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Resequencing of Common Bean Identifies Regions of Inter-Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding.

Lobaton JD, Miller T, Gil J, Ariza D, de la Hoz JF, Soler A, Beebe S, Duitama J, Gepts P, Raatz B.

Plant Genome. 2018 Jul;11(2). doi: 10.3835/plantgenome2017.08.0068.


Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia.

Dequigiovanni G, Ramos SLF, Alves-Pereira A, Fabri EG, Picanço-Rodrigues D, Clement CR, Gepts P, Veasey EA.

PLoS One. 2018 Jun 6;13(6):e0198593. doi: 10.1371/journal.pone.0198593. eCollection 2018.


Genetic Patterns of Common-Bean Seed Acquisition and Early-Stage Adoption Among Farmer Groups in Western Uganda.

Wilkus EL, Berny Mier Y Teran JC, Mukankusi CM, Gepts P.

Front Plant Sci. 2018 May 11;9:586. doi: 10.3389/fpls.2018.00586. eCollection 2018.


Spatial and Temporal Scales of Range Expansion in Wild Phaseolus vulgaris.

Ariani A, Berny Mier Y Teran JC, Gepts P.

Mol Biol Evol. 2018 Jan 1;35(1):119-131. doi: 10.1093/molbev/msx273.


Genomic history of the origin and domestication of common bean unveils its closest sister species.

Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A.

Genome Biol. 2017 Mar 29;18(1):60. doi: 10.1186/s13059-017-1190-6.


Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

Rodriguez M, Rau D, Bitocchi E, Bellucci E, Biagetti E, Carboni A, Gepts P, Nanni L, Papa R, Attene G.

New Phytol. 2016 Mar;209(4):1781-94. doi: 10.1111/nph.13713. Epub 2015 Nov 3.


Global agricultural intensification during climate change: a role for genomics.

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, de Oliveira AC, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Tuberosa R, Valliyodan B, Varshney RK, Yano M.

Plant Biotechnol J. 2016 Apr;14(4):1095-8. doi: 10.1111/pbi.12467. Epub 2015 Sep 11. Review.


Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects.

Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M.

Front Plant Sci. 2015 Aug 11;6:563. doi: 10.3389/fpls.2015.00563. eCollection 2015. Review.


Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.).

Ariani A, Gepts P.

Mol Genet Genomics. 2015 Oct;290(5):1771-85. doi: 10.1007/s00438-015-1038-2. Epub 2015 Apr 7.


A reference genome for common bean and genome-wide analysis of dual domestications.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, 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 MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA.

Nat Genet. 2014 Jul;46(7):707-13. doi: 10.1038/ng.3008. Epub 2014 Jun 8.


Current perspectives and the future of domestication studies.

Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Climer Vigueira C, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MT, Gremillion KJ, Lucas L, Lukens L, Marshall FB, Olsen KM, Pires JC, Richerson PJ, Rubio de Casas R, Sanjur OI, Thomas MG, Fuller DQ.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6139-46. doi: 10.1073/pnas.1323964111. Epub 2014 Apr 22.


Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico.

Kraft KH, Brown CH, Nabhan GP, Luedeling E, Luna Ruiz Jde J, Coppens d'Eeckenbrugge G, Hijmans RJ, Gepts P.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6165-70. doi: 10.1073/pnas.1308933111. Epub 2014 Apr 21.


The contribution of genetic and genomic approaches to plant domestication studies.

Gepts P.

Curr Opin Plant Biol. 2014 Apr;18:51-9. doi: 10.1016/j.pbi.2014.02.001. Epub 2014 Mar 15. Review.


Agriculture: Feeding the future.

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.

Nature. 2013 Jul 4;499(7456):23-4. doi: 10.1038/499023a. No abstract available.


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.

Gonçalves-Vidigal MC, Cruz AS, Lacanallo GF, Vidigal Filho PS, Sousa LL, Pacheco CM, McClean P, Gepts P, Pastor-Corrales MA.

Theor Appl Genet. 2013 Sep;126(9):2245-55. doi: 10.1007/s00122-013-2131-8. Epub 2013 Jun 13.


Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common Bean.

Gioia T, Logozzo G, Kami J, Spagnoletti Zeuli P, Gepts P.

