Paul Gepts

image of Paul Gepts

Professor of Plant Sciences and Geneticist/Breeder


Plant Sciences

Offices and Labs

1242 Plant and Environmental Sciences

Profile Introduction

My research and teaching is focused on studying the evolutionary factors that affect crop biodiversity, with particular emphasis on Phaseolus beans, including intrinsic plant factors such as gene flow and gene diversification, environmental correlations with crop biodiversity, and human effects on the maintenance and generation of diversity. Tools used are broad and range from field surveys to genomic tools. In turn, this information is applied to breeding programs to develop new varieties of beans for California and Eastern Africa.


1984 PhD Plant Breeding and Plant Genetics University of Wisconsin

Research Interests

Crop bioidversity and bean breeding

Since the beginning of agriculture, some 10,000 years ago, humans have molded the diversity of crop plants around them to suit their diverse needs for food and beverage, feed, clothing and other numerous uses. Starting with the process of domestication, crop biodiversity results from the fascinating interactions among humans, plants, and their environment. My research and teaching program is focused on elucidating the evolutionary processes that have shaped evolution of crop plants under cultivation. I focus particularly on Phaseolus beans because they are such an important part of the human diet, especially in developing countries, and provide many health benefits. Other crops of interest in my lab are additional crops from the Americas such as peppers (Capsicum), wild maize (teosinte), amaranth, and agaves. These provide a comparative dimension to studies of crop evolution because they encompass a wide range of reproductive systems, life histories, and human uses. On the more applied level, I look at the consequences of our findings for plant breeding. One of my main activities is a participation in the ABC-KT project (i.e., African Bean Consortium, funded by the Kirkhouse Trust), which seeks to develop a marker-assisted selection capability in East African bean breeding programs. I have recently taken over the grain legume breeding program at UC Davis, which focuses on the development of new varieties of lima and common bean and garbanzos for the state of California.


Distinguished Achievement Award, Bean Improvement Cooperative, 1991
Elected Fellow, American Association for the Advancement of Science, 2001
Elected Fellow, American Society of Agronomy, 2003
Elected Fellow, Crop Science Society of America, 2005
Poehlman Lecture, Missouri University, 2005
Morrison Lecture, USDA-ARS & ASHS, 2013
Calvin Sperling Memorial Biodiversity Lectureship, Crop Science Society of America, 2014


American Association for the Advancement of Science,
American Society of Agronomy
Crop Science Society of America
Society for Economic Botany
American Society for Horticultural Science
American Institute of Biological Sciences
Bean Improvement Cooperative

CBS Grad Group Affiliations

Integrated Genetics and Genomics
Plant Biology

Specialties / Focus

Plant Biology
  • Systematics and Evolutionary Biology

Graduate Groups not Housed in CBS

Ecology, International Agricultural Development, and Horticulture and Agronomy

Teaching Interests

Crop evolution. Plant genetics. Economic Botany.


PLB 143 Evolution of Crop Plants (Spring)
PLS/ECL 290 Molecular basis of plant phenotypic variation (seminar) (Winter)


11/6/2014 3:17:42 PM
  • 2014 Schmutz J, McClean P, Mamidi S, Wu G, Cannon S, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wan M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics 46:707-713. DOI:10.1038/ng.3008

  • 2014 Ddamulira G, Mukankusi C, Ochwo-Ssemakula M, Edema R, Sseruwagi P, Gepts P. Distribution and variability of Pseudocercospora griseola in Uganda. Journal of Agricultural Science 6:16-29. 

  • 2014 Okii D, Tukamuhabwa P, Odong P, Namayanja A, Mukabaranga J, Paparu P, Gepts P. Morphological diversity of tropical common bean germplasm. Afr. Crop Sci. J. 22 (1): 59-68. 

