proud of.

Harnessing the power of designer yeast

The synthetic yeast genome built through this innovative laboratory course offered a major paradigm shift in genetics and biotechnology, showcasing how to design and assemble synthetic DNA at scale. These synthetic chromosomes further facilitate testing genome fundamentals traditionally difficult to dissect in laboratory yeast strains. “Our knowledge about yeast genetics is largely based on our observation of the natural yeast genomes, which sometimes can be difficult to study. The synthetic yeast genome allows us to engineer the genomes to address societal challenges,” explains Cai. For example, Boeke made a bold choice to remove all the tRNA genes from the synthetic chromosomes and put them all on a new chromosome, allowing researchers to engineer it independently of all the other chromosomes. Now, Cai is testing yeast strains with tRNAs adapted to human codon usage to better express human proteins that can in turn be used in therapeutic applications to increase product yield.

Join us in congratulating Jef Boeke, who received the Elizabeth W. Jones Award for Excellence in Education, on behalf of Build-A-Genome, at The Allied Genetics Conference 2024 in Metro Washington, DC. And congratulations to the Build-a-Genome team whose members include Jessica Dymond of In-Q-Tel; Lisa Z. Scheifele of Loyola University Maryland; Eric Cooper of Hartwick College; Robert Newman of North Carolina Agricultural and Technical State University; Franziska Sandmeier of Colorado State University, Pueblo; Yu (Jeremy) Zhao of NYU Langone Health; Stephanie Lauer of St. Thomas Aquinas College; and Raquel Ordoñez of NYU Langone Health.


2024 GSA Awards Seminar Series

In a recent seminar, Jef Boeke, who received this award on behalf of Build-a-Genome, described how the course teaches students fundamental principles of genetics and how to perform, interpret, and troubleshoot an experiment when the outcome is unknown. He also touched on the history of the course and the resultant Network of Build-a-Genome courses, how it has affected students and instructors, and the course’s impact on the overarching International Sc2.0 project. Watch the recording here.


Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

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GSA and collaborators Personal Genetics Education & Dialogue and Reclaiming STEM Institute launch NSF-funded BIO-LEAPS project to support culture change in genetics  https://genestogenomes.org/gsa-and-collaborators-personal-genetics-education-dialogue-and-reclaiming-stem-institute-launch-nsf-funded-bio-leaps-project-to-support-culture-change-in-genetics/ Mon, 06 May 2024 14:00:00 +0000 https://genestogenomes.org/?p=87058 We are thrilled to announce that the Genetics Society of America (GSA) is collaborating with the Personal Genetics Education & Dialogue (PGED) based in the Department of Genetics at Harvard Medical School, and the Reclaiming STEM Institute (RSI) on a Leading Culture Change Through Professional Societies of Biology (BIO-LEAPS) grant from the U.S. National Science…]]>

We are thrilled to announce that the Genetics Society of America (GSA) is collaborating with the Personal Genetics Education & Dialogue (PGED)1 based in the Department of Genetics at Harvard Medical School, and the Reclaiming STEM Institute (RSI) on a Leading Culture Change Through Professional Societies of Biology (BIO-LEAPS) grant from the U.S. National Science Foundation (NSF). The two-year Design grant awarded to PGED’s home institution, Harvard Medical School, supports “Culture Change–Building a Relational and Inclusive Discipline through Genetics Engagement (CC-BRIDGE),” a capacity-building initiative that seeks to explore public engagement with science as a path for transformative culture change in the field of genetics. 

“As part of GSA’s mission to cultivate a community that creates and communicates the excitement and implications of discovery, CC-BRIDGE will help us better understand and develop ways to address issues our field faces surrounding public perception and a lack of trust in science and scientists. Through public engagement driven by this project, our members will be able to dialogue with each other and with the public more effectively, making our genetics community more inclusive, inviting, and better equipped to serve all,” says GSA President Mariana Federica Wolfner.   

Since 2020, GSA has collaborated with PGED to develop genetics-and-society programming through webinars, workshops, and other events. This grant will fund the development of a program that better equips scientists to effectively engage with their communities on topics of interest and relevance to genetics. Director of Programs at PGED Marnie Gelbart shares her enthusiasm, “PGED is thrilled to embark on this journey with GSA, RSI, and project advisors as we bring our collective expertise to explore the role of public engagement in cultivating a more inclusive and welcoming genetics culture.”  

Design Track projects funded by this grant support researchers in developing evidence-based approaches to culture change. Through webinars, workshops, and a symposium focused on historical and current social impacts of genetics research, CC-BRIDGE will pilot a reciprocal and inclusive public engagement program for scientists. Increasing evidence suggests that participation in science communication and outreach positively impacts the professional development and identity of scientists—which can in turn benefit scientific institutions and culture—while also building public understanding and positive perceptions of science. 

RSI Co-Executive Directors Evelyn Valdez-Ward and Robert Ulrich emphasize the importance of cultural transformation in genetics and its implications for those in STEM as well as broader societal impacts, saying, “Science, technology, engineering, and mathematics (STEM) are shaped by the values of the dominant U.S. cultural norms… [and] success in STEM fields privileges these [norms]. Public engagement is an undervalued way to change these conventions. CC-BRIDGE could be a critical first step in helping change the culture of genetics as a whole.” 