J Hered. 2013 Mar;104(2):273-86. doi: 10.1093/jhered/ess102. Epub 2012 Dec 12.


Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris).

Kwak M, Toro O, Debouck DG, Gepts P.

Ann Bot. 2012 Dec;110(8):1573-80. doi: 10.1093/aob/mcs207. Epub 2012 Sep 27.


Genetic structure and mating system of wild cowpea populations in West Africa.

Kouam EB, Pasquet RS, Campagne P, Tignegre JB, Thoen K, Gaudin R, Ouedraogo JT, Salifu AB, Muluvi GM, Gepts P.

BMC Plant Biol. 2012 Jul 24;12:113. doi: 10.1186/1471-2229-12-113.


The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1.

Repinski SL, Kwak M, Gepts P.

Theor Appl Genet. 2012 May;124(8):1539-47. doi: 10.1007/s00122-012-1808-8. Epub 2012 Feb 14.


Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.).

Nanni L, Bitocchi E, Bellucci E, Rossi M, Rau D, Attene G, Gepts P, Papa R.

Theor Appl Genet. 2011 Dec;123(8):1341-57. doi: 10.1007/s00122-011-1671-z. Epub 2011 Aug 10.


Leveraging genomic resources of model species for the assessment of diversity and phylogeny in wild and domesticated lentil.

Alo F, Furman BJ, Akhunov E, Dvorak J, Gepts P.

J Hered. 2011 May-Jun;102(3):315-29. doi: 10.1093/jhered/esr015. Epub 2011 Mar 30.


Different Seed Selection and Conservation Practices for Fresh Market and Dried Chile Farmers in Aguascalientes, Mexico.

Kraft KH, de Jesús Luna-Ruíz J, Gepts P.

Econ Bot. 2010 Dec;64(4):318-328. Epub 2010 Oct 16.


Linkage mapping of the Phg-1 and Co-1(4) genes for resistance to angular leaf spot and anthracnose in the common bean cultivar AND 277.

Gonçalves-Vidigal MC, Cruz AS, Garcia A, Kami J, Vidigal Filho PS, Sousa LL, McClean P, Gepts P, Pastor-Corrales MA.

Theor Appl Genet. 2011 Mar;122(5):893-903. doi: 10.1007/s00122-010-1496-1. Epub 2010 Nov 28.


Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis).

Hufford MB, Gepts P, Ross-Ibarra J.

Mol Ecol. 2011 Jan;20(1):46-55. doi: 10.1111/j.1365-294X.2010.04924.x. Epub 2010 Nov 11.


Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity.

Burle ML, Fonseca JR, Kami JA, Gepts P.

Theor Appl Genet. 2010 Sep;121(5):801-13. doi: 10.1007/s00122-010-1350-5. Epub 2010 May 26.


Cytogenetic map of common bean (Phaseolus vulgaris L.).

Fonsêca A, Ferreira J, dos Santos TR, Mosiolek M, Bellucci E, Kami J, Gepts P, Geffroy V, Schweizer D, dos Santos KG, Pedrosa-Harand A.

Chromosome Res. 2010 Jun;18(4):487-502. doi: 10.1007/s10577-010-9129-8. Epub 2010 May 7.


Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers.

Hanai LR, Santini L, Camargo LE, Fungaro MH, Gepts P, Tsai SM, Vieira ML.

Mol Breed. 2010 Jan;25(1):25-45. Epub 2009 Jul 3.


Dispersal of transgenes through maize seed systems in Mexico.

Dyer GA, Serratos-Hernández JA, Perales HR, Gepts P, Piñeyro-Nelson A, Chávez A, Salinas-Arreortua N, Yúnez-Naude A, Taylor JE, Alvarez-Buylla ER.

PLoS One. 2009 May 29;4(5):e5734. doi: 10.1371/journal.pone.0005734.


Cytogenetic mapping of common bean chromosomes reveals a less compartmentalized small-genome plant species.

Pedrosa-Harand A, Kami J, Gepts P, Geffroy V, Schweizer D.

Chromosome Res. 2009;17(3):405-17. doi: 10.1007/s10577-009-9031-4. Epub 2009 Mar 28.


Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations.