  • 2014 Okii D, Tukamuhabwa P, Kami J, Namayanja A, Paparu P, Ugen M, Gepts P. The genetic diversity and population structure of common bean (Phaseolus vulgaris L.) germplasm in Uganda. African Journal of Biotechnology 29 (35): 2935-2949. DOI: 10.5897/AJB2014.13916 

  • 2014 Ddamulira G, Mukankusi C, Ochwo-Ssemakula M, Edema R, Sseruwagi P, Gepts P. Identification of new sources of resistance to angular leaf spot among Ugandan common bean landraces. Canadian Journal Plant Breeding 2(2): 55-65. 

  • 2012 Worthington M, Soleri D, Aragón-Cuevas F, Gepts P. Genetic composition and spatial distribution of farmer-managed Phaseolus bean plantings: an example from a village in Oaxaca, Mexico. Crop Sci 52: 1721-1735 doi:10.2135/cropsci2011.09.0518
  • 2012 Kouam EB, Pasquet RS, Campagne P, Tignenegre JB, Thoen K, Gaudin R, Oedraogo JT, Salifu AB, Muluvi GM, Gepts P. Genetic structure and mating system of wild cowpea populations in West Africa. BMC Plant Biology 12: 113 DOI: 10.1186/1471-2229-12-113
  • 2012 Kwak M, Toro O, Debouck D, Gepts P. Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris L.). Annals of Botany 110: 1573-1580. doi:10.1093/aob/mcs207.
  • 2013 Gioia T, Logozzo G, Kami J, Zeuli PS, Gepts P. Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common bean. Journal of Heredity 104: 273-286. DOI: 10.1093/jhered/ess102
  • 2013 Kraft, K.H., J.D. Luna-Ruiz, and P. Gepts. A new collection of wild populations of Capsicum in Mexico and the southern United States. Genetic Resources and Crop Evolution 60: 225-232. doi:10.1007/s10722-012-9827-5.
  • 2013 Gonçalves-Vidigal MC, Cruz AS, Lacanallo GF, Vidigal Filho PS, Sousa LL, Pacheco CMNA, McClean P, Gepts P, Pastor Corrales MA. Co-segregation analysis and mapping of the anthracnose Co-10 and angular leaf spot Phg-ON disease-resistance genes in the common bean cultivar Ouro Negro. Theoretical and Applied Genetics:online DOI 10.1007/s00122-013-2131-8
  • 2013 McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D. Agriculture: Feeding the future. Nature 499:23-24
  • 2013 Nascimento W, Rodrigues J, Koehler S, Gepts P, Veasey E. Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil. Genetic Resources and Crop Evolution:1-16.
  • Gepts P. 2002. A comparison between crop domestication, classical plant breeding, and genetic engineering. Crop Sci. 42: 1780-1790.
  • Gepts P. 2003. Ten thousand years of crop evolution. In: M. Chrispeels and D. Sadava (eds.), Plants, Genes, and Crop Biotechnology (2nd ed.). Bartlett and Jones, Sudbury, MA; Chapter 13: pp. 328-359
  • McClean PE, Lee R, Otto C, Gepts P, Bassett MJ. 2002. STS and RAPD mapping of genes controlling seed coat color and patterning in common bean. J. Hered 93: 148-152.
  • Miklas PE, Johnson WC, Delorme R, and P Gepts. 2001. Identification of QTL conditioning physiological resistance and avoidance to white mold in dry bean. Crop Science. 41:309-315
  • Yu K, Park SJ, Poysa V, and P Gepts. 2000. Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). Journal of Heredity. 91:429-434
  • Geffroy V, Sévignac M, De Oliveira JCF, Fouilloux G, Skroch P, Thoquet P, Gepts P, Langin T, and M Dron M. 2000. Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of QTL with genes involved in specific resistance. Molecular Plant-Microbe Interactions 13, 287-296.
  • Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J. 2003. Beans (Phaseolus spp.) - Model food legumes. Plant Soil 252: 55-128.
