Merritt Khaipho-Burch
I am a Ph.D. Candidate in Ed Buckler’s lab in the Section of Plant Breeding and Genetics at Cornell University. My research investigates the extent to which pleiotropy controls phenotypes within the maize genome and the role of transposable elements in regulating gene expression. I have a passion for designing and implementing models to understand the genetic basis and regulation of complex quantitative traits. In my free time I enjoy hiking, baking, and creating beadwork.
To see my full CV, click here.
Contact me at: mbb262@cornell.edu
Socialization
Skills
- QTL Mapping
- Association Mapping (mixed, general, matrix eQTL)
- Genomic Prediction (SNP, expression, metabolite)
- RNA and DNA Sequence Analysis
- Machine Learning (random forest, gradient boosting models)
- R
- R Studio
- bash
- git
- windows
- apple
- linux
- github
- Bitbucket
Limited contribution of transposable elements to regulatory adaptation in maize inbreds and hybrids
Transposable elements (TEs) make up ~85% of the maize genome, however, little is known of their effects on gene expression under non-stressed conditions.
Elucidating the patterns of pleiotropy and its biological relevance in maize
Using association mapping of common alleles in over one hundred thousand traits, we show little evidence that pleiotropy is a common phenomenon in maize.
The perils and promise of single-gene solutions to crop yield: extraordinary claims require extraordinary evidence.
I lead a large collaborative effort to write a policy/perspective piece on the common reasons how crop productivity studies can be inaccurately measured and suggest testing guidelines moving forward.
Teaching and Outreach
I have communicated many different scientific concepts to the broader community through numerous teaching and outreach events.
Zines
I have created numerous zines for different projects and outreach events as a way to communicate my science to broader audiences.
Publications
A short collection of publications. My full list of publications is available on Google Scholar.
Paper - Elucidating the patterns of pleiotropy and its biological relevance in maize
Paper - The perils and promise of single-gene solutions to crop yield: extraordinary claims require extraordinary evidence
Paper - Genomic mapping of the modifiers of teosinte crossing barrier 1 (Tcb1)
Paper - Predictive breeding for maize: Making use of molecular phenotypes, machine learning, and physiological crop models
Experience
Graduate Research Assistant
Elucidating the patterns of pleiotropy and its biological relevance in maize AND Regulatory Adaptation of Transposable Elements and Their Effect on Gene Expression in Maize and the Andropogoneae.
- I curated and mapped 120,549 traits across two diverse maize populations to uncover the patterns of pleiotropy. Created machine learning models to describe how pleiotropic loci were biologically regulated.
- Developed a novel gene expression quantification pipeline suited towards highly diverse genomes to test how transposable elements impact gene expression.
- Lead a highly collaborative team to write a perspective on why genomic prediction will be the solution to increasing intrinsic crop yield.
Graduate Teaching Assistant
Taught two sections of Plant Genetics (PLBRG 2250). Responsibilities included:
- Created lab materials (quizzes, lab lectures, slides, pre-lab videos).
- Graded exams.
- Ran experiments with students.
Graduate Research Assistant
Used QTL mapping to identify modifiers of the teosinte crossing barrier 1 locus in maize using the Intermated B73 x Mo17 population and identified numerous candidate loci. For my second project, I sequenced and assembled the genomes of two male gametophyte mutants and identified candidate causal loci for pollen development.
Research Student Assistant
Investigating axis formation in Mediterranean fruit flies.
- Designed and analyzed experimental data for a time series gene expression experiment on fruit-fly eggs.
- Validated numerous RNAi experiments through gene expression assays.
REU Research Scholar
Worked on multiple projects looking at Arabidopsis thaliana snRNA processing and miRNA biogenesis and activity. Screened and backcrossed mutants defective in pollen and embryo development.
Laboratory Assistant
Taught two workshops on DNA extraction for the non-science community (East Hawaii 4-H club, UH Hilo outreach day). I also ran and taught core facility users how to perform DNA extractions, design RT-PCR experiments, set up IonTorret sequencing libraries and runs, and use facility instruments.
Molecular Laboratory Assistant
Using DNA extraction, PCR, and Sanger sequencing I amplified genetic markers to create and deliver phylogeographic trees of Metrosideros polymorpha to understand the speciation process of these trees across the Hawaiian Islands.
REU Research Scholar
Plant microbe interactions affect the biomass production of Spartina pectinata, a potential bioenergy crop.
- Collected and analyzed data on phosphorous content in roots and shoots, arbuscular mycorrhizae prevalence, and harvested tissue for RNA sequencing.
Education
Cornell University
Expected Graduation: December 2023
South Dakota State University
University of Hawaii at Hilo