Faculty: Alan Pepper2016-12-22T13:46:28+00:00
Alan Pepper

Alan Pepper

Associate Professor

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

Curriculum Vitae

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.


Faculty of Genetics
Faculty of Molecular and Environmental Plant Sciences

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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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 .
  6. 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.
  7. 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 .
  8. 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.
  9. 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 .
  10. 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 .
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