  • Papa R, Gepts P. 2003. Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor. Appl. Genet. 106:239-­250
  • Kelly JD, Gepts P, Miklas PN, and Coyne DP. 2003. Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Res. 82, 135­-154.
  • Blair, M.W., F. Pedraza, H.F. Buendía, E. Gaitán-Solís, S.E. Beebe, P. Gepts, and J. Tohme. 2003. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362 - 1374.
  • For an up-to-date list:
  • 2011 Alo F, Furman BJ, Akhunov E, Dvorak J, Gepts P. Leveraging genomic resources of model species for the assessment of phylogeny in wild and domesticated lentil. J Hered 102: 315-329. DOI: 10.1093/jhered/esr015
  • 2011 Nanni, L., Bitocchi, E., Bellucci, E., Rossi, M., Rau, D., Attene, G., Gepts, P., Papa, R. Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.). Theor. Appl. Genet.: published online. DOI: 10.1007/s00122-011-1671-z.
  • 2010 Kraft KH, Gepts P, Luna Ruíz J. Seed selection among commercial chile farmers in Aguascalientes, Mexico. Econ Bot 64: 318-328. DOI: 10.1007/s12231-010-9136-x.
  • 2009 Piñeyro-Nelson A, van Heerwaarden J, Perales H, Serratos J, Rangel A, Hufford M, Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Alvarez-Buylla E. Resolution of the Mexican transgene detection controversy: error sources and scientific practice in commercial and ecological contexts. Molec. Ecology 18: 4145-4150.
  • 2009 Dyer GA, Serratos-Hernández JA, Perales HR, Gepts P, Piñeyro-Nelson A, Chávez A, Salinas-Arreortua N, Yúnez-Naude A, Taylor JE, and Alvarez-Buylla ER. Dispersal of transgenes through maize seed systems in Mexico. PloS One 4(5): e5734. doi:10.1371/journal.pone.0005734 .
  • Phaseolus vulgaris is located in the Lerma-Santiago Basin of Mexico. Crop Sci 49: 554-563. DOI: 10.2135/cropsci2008.07.0421 .
  • 2008 Piñeyro-Nelson A, van Heerwaarden J, Perales H, Serratos J, Rangel A, Hufford, M, Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Alvarez-Buylla E. Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations. Molec Ecol 18, 750–761. doi: 10.1111/j.1365-294X.2008.03993.
  • 2011 Nanni, L., Bitocchi, E., Bellucci, E., Rossi, M., Rau, D., Attene, G., Gepts, P., Papa, R. Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.). Theor. Appl. Genet.123: 1341-1357. DOI: 10.1007/s00122-011-1671-z.
  • 2011 Nzungize J, Gepts P, Buruchara R, Buah S, Ragama P, Busogoro JP, Baudoin JP. Pathogenic and molecular characterization of Pythium species inducing root rot symptoms of common bean in Rwanda. African J Microbiol Res 5: 1169-1181.
  • 2011 Miklas PN, Fourie D, Trapp J, Larsen RC, Chavarro C, Blair MW, Gepts P. Genetic characterization and molecular mapping Pse-2 gene for resistance to halo blight in common bean. Crop Sci 51: 2439-2448. doi: 10.2135/cropsci2011.01.0046
  • 2011 Burle ML, Fonseca JR, Peloso MJ, Melo LC, Temple SR, Gepts P. Integrating phenotypic evaluations with a molecular diversity assessment of a Brazilian collection of common bean (Phaseolus vulgaris L.) landraces. Crop Sci 51: 2668-2680. doi: 10.2135/cropsci2010.12.0710
  • 2012 Gepts P, Famula TR, Bettinger RL, Brush SB, Damania AB, McGuire PE, Qualset CO (eds) (2012) Biodiversity in agriculture: domestication, evolution, and sustainability. Cambridge University Press, Cambridge, U.K.
  • 2012 Repinski S, Kwak M, Gepts P. The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1. Theor Appl Genet 124: 1539-154. DOI 10.1007/s00122-012-1808-8