Graduate Student Profiles
B.S. Life Sciences (Computational Biology), National University of Singapore
Lab: Dr. Fikret Isik
Among various locations and programs to choose for her doctoral study, Khushi elected to join the NC State Genetics Program because of the breakthrough research being done in population and quantitative genetics. She knew being a part of the competitive community would help refine and prepare her as a scientist. As an added bonus, she was excited about being able to utilize NC State’s proximity, connections, and presence within the Research Triangle while pursuing her degree. After arriving and beginning the program, she realized the program not only offers a diverse scientific community, but a supportive one made up of faculty, postdocs, and other students who are always willing to assist with research questions and personal endeavors.
Now that her own project is well under way, she credits NC State Genetics to expanding her expertise in ways she didn’t expect. “Being from a computational biology background, I have had the opportunity to really branch out and apply my previous knowledge to different aspects of genetics like forensic and statistical genetics”. She goes on further to say that this broad exposure has helped hone her skills and more acutely shape her career goals.
Specifically, Khushi enjoys having transitioned from being a desk-bound researcher to one who does important, hands-on work. As part of NC State’s Tree Improvement Program, her research focuses on developing an algorithm for efficient mate selecting and managing inbreeding in Pinus tadeda, or the loblolly pine tree. “I get to use cranes to work with gigantic loblolly pine trees in vast open fields, the peace and quiet is rejuvenating!” Her field work with loblolly pines is not only beneficial to her project, but she is able to use her research to help current pine breeders incorporate solutions for their problems with genetic gain and inbreeding.
At the recent National Association of Plant Breeders Annual Meeting (NAPB 2019), Khushi was one of the only four graduate students selected to give a talk to a wide and diverse audience of 400+ breeders, professors, industry, stakeholders and students. Her talk titled, “Arranged Marriages for Monoecious Plant Species: an example of Loblolly Pine” was highlighted for plant breeding innovations. The abstract for this talk can be read below:
Loblolly pine (Pinus taeda) is the most important tree crop in the US, planted over 25 million acres in the south. It is responsible for 58% of domestic wood supply and 16% of the global wood supply. The Tree Improvement Program at North Carolina State University manages the genetic improvement of Loblolly pine. Loblolly pine has a high genetic load and suffers greatly from inbreeding depression. It is a challenge to balance two important but contrasting goals of capturing as much genetic gain as possible while managing short- and long- term inbreeding. While methods and algorithms for animal breeding are well-established, an efficient algorithm suited to this species remains elusive. Developing an algorithm to design mating that optimizes genetic gain whilst putting constraints on relatedness is imperative for loblolly pine breeding. Towards this goal, we have adopted evolutionary genetic algorithms for optimized mating design. The optimization algorithm developed can utilize pedigree-based relationships to create optimal mating list for future breeding. Modified differential evolution (DE) algorithm has been applied to create mating lists that can be realized to give maximum return of genetic gain in future progeny while minimizing the increase in average co-ancestry in the population. Using the algorithm and optimizing the mating list from 964 monoecious loblolly pine tree candidates, resulted in 69.8% increase in genetic gain and no inbred progeny. The completion of this study will see the development of a suite of software that is able to not only utilize genetic relationships from pedigree but also utilize genomic relationships derived from Single Nucleotide Polymorphisms (SNPs). The framework and methods adapted for loblolly pine breeding have relevance to breeding of other monoecies species as well.
B.S. Genomic Sciences, Universidad Nacional Autónoma de México
Lab: Dr. Reade Roberts
The NC State Genetics Program appealed to Aldo because of its course structure and research opportunities available. He preferred the expansive curriculum, immersing students in all areas of genetics, such as molecular, developmental, and quantitative genetics. He knew that choosing NC State meant being a part of a diverse scientific community with endless research possibilities, one where he ultimately decided to focus on evolutionary genetics research projects.
Now in his 3rd year, Aldo commends the program for being integrative. In addition to learning from faculty who are passionate experts in their fields, he emphasizes the value of his experiences outside the classroom. “I can compliment my academic training by attending seminars and interacting with [people] from other programs, such as the Toxicology Program and the Bioinformatics Research Center.” He continues, “I have had the opportunity gain teaching experience and be in contact with the industry [partners] around the Triangle area.” Aside from academics and professional development, Aldo thinks highlighting the strong sense of community within the program is also important. All of the graduate students work together through the Genetics Graduate Student Association (GGSA) to coordinate social events, play on intramural sports teams, plan symposiums, and assist with the program’s recruitment and outreach. Through all of this, the Genetics Program at NC State offers its students a uniquely comprehensive graduate school experience.
