Sam Leiboff, PI

We use mutant plant varieties to understand the genes necessary to make a normal, healthy corn plant. We use 1) next generation sequencing, long-read Oxford Nanopore, and chromatin structural sequencing to identify the genetic changes that cause mutations while we 2) capture comprehensive image-based measurements and fit mathematical models to compare normal and mutant development. Our work is split 60/40 between indoor laboratory work and field-based sampling in our nearby corn nursery .

Lab website: Sam Leiboff

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Project

Students will use advanced genetic pedigrees to map and characterize mutant maize phenotypes. Mapping tasks will include experimental work to prepare DNA for sequencing and/or the bioinformatic analysis of the map data to identify potential causative mutations. Mutant characterization will include high-throughput genotyping with molecular markers, field-based measurements of plant growth, high-throughput imaging of live plant tissue followed by computational image processing and modeling to identify and model mutant vs normal plant tissue shape.

Learning

Students will design and execute hypothesis-driven research with a variety of techniques. Over the summer, students will learn and deploy basic to advanced concepts in genetics and plant development, including mutant analysis of organ production and mapping-by-sequencing.

  • Molecular training will include DNA extraction, PCR, restriction digest, Sanger sequencing, with potential preparation of Illumina sequencing libraries.
  • Computational training will include the design or deployment of analytical pipelines to align genomic DNA sequences to a refence genome, identify sequence variants, map mutations using variant allele frequency, automated image processing, and statistical shape description with R.
  • Field training will include pedigree management, sampling logistics, and fundamentals of maize propagation.