Faculty Directory

Andy Pereira

Andy Pereira


Anheuser-Busch and Arkansas Wholesalers Professorship in Plant Molecular Genetics

(DREX)-Director Experiment Station

(CSES)-Crop, Soil and Environmental Sciences

Phone: 479-575-2354

Fax: (479) 575-7465

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  • Andrill Climate Change -teachers training program: Presented climate change related research to school teachers “Crop water use efficiency in response to climate change”, November 1-2, 2010
  • First USA Science and Engineering Festival: participated in hands on demonstration of “plant science research for climate change” (http://www.epa.gov/research/sciencefestival/), October 23-24, 2010
  • Kids Tech University: Demonstrated “Mutants of Plants” to ~200 school students (March 2009) http://kidstechuniversity.vbi.vt.edu/
  • VBI High school days: Taught High school students (15 in 2007, 12 in 2009) from Montgomery County, Virginia; representing 9th and 10th grade students as well as students from underrepresented groups. Guided the students through a practical course “Mutants of Plants reveal how Genes Function” where students discussed the significance of genetic analysis of mutants to plant biology.
  • Multicultural Academic Opportunities Program (MAOP-VT): Hosted MAOP student for Bioinformatics training during summer and mentoring during the year, resulting in poster presentation at national conference:
  • Udiani O, Krishnan A, Pereira A (2008) Investigating the conservation of transcription factor binding sites between evolutionary related species, The Annual Biomedical Research Conference for Minority Students (ABRCMS), November 5-8, 2008, Orlando, Florida.
  • High/Middle School student training: Provide laboratory training for students (4 students in 2008) in scientific principles, doing experiments with plants (Stress testing), the use of statistics and computer programs.
  • Undergraduate VT student training: Provide undergraduate assistantships to offer selected students to learn genomics and genetics techniques in the laboratory, enabling job and graduate placement in reputed labs elsewhere.


  • Sixth International Rice Genetics Symposium, November 16-19, 2009; Manila, Philippines, Convener –Translational Genomics session.
  • 1st EPOBIO Workshop: ‘Products from Plants - the Biorefinery Future’, 22-24 May 2006, Wageningen, The Netherlands, Local Organizer.
  • Fourth Plant GEMS (Plant Genomics European Meetings), Amsterdam 20-23 September 2005, Local organization committee.
  • First International Symposium on Rice Functional Genomics, Shanghai, China, November 19-21, 2003. Co-organizer symposium.
  • ‘Transposition, Recombination and Application to Plant Genomics’, 5th Plant Sciences Institute Symposium, June 5-8, 2003, Ames, ISU, USA. Co-organizer symposium.
  • EMBO Workshop: "Novel Applications of Homologous and Specific Recombination in Plants", 13-16 Sept. 1998, Lunteren, The Netherlands. Co-Organizor and Session Chairman.
  • 4th International Symposium on the Molecular Biology of the Potato, July 18, 1995, Wageningen. Session Chairman.
  • ‘Gene Targeting’ Workshop, VII International Congress on Plant Tissue and Cell Culture, June 24-29, 1990, Amsterdam, Workshop organizer.

Research Emphasis

  • Drought stress systems biology using the plant models Arabidopsis and rice: Dissect drought response, resistance and water use efficiency pathways using transcriptome analysis and regulatory genes with conserved functions across plants.
  • Gene function network analysis to dissect complex biological pathways, using regulatory genes as genetic perturbations to experimentally validate and improve predicted networks
  • Reproductive drought stress response and resistance pathways: comparative analysis in the cereals maize and rice
  • Systems analysis of regulatory pathways of cellulose, lignin and other cell wall components
  • Development of heterologous transposon tagging systems in plants using En-I(Spm) and Ac-Ds maize transposons for knockout mutagenesis, activation tagging and gene detection
  • Forward genetics strategies for identification and analysis of gene functions for important crop traits like disease resistance, abiotic stress, regulators of metabolic pathways, plant architecture, meristem identity etc.
  • Development of Reverse genetics strategies by generation of insertion flanking sequence tag FST databases in Arabidopsis, rice and tomato
  • Potato molecular genetics: QTL mapping of Phytophthora and nematode resistance genes, isolation of resistance genes by map-based cloning and transposon tagging approaches
  • Arabidopsis-pathogen interaction: isolation of non-race specific pathogen resistance genes
  • Characterization of the cuticular wax CER genes and their role in plant protection mechanisms by validation in Arabidopsis, rice and tomato
  • QTL analysis of physiological parameters for drought tolerance/avoidance in rice
  • Functional genomics of agronomic traits in rice

