Alan Pepper
Associate Professor
Department of Biology
Faculty of Genetics
Faculty of Molecular and Environmental Plant Sciences
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B.A. Biochemistry, University of California at Berkeley
Ph.D. Genetics, University of California at Davis
NSF Post-doctoral Fellow, The Salk Institute for Biological Studies
Developmental Responses to the Environment:
In plants, phenotype is strongly influenced by environmental factors (such as light,
temperature and water availability) as well as genetic determinants. This is known as
phenotypic plasticity. My laboratory is investigating the molecular basis of plant
developmental responses to light using genetic and genomic tools available in the model
plant Arabidopsis thaliana.
Developmental and evolutionary genetics and genomics of cotton (Gossypium spp.)
Cottons are a close evolutionary relative of Arabidopsis. We are using genetic tools
(such as DNA-based molecular markers including microsatellites, AFLPs and SNPs) to investigate
the genomic and developmental evolution of cultivated cottons (Gossypium spp.) during
domestication. Genes identified through this study may play a role in the improvement of elite
cotton varieties.
Ecological and Evolutionary Genetics and Genomics in wild relatives of Arabidopsis:
We are also investigating the genetic mechanisms of plant adaptation to extreme environments
such as drought stress, low mineral nutrients and heavy metals, in wild relatives of Arabidopsis,
such as the rare endemic plant Caulanthus amplexicaulis (Brassicaceae).
J. Spencer Johnston, Alan E. Pepper, Anne E. Hall, Jeffrey Chen, George Hodnett, Janice Drabek, Rebecca Lopez, and H. James Price (2004) Evolution of genome size in the Brassicaceae. In press, Annals of Botany.
Alan E. Pepper, Ning Kang and Robert Corbett (2002) Natural variation in Arabidopsis seedling photomorphogenesis reveals a role for TED1 in phytochrome signaling. Plant, Cell and Environment 25: 591-600.
Alan E. Pepper and Laura E. Norwood (2001) Evolution of Caulanthus amplexicaulus var. barbarae (Brassicaceae), a rare serpentine endemic plant: a molecular phylogenetic perspective. American Journal of Botany 88: 1479-1489.
Alan E. Pepper, Mi-seon Seong, Stephanie M. Hebst, Kathryn Ivey, Su-Jin Kwak, and Denise Broyles (2001) shl, a new class of Arabidopsis mutants with exaggerated developmental responses to available red, far-red and blue light. Plant Physiology 127: 295-304.
Javed Iqbal, O. Umesh K. Reddy, Kamal M. El-Zik and Alan E. Pepper (2001). A genetic bottleneck during the evolution under domestication of upland cotton Gossypium hirsutum (L.) examined by DNA fingerprinting. Theoretical and Applied Genetics 103: 547-554.
Abdalla M. Abdalla, O. Umesh K. Reddy, Kamal M. El-Zik and Alan E. Pepper (2001) Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP. Theoretical and Applied Genetics 102: 222-229.
Michael Neff, Joseph D. Neff, Joanne Chory, and Alan E. Pepper (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. The Plant Journal 14: 387-392.
Alan E. Pepper and Joanne Chory (1997) Extragenic suppressors of the Arabidopsis det1 mutant identify elements of flowering-time and light-response regulatory pathways. Genetics 145: 1125-1137.
