Pepper, Alan individual record
Associate Professor

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.

selected publications
Academic Articles56
  • Janga, M. R., Pandeya, D., Campbell, L. M., Konganti, K., Villafuerte, S. T., Puckhaber, L., ... Rathore, K. S. (2019). Genes regulating gland development in the cotton plant.. Plant Biotechnol J. 17(6), 1142-1153.
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  • Swope, S. M., Pepper, A. E., Lee, G. T., Burnett, B. A., & Horten, H. M. (2019). Development of 15 microsatellite loci in the endangered Streptanthus glandulosus subsp. niger (Brassicaceae).. Appl Plant Sci. 7(2), e01215-e01215.
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  • Hinze, L. L., Hulse-Kemp, A. M., Wilson, I. W., Zhu, Q., Llewellyn, D. J., Taylor, J. M., ... Stelly, D. M. (2017). Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.. BMC Plant Biol. 17(1), 37.
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  • Miao, Q., Deng, P., Saha, S., Jenkins, J. N., Hsu, C., Abdurakhmonov, I. Y., ... Ma, D. (2017). Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line.. PLoS One. (6), e0179381-e0179381.
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  • Y., I., T., Z., E., S., A., A., Urmonov, K., Kushanov, F., ... Ullo, M. (2012). Genetic Diversity in Gossypium genus. Genetic Diversity in Plants. 313-338. InTech.
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Conference Papers1
  • Chory, J., Chatterjee, M., Cook, R. K., Elich, T., Fankhauser, C., Li, J., ... Vitart, V. (1996). From seed germination to flowering, light controls plant development via the pigment phytochrome. 93(22), 12066-12071.
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Repository Documents / Preprints1
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mailing address
Texas A&M University; Biology; 3258 TAMU
College Station, TX 77843-3258