Aldo’s main research interests in the program include evolutionary genetics, genomics, and bioinformatics. He has participated in poster presentations at several events, including the NCSU Latin American Symposium and the Triangle Zebrafish Symposium. He recently gave a talk about his research at the 9th Annual Fall Genetics Program Retreat titled, The genetic basis of gut length divergence across trophic levels in cichlid fishes. His abstract can be read below:
Trophic specialization is key to the phenotypic and species diversity observed across life. Several characteristics of gut morphology and physiology correlate with trophic levels. The most common example of these correlations is found in vertebrates, where organisms with a plant-based diet generally have longer digestive tracts compared to animals at higher trophic levels. Despite its importance, very few studies have explored the genetic basis of diet adaptation. In this study, we used recently diverged Malawi cichlid species as a model to identify candidate genes involved in gut length variation with a forward genetics approach. We performed QTL mapping of gut length on an F2 mapping population from a hybrid cross between carnivorous and omnivorous species of cichlids, and identified QTL contributing to variation in gut length. This analysis represents the first identification of naturally evolved, adaptive genetic variants associated with gut length. We are now integrating these mapping results with comparative genomic and transcriptomic studies to pinpoint the genes and gene networks driving evolution of the gut.
M.S. Marine Biology, College of Charleston
B.S. Marine Biology, College of Charleston
Lab: Dr. Fred Gould
As a 6th year Genetics PhD student, Jennifer has had many valuable experiences during her time at NC State. She says she “was drawn to NC State because of the wide variety of research topics being studied by professors here. I knew that I did not want to focus on classical medical research. I was much more interested in pursuing evolutionary and ecologically focused research questions. I also really liked that the program required rotations during the first semester so that I would get to “try out” different labs to make sure that the one I joined was a good fit both professionally and personally.”
Jennifer considers the people and research to be the program’s crown jewel; she has been able to learn and work with incredible seminar speakers and scientists. I am most proud of helping Dr. Gould our collaborators write a new NIH-RO1 grant based on the data generated during her dissertation,” she says. This 5-year grant will fully support her post-doctoral position, allowing her to continue working on her PhD research. She has also been recognized twice for presenting her research, winning best poster presentation awards by the Entomological Society of America in Denver, CO and BASF in Raleigh, NC. Jennifer also has several publications which are listed below:
– Baltzegar, J., J. Elsensohn, N. Gutzmann, and S. Webster. 2018. 2016 International Student Debates—Solving Problems without Borders: “What is the Single Best Strategy for Decreasing Dengue Fever Virus (Breakbone Fever) incidence worldwide? Genetically Engineered Mosquitoes with Lethal Genes.” American Entomologist 64(3): 165-175. doi: 10.1093/ae/tmy040.
– Baltzegar, J., J. Cavin Barnes, J. E. Elsensohn, N. Gutzmann, M. S. Jones, S. King, and J. Sudweeks. 2018. “Anticipating Complexity in the Deployment of Gene Drive Insects in Agriculture.” Journal of Responsible Innovation. 5(sup1): S81-S97. doi: 10.10180/23299460.2017.1407910.
– Gutzmann, N., J. Elsensohn, J. Barnes, J. Baltzegar, M. Jones, and J. Sudweeks. 2017. CRISPR- based gene drive in agriculture will face technical and governance challenges. EMBO Reports 18(9): 1479-1480. doi: 10.15252/embr.201744661.
– Baltzegar, J., J. Elsensohn, and S. Webster. 2017. 2015 Student Debates—Molecular Biology and Entomology: Partnering for Solutions: Con Team: “With the Development of Tools Like RNAi, in the Future We May be Capable of Eradicating Species. If We Can Eradicate a Species, Should We?” American Entomologist 63(2): 114-123. doi: 10.1093/ae/tmx028.
– Fritz, M. L., S. Paa, J. Baltzegar, and F. Gould. 2016. Application of a Dense Genetic Map for Assessment of Genomic Responses to Selection and Inbreeding in Heliothis virescens. Insect Molecular Biology 25(4): 385-400. doi: 10.1111/imb.12234.
– Fountain, J., T. Darden, W. Jenkins, and M. Denson. 2009. Three Multiplexed Microsatellite Panels for Striped Bass. Southeastern Naturalist 8(4): 671-676. doi: 10.1656/058.008.0408.