Genomics, Genetics, Stress Biology, Plant Functional Genomics

Other Information


  • ‘Abiotic stress tolerance mechanisms: from model to crop’ European networking summer school 2005, August 22-31, 2005, Ljubljana, Slovenia.
  • ‘Advanced Genetics’ Post-graduate course Natural Products and Biotechnology,  Mediterranean Agronomic Institute of Chania (MAICH), May 24-28, 2004, Crete, Greece.
  • ‘Advaned Genetics’ Post-graduate course Natural Products and Biotechnology, MAICH, December 3-7, 2002, Crete, Greece.
  • ‘Advanced Genetics and Genomics’ Post-graduate course Natural Products and Biotechnology, MAICH, December 16-20, 2001, Crete, Greece.
  • ‘Phenotyping gene functions’ PhD Summerschool “Environmental Signaling: Arabidopsis as a model”. Utrecht, The Netherlands, August 2001.
  • ‘Functional genomics with transposons in model plants: Arabidopsis and Rice’, Post-graduate course Natural Products and Biotechnology, MAICH, May 14-16, 2001, Crete, Greece.
  • ‘Functional Genomics with Transposons’ Winterschool Bioinformatics, Dec 14, 2000, Wageningen
  • ‘Arabidopsis a source of genes: Gene isolation strategies’ Seed Master Class, Wageningen Seed Centre, Nov 15, 1999, Wageningen.
  • ‘Functional analysis of the Arabidopsis genome for the identification of genes useful for agriculture’ UNESCO Course on: Molecular Plant Genome Analysis; International symposium and training course, June 22, 1998, Godollo, Hungary.
  • ‘Transposable Elements: an overview’ PhD Autumn school on Molecular and Genetic Analysis of Plant Genomes, Nov. 30, 1995, IAC, Wageningen.
  • ‘New Cloning Strategies'; EPW AIO/OIO course on `Development Biology’, Dept. Molecular Biology WAU, Sept. 7, 1995, Wageningen.
  • ‘Transposon Tagging with En-I: from Maize to Arabidopsis’; Gene Engineering for Low Environmental Impact Crops, Institute of Plant Molecular Biology of the Academy of Sciences of the Czech Republic, Oct. 24-27, 1993, Ceske Budejovice, Czech Republic.
  • ‘Transposon Tagging and RFLPs’, Plant Breeding Lectures (LUW), Nov. 1992, Wageningen.


