• A.B., 1982, University of California, Berkeley, Biochemistry.
  • Ph.D., 1990, University of California, Davis, Genetics.
  • Postdoctoral research: Salk Institute, La Jolla, CA.

Joined the department in 1995.

Associations: Faculty of Genetics, Faculty of Molecular and Environmental Plant Sciences.

Research Interests

My laboratory uses genetic, molecular, and genomic tools to study how terrestrial plants adapt, both in a short-term sense (phenotypic plasticity) and in a long-term sense (adaptive evolution), to the vast diversity of environments found on our planet.

My laboratory is studying the molecular and physiological mechanisms of ‘downstream’ developmental responses to light using genetic and molecular tools available in the model plant Arabidopsis thaliana. In another project, we are using comparative genomics to investigate the genetic basis of the evolution-under-domestication of developmental processes in cultivated cottons (Gossypium spp.) and their wild relatives. Gossypium is in the Malvaceae family and, as such, shares a recent common ancestor with Arabidopsis and other plants in the Brassicaceae family.

We are also investigating the genetic mechanisms of plant adaptation to the stresses of extreme environments such as drought, low mineral nutrients (N,P,K) and heavy metals, in wild relatives of Arabidopsis, such as the rare endemic plant Caulanthus amplexicaulis (Brassicaceae.) This work has led us to become more broadly interested in the conservation and ecological genetics of rare plants, particularly geoendemics.

  1. Abdurakhmonov, IY, Ayubov, MS, Ubaydullaeva, KA, Buriev, ZT, Shermatov, SE, Ruziboev, HS et al.. RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.). Front Plant Sci. 2016;7 :202. Epub 2016/2/22. doi: 10.3389/fpls.2016.00202. PubMed PMID:26941765 PubMed Central PMC4762190.
  2. Burrell, AM, Pepper, AE, Hodnett, G, Goolsby, JA, Overholt, WA, Racelis, AE et al.. Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Mol. Ecol. 2015;24 (9):2177-93. doi: 10.1111/mec.13167. PubMed PMID:25864837 .
  3. Logan-Young, CJ, Yu, JZ, Verma, SK, Percy, RG, Pepper, AE. SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing. Appl Plant Sci. 2015;3 (3):. Epub 2015/3/9. doi: 10.3732/apps.1400077. PubMed PMID:25798340 PubMed Central PMC4356317.
  4. Yu, JZ, Ulloa, M, Hoffman, SM, Kohel, RJ, Pepper, AE, Fang, DD et al.. Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population. Mol. Genet. Genomics. 2014;289 (6):1347-67. doi: 10.1007/s00438-014-0930-5. PubMed PMID:25314923 .
  5. Ryan, DE, Pepper, AE, Campbell, L. De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis. BMC Genomics. 2014;15 :888. doi: 10.1186/1471-2164-15-888. PubMed PMID:25306556 PubMed Central PMC4203930.
  6. Abdurakhmonov, IY, Buriev, ZT, Saha, S, Jenkins, JN, Abdukarimov, A, Pepper, AE et al.. Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L. Nat Commun. 2014;5 :3062. doi: 10.1038/ncomms4062. PubMed PMID:24430163 .
  7. Ivalú Cacho, N, Millie Burrell, A, Pepper, AE, Strauss, SY. Novel nuclear markers inform the systematics and the evolution of serpentine use in Streptanthus and allies (Thelypodieae, Brassicaceae). Mol. Phylogenet. Evol. 2014;72 :71-81. doi: 10.1016/j.ympev.2013.11.018. PubMed PMID:24333439 .
  8. Burrell, AM, Hawkins, AK, Pepper, AE. Genetic analyses of nickel tolerance in a North American serpentine endemic plant, Caulanthus amplexicaulis var. barbarae (Brassicaceae). Am. J. Bot. 2012;99 (11):1875-83. doi: 10.3732/ajb.1200382. PubMed PMID:23125430 .
  9. Burrell, AM, Taylor, KG, Williams, RJ, Cantrell, RT, Menz, MA, Pepper, AE et al.. A comparative genomic map for Caulanthus amplexicaulis and related species (Brassicaceae). Mol. Ecol. 2011;20 (4):784-98. doi: 10.1111/j.1365-294X.2010.04981.x. PubMed PMID:21284744 .
  10. Friedman, JM, Roelle, JE, Gaskin, JF, Pepper, AE, Manhart, JR. Latitudinal variation in cold hardiness in introduced Tamarix and native Populus. Evol Appl. 2008;1 (4):598-607. Epub 2008/8/21. doi: 10.1111/j.1752-4571.2008.00044.x. PubMed PMID:25567800 PubMed Central PMC3352386.
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Alan Pepper

Alan Pepper
Associate Professor

2123 TAMU
College Station, TX 77843-2123

Office:
Biological Sciences Building East
Room 214B
979-845-2518

Lab:
Biological Sciences Building East
Room 214
979-845-2683

Fax: 979-845-2891
Email: apepper@bio.tamu.edu

Curriculum Vitae