Piñeyro-Nelson A, Van Heerwaarden J, Perales HR, Serratos-Hernández JA, Rangel A, Hufford MB, Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Alvarez-Buylla ER.

Mol Ecol. 2009 Feb;18(4):750-61. doi: 10.1111/j.1365-294X.2008.03993.x. Epub 2008 Dec 18.


Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae).

Kwak M, Gepts P.

Theor Appl Genet. 2009 Mar;118(5):979-92. doi: 10.1007/s00122-008-0955-4. Epub 2009 Jan 8.


BAC end sequences corresponding to the B4 resistance gene cluster in common bean: a resource for markers and synteny analyses.

David P, Sévignac M, Thareau V, Catillon Y, Kami J, Gepts P, Langin T, Geffroy V.

Mol Genet Genomics. 2008 Dec;280(6):521-33. doi: 10.1007/s00438-008-0384-8. Epub 2008 Sep 24.


Long-distance pollen flow assessment through evaluation of pollinator foraging range suggests transgene escape distances.

Pasquet RS, Peltier A, Hufford MB, Oudin E, Saulnier J, Paul L, Knudsen JT, Herren HR, Gepts P.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13456-61. doi: 10.1073/pnas.0806040105. Epub 2008 Sep 3.


Ecology. Harvesting data from genetically engineered crops.

Marvier M, Carrière Y, Ellstrand N, Gepts P, Kareiva P, Rosi-Marshall E, Tabashnik BE, Wolfenbarger LL.

Science. 2008 Apr 25;320(5875):452-3. doi: 10.1126/science.1154521. No abstract available.


Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris).

Kwak M, Velasco D, Gepts P.

J Hered. 2008 May-Jun;99(3):283-91. doi: 10.1093/jhered/esn005. Epub 2008 Mar 2.


Genetic mapping of a new set of microsatellite markers in a reference common bean (Phaseolus vulgaris) population BAT93 x Jalo EEP558.

Grisi MC, Blair MW, Gepts P, Brondani C, Pereira PA, Brondani RP.

Genet Mol Res. 2007 Sep 30;6(3):691-706.


Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples.

Papa R, Bellucci E, Rossi M, Leonardi S, Rau D, Gepts P, Nanni L, Attene G.

Ann Bot. 2007 Nov;100(5):1039-51. Epub 2007 Aug 1.


Detecting (trans)gene flow to landraces in centers of crop origin: lessons from the case of maize in Mexico.

Cleveland DA, Soleri D, Cuevas FA, Crossa J, Gepts P.

Environ Biosafety Res. 2005 Oct-Dec;4(4):197-208; discussion 209-15. Epub 2006 Jun 22.


Development of four phylogenetically-arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris.

Kami J, Poncet V, Geffroy V, Gepts P.

Theor Appl Genet. 2006 Apr;112(6):987-98. Epub 2006 Jan 11.


A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica.

Papa R, Acosta J, Delgado-Salinas A, Gepts P.

Theor Appl Genet. 2005 Oct;111(6):1147-58. Epub 2005 Oct 11.


Legumes as a model plant family. Genomics for food and feed report of the Cross-Legume Advances Through Genomics Conference.

Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young ND.

Plant Physiol. 2005 Apr;137(4):1228-35. No abstract available.


Who owns biodiversity, and how should the owners be compensated?

Gepts P.

Plant Physiol. 2004 Apr;134(4):1295-307. No abstract available.


Genetics of resistance to the geminivirus, Bean dwarf mosaic virus, and the role of the hypersensitive response in common bean.

Seo YS, Gepts P, Gilbertson RL.

Theor Appl Genet. 2004 Mar;108(5):786-93. Epub 2003 Nov 19.


Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.).

Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, Gepts P, Tohme J.

Theor Appl Genet. 2003 Nov;107(8):1362-74. Epub 2003 Sep 20.


Protein structures of common bean (Phaseolus vulgaris) alpha-amylase inhibitors.

Lee SC, Gepts PL, Whitaker JR.

J Agric Food Chem. 2002 Oct 23;50(22):6618-27.


Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.).

McClean PE, Lee RK, Otto C, Gepts P, Bassett MJ.

J Hered. 2002 Mar-Apr;93(2):148-52.


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