  • “Systems biology of conserved drought stress response and resistance in plants”, International Plant Molecular Biology Congress, St. Louis, USA, October 25-30, 2009.
  • “Validation of drought response/resistance pathway genes by phenotypic analysis of mutants” Generation Challenge Program Annual Meeting, Bamako, Mali, September 20-23, 2009.
  • “Systems biology of conserved drought stress resistance in plants”, International Symposium in Commemoration of 150th Birth Anniversary of Sir J.C. Bose: A journey from Plant Physiology to Plant Biology, Kolkatta, India, November 24-28, 2008.
  • “Comparative functional genomics of drought stress response and resistance pathways in rice”, 6th International Rice Functional Genomics Symposium, Jeju, S. Korea, November 10-12, 2008.
  • “Improvement of water use efficiency in rice”, Salt & Water Stress In Plants, Gordon Research Conference, Big Sky, MT, September 7-12, 2008.
  • “Comparative functional genomics of drought stress response and resistance pathways in plants”, Soy2008: 12th Biennial Molecular and Cellular Biology of the Soybean Conference, Indianapolis, IN, July 20-23, 2008.
  • ‘Improvement of Water Use Efficiency and Drought Resistance in Rice’, Challenge Program Workshop, Plant & Animal Genomes XVI Conference, January 12-16, 2008, San Diego, USA
  • ‘From genomics to traits for sustainable rice crop production’ International Symposium on “Breeding Rice – Progress and Strategies for the future”, July 17-17, 2007, New Delhi, India.
  • ‘Improvement of water use efficiency together with drought resistance in rice’, 4th International Rice Functional Genomics Symposium, October 9-11, 2006, Montpellier, France
  • ‘Improvement of water-use efficiency in crop plants’, 5th Plant Genomics European Meetings, October 11-14, 2006, Venice, Italy
    ‘Discovery of stress tolerance genes using global collections of rice mutants’, Fifth International Rice Genetics Symposium, November 19-23, 2005, Manila, Philippines
  • ‘New Initiatives: IRFGC’ Second International Symposium on Rice Functional Genomics. November 14-17, 2004, Tucson. AZ, USA. ‘Functional genomics using gain-of-function transposon mutagenesis’. XLVIII Annual Congress of the Italian Society of Agricultural Genetics (SIGA). Lecce, Italy, September 2004.
  • ‘Rice Genomics’, Workshop on Rice Research, June 28-30, 2004, Pavia, Italy.
  • ‘Plant Biotechnology for Multiple End Users’ US-EC Workshop on Applications of Molecular Biology for the Production of Plants for Biobased Products and Bioenergy; April 28-30, 2004, USDA-ARS, Albany, CA, USA.
  • ‘EU consortium on rice functional genomics’ The First International Symposium on Rice Functional Genomics. November 19-21, 2003, Shanghai, China.
  • ‘Gain-of-function mutagenesis strategy for gene function discovery’ The CAAS-WUR Autumn workshop. Plant Genomics: from crop production to healthy food. November 10-15, 2003, Beijing, China
  • ‘Transposon mediated activation tagging for high efficiency gain-of-function mutants’ 5th International Symposium in the Series -Recent Advances in Plant Biotechnology, September 7-13, 2003, Stara Lesna, Slovak Republic
  • ‘Transposon Mediated Activation Tagging for High Efficiency Gain-of-function Mutants’ Transposition, Recombination and Application to Plant Genomics, 5th Plant Sciences Institute Symposium, June 5-8, 2003. Ames, ISU, USA.
  • ‘Impacts of biotechnology on fertilizer use: genomics & biotechnology’ IFA-FAO Agriculture Conference: Global Food Security and the Role of Sustainable Fertilization. 26-28 March 2003, Rome, Italy.
  • ‘EU consortium on rice transposon mutagenesis’ Towards Building a Global Rice Gene Machine - An International Workshop. November 11-12, 2002, CSIRO Plant Industry, Canberra, Australia.