This pilot program will draw on input from a multidisciplinary advisory group comprising experts in genetics and the broader life sciences with vast knowledge in inclusive public engagement, science communication, pedagogy, and professional development. The group represents various career stages, sectors, identities, and lived experiences, and includes representatives from other organizations like AAAG, AABA, ASTC, Alliance for Genomic Justice, Black In Genetics, CienciaPR, Gallaudet University, and SACNAS.2 PGED Public Engagement Associate Rob O’Malley shares, “I’m particularly excited to co-develop new programming with GSA to support members in how they approach conversations on emerging issues in genetics with the public and with each other, and to highlight a wide range of voices and perspectives from beyond the discipline.”

We are excited to collaborate with our partners in these endeavors and we extend our gratitude to NSF for their generous support. GSA Executive Director Tracey DePellegrin underscores the importance of scientific societies like ours taking a leadership role in creating culture change in the sciences, “Given our broad impact and reach, it is incumbent upon GSA to provide a platform for members to share their lived experiences. Because these experiences actively shape how scientists conduct research and engage with others, by fostering an environment that amplifies their unique perspectives, we fuel progress both within and outside of our field.”

NSF awarded this grant under the BIO-LEAPS program, which leverages the reach of professional societies like GSA to advance diversity, equity, and inclusion in the biological sciences. CC-BRIDGE program activities started in April 2024.

  1.  Formerly Personal Genetics Education Project ↩
  2.  AAAG: American Association of Anthropological Genetics; AABA: American Association of Biological Anthropologists; ASTC: Association of Science and Technology Centers; CienciaPR: Ciencia Puerto Rico; SACNAS: Society for the Advancement Chicanos/Hispanics and Native Americans in Science. ↩
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Parrot plumage study aids breeders and endangered natural populations https://genestogenomes.org/parrot-plumage-study-aids-breeders-and-endangered-natural-populations/ Thu, 11 Apr 2024 14:58:24 +0000 https://genestogenomes.org/?p=87023 Yellow coloration is maladaptive in the wild but prized by breeders.]]>

People have long been fascinated with birds, which exhibit one of the widest ranges of coloration among vertebrates. Parrots, in particular, have captivated humans by their ability to mimic human speech and spectacular plumage.

Brightly colored feathers are used primarily to attract mates, intimidate competitors, and protect birds from predators. Coloration is both environmentally and genetically mediated, and research into its genetic control can help us better understand its role in adaptation and survival.

Blue and yellow pigmentation combine to create the green hue—which blends well with the tree canopy—most commonly seen in wild parrots. In contrast, yellow alone is a popular color for captive-bred parrots. A study published in the February issue of G3: Genes|Genomes|Genetics investigates the molecular basis of yellow color variations in three species of captive-bred parrots.

Parrots’ yellow coloration has connections to albinism in humans

Researchers at the University of the Negev, led by principal investigator Uri Abdu, report that a mutation in SLC45A2 is responsible for the sex-linked yellow phenotype seen in Psittacula krameri and two other parrot species.

Although most birds employ dietary carotenoid pigments for yellow coloration, parrots use a unique group of pigments called psittacofulvins. The blue color of parrot plumage is partly due to light scattering by nanostructures within the feathers. Data suggested that the presence of melanosomes also plays a role in producing blue coloration. In contrast, the absence of melanosomes allows the solitary expression of yellow coloration.

Breeder data indicates that the yellow parrot phenotype is usually sex-linked. Unlike humans, sex chromosomes in birds are designated as Z and W. The male is the homomorphic sex (ZZ), and the female is heteromorphic (ZW). Pedigree analysis from breeders who supplied birds for the study implied that the sex-linked yellow locus resided on the Z chromosome. Therefore, the researchers hypothesized that a defect in a melanin synthesis gene located on the Z chromosome was primarily responsible for the yellow phenotype.

Using whole-genome sequencing, researchers zeroed in on one Z-chromosome gene with the help of previously annotated budgerigar genome data. They found one protein-terminating nonsense mutation and three nonsynonymous SLC45A2 polymorphisms in yellow parrots that were absent in wild-type parrots. Parrots with this mutation “lose melanin in their entire bodies,” Abdu explains.

In humans, changes in this gene can lead to oculocutaneous albinism type 4 (OCA4), which causes very little pigmentation. One of the mutations found in yellow Psitticula krameri is reported in the human albinism database and is associated with OCA4. Although mutations that can lead to albinism affect many species, this study provides the first evidence of parrot color variation involving SLC45A2.

Better genetic understanding supports breeding and conservation efforts

Shatadru Ghosh Roy, a Ph.D. candidate in Abdu’s lab, explains that this research can save breeders time and produce healthier hatchlings. To maintain the coveted yellow color mutation, breeders traditionally bred siblings, which led to unhealthy hatchlings that often died from lethal mutations. Now that breeders know the genetic basis of yellow coloration, they can breed parrots from distinct bloodlines and avoid the negative effects of inbreeding.

