Plant Pathology/Genomics Ph.D. Position at North Carolina State University
North Carolina State University is offering a Ph.D. position for a student to work on the population genetics of Cronartium quercuum fusiforme fungus (Cqf) and the identification of putative effector loci in the genome. Cqf infects multiple pine species in the southern United States, causing significant damage to pine farming in the region. The project is led by Fikret Isik (quantitative genetics) in collaboration with a strong team. Ralph Dean (plant host-pathogen interactions), Peter Balint-Kurti (genetic bases of disease resistance in maize), and Amanda Hulse-Kemp (computational biology).
As a Ph.D. student, you will work with a strong interdisciplinary research team, including a post-doctoral scientist specializing in PacBio sequence data analysis and reference genome assembly of the pathogen. You will play a crucial role in generating complete reference pangenomes of Cqf using long-read PacBio sequencing of four haploid fungal isolates.
Additionally, you will work to identify pathogen virulence genes and understand their effects on the known host (Pinus taeda) QTL, conferring disease resistance.
Your responsibilities will include leading and coordinating DNA extraction from about 6K samples, collecting and organizing disease phenotypic data (presence and absence of galls on seedlings), and genotyping 6K megagametophytes using the Pita50K Axiom SNP array developed for Pinus taeda. You'll also validate two major QTLs previously discovered in the same pedigree and test the Mendelian segregation ratios for two QTLs located on the same linkage group in repulsion-phase linkage. Finally, you will conduct population genetic analysis using whole-genome sequence data in collaboration with the research team.
To qualify for this position, you should have a background in plant pathology, genetics &
genomics, plant breeding, bioinformatics, or related fields. Strong computing skills, including familiarity with the Linux command line and working with sequence data analysis, are essential.
Excellent writing skills and familiarity with QTL mapping are also required. You should be fluent in written and spoken English. We offer a competitive salary, health insurance, and fees. The position is for three years, with a likely extension for one more year.
To apply, please send a package including a CV, a cover letter, academic records, and three letters of recommendation (two of which must be from academic advisors) to Professor Fikret Isik (fisik@ncsu.edu). The application will remain open until a candidate is found.