  • ‘European Union consortium on rice functional genomics: status and progress’ The International Rice Congress 2002, September 16-18 2002, Beijing, China.
  • ‘Functional genomics strategies with transposons in rice’ RicEU Conference. 6-8 June, 2002. Turin, Italy.
  • ‘An Activation Tagging System in Arabidopsis to Bridge the Phenotype Gap to Metabolomics’ First International Congress on Plant Metabolomics. 8 April 2002, Wageningen, The Netherlands.
  • ‘Transposon insertional mutagenesis in Arabidopsis and Rice’ 23 November 2001, NIAS-COE/BRAIN Joint International Symposium. Tsukuba, Japan
  • ‘Functional Genomics for Plant Breeding’ Korean Horticultural Society. 26 October 2001, Korea
  • ‘Functional Genomics for transposons in rice’ August 10 2001, ICRISAT, India
  • ‘Activation tagging for novel phenotypes in Arabidopsis’ EU-NSF Tomato Consortium. 28 July, 2001, Toulouse, France.
  • ‘Transposons and Functional Genomics in Rice’ 4th International Rice Genetics Symposium, 22-27 Oct. 2000, IRRI, Los Baños, Philippines.
  • ‘Functional genomics in model plants’ China-EBNIC Workshop on Plant Genome Research, Session Chair, 6-8 Dec, 1999, Wuhan, China.
  • ‘Functional genomics with transposon in rice’. Rockefeller General Meeting of The International Program on Rice Biotechnology. Phuket, Thailand, September 1999.
  • ‘Functional Genomics with Transposons in Model Plants: Arabidopsis and Rice’ CHI symposium: Molecular Biology’s role in Enhancing Agricultural Productivity’, 14-16 March, 1999, Amsterdam.
  • EMBO Workshop: "Novel Applications of Homologous and Specific Recombination in Plants" Co-Organizor and Chairman Session Tagging, 13-16 Sept. 1998, Lunteren, The Netherlands.
  • `Identification and Engineering of Resistance genes in Potato'; Chairman Session Resistance: 5th International Symposium on the Molecular Biology of the Potato. 2-6 Aug.1998, Bogensee, Germany.
  • `Sequence Selected Insertional Mutagenesis with the En-I system in Arabidopsis'; The Arabidopsis Genome: From Sequence to Function; 11-14 Dec 1997. Cold Spring Harbor Laboratory, USA.
  • `The EU Rice Transposon Mutagenesis Network'; Rice Genome Workshop, 5th International Congress of Plant Molecular Biology, Sept. 21-27, 1997, Singapore.
  • 'Functional Analysis of the Arabidopsis Genome using the En-I Transposon Mutagenesis System'; 5th International Congress of Plant Molecular Biology, Sept. 21-27, 1997, Singapore.
  • `Gene Detection with Transposons in Rice'; International Program on Rice Biotechnology, Rockefeller sponsored, Sept 15-19, 1997, Malacca, Malaysia.
  • `Insertional Mutagenesis with the En-I System'; 8th International Conference on Arabidopsis Research, 25-29 June 1997, Madison, USA.
  •  `Targeted Insertion Mutagenesis with the En-I Transposon System in Arabidopsis'; Plant & Animal Genome V, Jan 12-16, 1997, San Diego, USA.
  • `Targeted tagging with the En-I transposon system'; 7th International Conference on Arabidopsis Research, June 23-27, 1996, Norwich, UK.
  • `Another Tagging System: En-I', Transposon Tagging Workshop, 5th International Conference on Arabidopsis Research, Aug 19-22, 1993, Ohio, USA.
  • `Towards the isolation of resistance genes by transposon targeting in potato'; Advances in Potato Crop Protection, International Symposium organized by the Royal Netherlands Society of Plant Pathology and by the Sections Pathology and Virology of the EAPR, Sept. 1-6, 1991, Wageningen.
  • `Transposon Targeting in Potato', 2nd International Potato Molecular Biology Symposium, Aug. 11-15, 1991, St. Andrews, Scotland.
    `Gene Targeting' Workshop organizer, VII International Congress on Plant Tissue and Cell Culture, June 24-29, 1990, Amsterdam.