Another takeaway from this work concerns the parrot as a model organism. Abdu considers the parrot an ideal model system for studying the physical and genetic mechanisms underlying avian coloration. After all, parrots have been bred in captivity for decades—indeed, half of all parrots alive live in captivity—and breeders can provide abundant genetic information. Hopefully, more basic biological studies on parrots will add to the knowledge needed to keep parrots alive in the wild. Coloration is part of the parrot puzzle, and additional genetic research into these fascinating birds may uncover strategies to fight the extinction of natural populations. With almost one-third of wild parrot species threatened with extinction, Polly needs all the help she can get.

References

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Steven Munger joins G3 as an associate editor https://genestogenomes.org/steven-munger-joins-g3-as-an-associate-editor/ Mon, 08 Jan 2024 17:00:00 +0000 https://genestogenomes.org/?p=86448 A new associate editor is joining G3: Genes|Genomes|Genetics. We’re excited to welcome Steven Munger to the editorial team. Steven MungerAssociate Editor Steven Munger, PhD, is an Associate Professor at The Jackson Laboratory in Bar Harbor, Maine, where he applies a systems genetics approach that integrates multi-scale genomics and genetic data from genetically diverse mice and…]]>

A new associate editor is joining G3: Genes|Genomes|Genetics. We’re excited to welcome Steven Munger to the editorial team.

Steven Munger
Associate Editor

Steven Munger, PhD, is an Associate Professor at The Jackson Laboratory in Bar Harbor, Maine, where he applies a systems genetics approach that integrates multi-scale genomics and genetic data from genetically diverse mice and embryonic stem cells to define the genetic and molecular bases of pluripotency and cell fate decisions. Munger received his BS in Biology from the University of Michigan and his PhD in Genetics from Duke University. As a first-generation college graduate from a small town in rural Michigan, he is acutely sensitive to the systemic barriers and personal obstacles that make it difficult for students from economically disadvantaged and underrepresented communities to enter and succeed in STEM fields. In his own lab and through his service to GSA, Steve is committed to finding solutions to lower these barriers and actively support and promote the next generation of talented young researchers from diverse backgrounds. Outside of the lab, Steve enjoys traveling, cooking, playing with his golden retriever Higgins, and starting and almost finishing DIY house projects.

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Congratulations to the Fall 2022 DeLill Nasser Awardees! https://genestogenomes.org/congratulations-to-the-fall-2022-delill-nasser-awardees/ Wed, 08 Mar 2023 16:52:52 +0000 https://genestogenomes.org/?p=85024 GSA is pleased to announce the recipients of the DeLill Nasser Award for Professional Development in Genetics for Fall 2022! Given twice a year to graduate students and postdoctoral researchers, DeLill Nasser Awards support attendance at meetings and laboratory courses. The award is named in honor of DeLill Nasser, a long-time GSA supporter and National Science Foundation…]]>

GSA is pleased to announce the recipients of the DeLill Nasser Award for Professional Development in Genetics for Fall 2022! Given twice a year to graduate students and postdoctoral researchers, DeLill Nasser Awards support attendance at meetings and laboratory courses.

The award is named in honor of DeLill Nasser, a long-time GSA supporter and National Science Foundation Program Director in Eukaryotic Genetics. Nasser was regarded by some as the “patron saint of real genetics,” shaping the field through more than two decades of leadership. She was especially supportive of young scientists, people who were beginning their careers, and those trying to open new areas of genetic inquiry. For more about Nasser, please see the tribute from Scott Hawley, published in the August 2001 issue of GENETICS.


Meareg Amare

University of Wisconsin-Madison

“Leveraging conserved inhibitor of apoptosis proteins to characterize the programmed cell death pathway in fungi.”


Puja Biswas

University of British Columbia

“Males and females have different levels of body fat storage which affect their lifespan and reproduction.”


Małgorzata Gazda

Institut Pasteur

“I study how biology is coded in the genome and how gene expression modulates phenotypical traits.”


Lydia Grmai

University of Pittsburgh/Duke University

“My research aims to leverage the power of Drosophila genetics to dissect the complex interorgan regulatory networks that link metabolism and reproduction.”


James Held

Vanderbilt University

“My research focuses on understanding how the quality of mitochondria, the cell’s energy producers, is maintained in healthy cells and under stressful conditions.”


Zoe Irons

University of Oregon

“My work centers around understanding the ways in which multiple tissues coordinate during development to form the correct body shape.”


Sarah Neuman

University of Wisconsin-Madison

“I study the role of lipid transport during animal development.”


Ana-Maria Raicu

Michigan State University

“I am studying how cancer-causing retinoblastoma proteins turn gene expression off in different cell types using the fruit fly.”


Carla Bautista Rodriguez

Université Laval

“Evolutionary dynamics of yeast hybrids facing harsh environments.”


Katheryn Rothenberg

University of Toronto

“I study how cells communicate and coordinate as a group to heal wounds.”

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