User:James C. Schnable

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Research interests

On the left and right are the specialized male and female inflorescences of maize respectively. In the center, for comparison is the single inflorescence produced by sorghum, a closely related grass species

I am a graduate student in Dr. Michael Freeling's lab at the University of California, Berkeley where I am studying what makes the two subgenomes within ancient tetraploid species such as maize different from each other. By taking advantage of the huge datasets that are now routinely generated by research groups using 2nd generation sequencers, I am studying how homeologs (duplicate genes created by a whole genome duplication, also known as ohnologs) on the two subgenomes of maize behave differently.

In addition to having lots of well characterized mutants and a relative abundance of RNA-seq data, studying the evolutionary and genomic consequences of polyploidy in maize also benefits from the fact that the grass family (Poaceae), of which maize is a member, are represented by the most complete genome sequences of any plant family (which only makes sense when you consider the crucial roles grasses play in both agriculture and ecology). Using comparative genomics to identify and compare orthologous regions of different grass genomes, we can identified duplicate genes which were completely or partially removed from the maize genome following its ancient whole genome duplication, as well as conserved noncoding sequences thought to be involved in regulating the expression of genes.

In the long term, my goal is to test the hypothesis that duplicated transcription factors from the maize whole genome duplication underly the emergence of two separate and morphologically distinct inflorescences in maize (the ear and tassel) when most other members of the Andropogoneae (the grass tribe to which maize, sorghum, and sugar cane belong to) have only a single style of inflorescence.

The comparison of maize an sorghum inflorescences on the right is a Creative Commons Licensed Image. See it in its original context.


  • In Progress, PhD, University of California-Berkeley, Plant Biology
  • 2008, BA, Cornell University, Biology


  1. Eichten SR,* Swanson-Wagner RA,* Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh C, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. (2011) Heritable epigenetic variation among maize inbreds. PLoS Genetics DOI: 10.1371/journal.pgen.1002372
  2. Schnable JC, Lyons E. 2011. "Comparative genomics with maize and other grasses: from genes to genomes" Maydica 56(2) 183-200 (Link is directly to PDF)
  3. Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. 2011. Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics DOI: 10.1186/1471-2105-12-102
  4. Schnable JC, Pedersen BS, Subramaniam S, Freeling M. 2011. Dose-sensitivity, conserved noncoding sequences and duplicate gene retention through multiple tetraploidies in the grasses. Frontiers in Plant Science DOI: 10.3389/fpls.2011.00002
  5. Schnable JC, Freeling M. 2011. Genes identifed by visible mutant phenotypes show increased bias towards one of two maize subgenomes. PLoS One DOI: 10.1371/journal.pone.0017855
  6. Schnable JC, Springer NM, Freeling M. 2011 Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1101368108
  7. Woodhouse MR,* Schnable JC,* Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biology DOI: 10.1371/journal.pbio.1000409
  8. The International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature DOI: 10.1038/nature08747

My google scholar profile has information on which other publications have cited my work.

Contact Info

James C. Schnable (an artistic interpretation)
  • 434 Koshland Hall (mail to: 111 Koshland Hall)
  • University of California
  • Berkeley, CA 94720