  • 1981-1986: Ph.D., Plant Breeding and Cytogenetics, minor Biochemistry, Department of Plant Breeding & Cytogenetics, Iowa State University, USA   Thesis: Molecular isolation, DNA sequence and organization of the transposable element Enhancer of Zea mays.
  • 1979-1981: M.S. Genetics, major Cytogenetics, minor Biochemistry, Dept. of Genetics, Indian Agricultural Research Institute, New Delhi, India   Thesis: Cytogenetic and Biochemical studies on some of the American and Oriental genera of Maydeae.
  • 1974-1979: B.Sc. Agriculture and Animal Husbandry, Genetics & Plant Breeding electives, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India


  • Pereira A (2016) Plant Abiotic Stress Challenges from the Changing Environment. Front Plant Sci 7:1123. doi: 10.3389/fpls.2016.01123. PMID: 27512403
  • Basu S, Ramegowda V, Kumar A, Pereira A (2016) Plant adaptation to drought stress. F1000Res. 5. pii: F1000 Faculty Rev-1554. doi: 10.12688/f1000research.7678.1.
  • Moraes de Freitas GP, Basu S, Ramegowda V, Braga EB, Pereira A. (2016) Comparative analysis of gene expression in response to cold stress in diverse rice genotypes. Biochem Biophys Res Commun. 471(1):253-9. doi: 10.1016/j.bbrc.2016.02.004. PMID: 26855133
  • Lozano-Sotomayor P, Chávez Montes RA, Silvestre-Vañó M, Herrera-Ubaldo H, Greco R, Pablo-Villa J, Galliani BM, Diaz-Ramirez D, Weemen M, Boutilier K, Pereira A, Colombo L, Madueño F, Marsch-Martínez N, de Folter S. (2016) Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana. Plant J. doi: 10.1111/tpj.13264. PMID: 27402171.
  • Ramegowda V, Basu S, Gupta C, Pereira A. (2015) Regulation of grain yield in rice under well-watered and drought stress conditions by GUDK. Plant Signal Behav. 10(11):e1034421. doi: 10.1080/15592324.2015.1034421. PMID: 26633564
  • Bevilacqua CB, Basu S, Pereira A, Tseng TM, Zimmer PD, Burgos NR. (2015) Analysis of Stress-Responsive Gene Expression in Cultivated and Weedy Rice Differing in Cold Stress Tolerance. PLoS One. 10(7):e0132100. doi: 10.1371/journal.pone.0132100. PMID: 26230579
  • Ambavaram M, Basu S, Krishnan A, Ramegowda V, Batlang U, Rahman L, Baisakh N, Pereira A (2014) Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress. Nature Commun. 5:5302. doi: 10.1038/ncomms6302
  • Ramegowda V, Basu S, Krishnan A, Pereira A (2014) The rice receptor-like cytoplasmic kinase GUDK is required for drought tolerance, and grain yield under normal and drought stress conditions. Plant Physiol. 166:1634-45.
  • Srivastava SK, Wolinski P, Pereira A (2014) A strategy for genome-wide identification of gene based polymorphisms in rice reveals non-synonymous variation and functional genotypic markers. PLoS One. 9(9):e105335.
  • Basu S, Krishnan A, Ambavaram M, Rahman L, Ramegowda V, Pereira A (2014) Identification of genes directly regulated by a transcription factor in rice. Prot. Exchange doi:10.1038/protex.2014.039. http://www.nature.com/protocolexchange/protocols/3423 
  • Trijatmiko KR, Supriyanta, Prasetiyono J, Thomson MJ, Vera Cruz, CM, Moeljopawiro S, Pereira A (2014) Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population. Mol Breed. 34:283-295.
  • Marsch-Martínez N, Zúñiga-Mayo VM, Herrera-Ubaldo H, Ouwerkerk PB, Pablo-Villa J, Lozano-Sotomayor P, Greco R, Ballester P, Balanzá V, Kuijt SJ, Meijer AH, Pereira A, Ferrándiz C, de Folter S. (2014) The NTT transcription factor promotes replum development in Arabidopsis fruits. Plant J. 80(1):69-81. doi: 10.1111/tpj.12617. PubMed PMID: 25039392.
  • Batlang U, Ambavaram MM, Krishnan A, Pereira A (2014) Drought responsive genes and their functional terms identified by GS FLX Pyro sequencing in maize. Maydica 59: 306-314
  • Choudhary S, Pereira A, Basu S (2014) Effect of cryogenic and conventional grinding on the anti-oxidative potential of coriander and turmeric. International J. Seed Spices 4(2): 85-90.
  • Lu N, Carter JD, Boluarte Medina T, Holt SH, Manrique-Carpintero NC, Upham KT, Pereira A, Shulaev V, Veilleux RE. (2014) Transposon based activation tagging in diploid strawberry and monoploid derivatives of potato. Plant Cell Rep. 33(7):1203-16. PMID: 24728112.
  • Carter JD, Pereira A, Dickerman AW, Veilleux RE (2013) An active Ac/Ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation. Plant Physiol. 162(1):145-56. doi: 10.1104/pp.113.213876. PMID: 23569107
  • Harb A, Pereira A (2013) Activation tagging using the maize En-I transposon system for the identification of abiotic stress resistance genes in Arabidopsis. Methods Mol Biol. 1057:193-204. doi: 10.1007/978-1-62703-568-2_14. PMID: 23918430.
