Profile Photo of Alan Pepper
Alan Pepper


Fax: 979-845-2891

2123 TAMU
Biological Sciences Building East
Room 214B

Biological Sciences Building East
Room 214

Joined the Department in 1995

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


Core Faculty, Doctoral Degree Program in Ecology and Evolutionary Biology (EEB)
Faculty of Genetics
Faculty of Molecular and Environmental Plant Sciences

My laboratory uses genetic, genomic and molecular tools to study the mechanisms of how terrestrial plants adapt to extreme environments. In particular, we are investigating the genetic mechanisms of plant adaptation to stresses such as drought, low levels of essential mineral nutrients (N, P, K, Ca), high and low light conditions, and heavy metals. Our key study organisms are Caulanthus amplexicaulis and related species in the tribe Thelypodieae of the Brassicaceae family (wild relatives of the model plant Arabidopsis thaliana). Species in this group show adaptation to a remarkable range of environments from deserts to cloud forests to barren sub-Antarctic islands. Further, these species are for the most part interfertile, allowing for sophisticated genetic and genomic investigation. This work has led us to become more broadly interested in the conservation and ecological genetics of rare plants, particularly geoendemics.

In a separate project, we are using comparative genomics to investigate the genetic basis of the evolution-under-domestication of 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, allowing genomic information gained from model plants to be applied to the complex genomes of cotton.

  1. Burrell, AM, Goddard, JHR, Greer, PJ, Williams, RJ, Pepper, AE. Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower). J Hered. 2019;110 (5):587-600. doi: 10.1093/jhered/esz029. PubMed PMID:31062855 .
  2. Swope, SM, Pepper, AE, Lee, GT, Burnett, BA, Horten, HM. Development of 15 microsatellite loci in the endangered Streptanthus glandulosus subsp. niger (Brassicaceae). Appl Plant Sci. 2019;7 (2):e01215. doi: 10.1002/aps3.1215. PubMed PMID:30828502 PubMed Central PMC6384297.
  3. Hawkins, AK, Garza, ER, Dietz, VA, Hernandez, OJ, Hawkins, WD, Burrell, AM et al.. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol. 2017;9 (12):3478-3494. doi: 10.1093/gbe/evx259. PubMed PMID:29220486 PubMed Central PMC5751042.
  4. Kushanov, FN, Buriev, ZT, Shermatov, SE, Turaev, OS, Norov, TM, Pepper, AE et al.. QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt. PLoS One. 2017;12 (10):e0186240. doi: 10.1371/journal.pone.0186240. PubMed PMID:29016665 PubMed Central PMC5633191.
  5. Hinze, LL, Hulse-Kemp, AM, Wilson, IW, Zhu, QH, Llewellyn, DJ, Taylor, JM et al.. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol. 2017;17 (1):37. doi: 10.1186/s12870-017-0981-y. PubMed PMID:28158969 PubMed Central PMC5291959.
  6. Kushanov, FN, Pepper, AE, Yu, JZ, Buriev, ZT, Shermatov, SE, Saha, S et al.. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers. BMC Genet. 2016;17 (1):141. doi: 10.1186/s12863-016-0448-4. PubMed PMID:27776497 PubMed Central PMC5078887.
  7. 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. doi: 10.3389/fpls.2016.00202. PubMed PMID:26941765 PubMed Central PMC4762190.
  8. Hulse-Kemp, AM, Lemm, J, Plieske, J, Ashrafi, H, Buyyarapu, R, Fang, DD et al.. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda). 2015;5 (6):1187-209. doi: 10.1534/g3.115.018416. PubMed PMID:25908569 PubMed Central PMC4478548.
  9. 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 .
  10. 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):. doi: 10.3732/apps.1400077. PubMed PMID:25798340 PubMed Central PMC4356317.
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