  • Trijatmiko, K.R., Pereira, A. (2013) Crop Traits: Gene Isolation. In: Encyclopedia of Sustainability Science and Technology, Ed. Robert A. Meyers, Springer, NY, pp. 667-698.
  • Droc, G., An, G., Wu, C.Y., Hsing, H.I., Hirochika, H., Pereira, A., Sundaresan, V., Han, C.D., Upadhyaya, N., Ramachandran, S., Comai, L., Leung, H., Guiderdoni, E. (2013) Mutant resources for functional analysis of the rice genome. In: Genetics and Genomics of Rice. Plant Genetics and Genomics: Crops and Models Volume 5, 2013, pp 81-115
  • Park SW, Li W, Viehhauser A, He B, Kim S, Nilsson AK, Andersson MX, Kittle JD, Ambavaram MM, Luan S, Esker AR, Tholl D, Cimini D, Ellerström M, Coaker G, Mitchell TK, Pereira A, Dietz KJ, Lawrence CB (2013) Cyclophilin 20-3 relays a 12-oxo-phytodienoic acid signal during stress responsive regulation of cellular redox homeostasis. Proc Natl Acad Sci U S A. 110(23):9559-64. doi: 10.1073/pnas.1218872110. PMID: 23671085; PubMed Central PMCID: PMC3677464.
  • Batlang U, Baisakh N, Ambavaram MM, Pereira A. (2013) Phenotypic and physiological evaluation for drought and salinity stress responses in rice. Methods Mol Biol. 956: 209-25. doi: 10.1007/978-1-62703-194-3_15. PMID: 23135854.
  • Baisakh N, RamanaRao MV, Rajasekaran K, Subudhi P, Janda J, Galbraith D, Vanier C, Pereira A (2012) Enhanced salt stress tolerance of rice plants expressing a vacuolar H+ -ATPase subunit c1 (SaVHAc1) gene from the halophyte grass Spartina alterniflora Löisel. Plant Biotechnol J. 2012 May;10(4):453-64. doi: 10.1111/j.1467-7652.2012.00678.x. PMID: 22284568.
  • Vanniarajan C, Vinod KK, Pereira A. (2012) Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). J. Genet. 91(1):9-19. PMID: 22546822.
  • Kakumanu A, Ambavaram MM, Klumas CM, Krishnan A, Batlang U, Myers E, Grene R, Pereira A (2012) Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol. 60: 846-67. (PMID: 22837360)
  • Yadeta KA, Hanemian M, Smit P, Hiemstra JA, Pereira A, Marco Y, Thomma BP. (2011) The Arabidopsis thaliana DNA-binding protein AHL19 mediates Verticillium wilt resistance. Mol Plant Microbe Interact. 24(12):1582-91.PMID: 21864046.
  • Ambavaram MM, Krishnan A, Trijatmiko KR, Pereira A (2010) Coordinated Activation of Cellulose and Repression of Lignin Biosynthesis Pathways in Rice. Plant Physiol. online 10.1104/pp.110.168641, PMID: 21205614
  • Harb, A., Krishnan, A., Ambavaram, M.M.R., Pereira A. (2010) Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiol. 154:1254-71.
  • Bassaganya-Riera J, Skoneczka J, Kingston DG, Krishnan A, Misyak SA, Guri AJ, Pereira A, Carter AB, Minorsky P, Tumarkin R, Hontecillas R. (2010) Mechanisms of action and medicinal applications of Abscisic Acid. Curr Med Chem. 17: 467-78
  • Krishnan A, E Guiderdoni, G An, YC Hsing, C-d Han, MC Lee, S-M Yu, N Upadhyaya, S Ramachandran, Q Zhang, V Sundaresan, H Hirochika, H Leung, A Pereira (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149: 165-170.
  • Krishnan A, R Greco, A Pereira (2009) Diversity of En/Spm transposons in maize and rice. Maydica 53: 181-187.
  • Krishnan A, A Pereira (2008) Integrative approaches for mining transcriptional regulatory programs in Arabidopsis. Brief Funct Genomic Proteomic. 7: 264-74.
  • Karaba A, S Dixit, R Greco, A Aharoni, K Trijatmiko, N Marsch-Martinez, A Krishnan, K Nataraja, M Udayakumar, A Pereira (2007) Improvement of water use efficiency in rice by expression of HARDY an Arabidopsis drought and salt tolerance gene. Proc. Natl Acad. Sci USA 104:15270-5.
  • Salentijn, EMJ, A Pereira, GC Angenent, CG van der Linden, F Krens, MJM Smulders, B Vosman (2007) Plant translational genomics: from model species to crops. Mol Breeding 20: 1-13.
  • Marsch-Martinez, N., R. Greco, JD Becker, S Dixit, JHW Bergervoet, A Karaba, S de Folter, A Pereira. (2006) BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways. Plant Mol. Biol. 62: 825-843.
  • Droc G, M Ruiz, P Larmande, A Pereira, P Piffanelli, JB Morel, A Dievart, B Courtois, E Guiderdoni, C Périn (2006) OryGenesDB: A database for rice reverse genetics. Nucl Acids Res 34: D736-740.
  • Greco R, PBF Ouwerkerk, A Pereira (2005) Suppression of an atypically spliced rice CACTA transposon transcript in transgenic plants. Genetics, 169: 2383-2387.
  • Enckevort LJG van, G Droc, P Piffanelli, R Greco, C Gagneur, C Weber, VM González, P Cabot, F Fornara, S Berri, B Miro, P Lan, M Rafel, T Capell, P Puigdomènech, PBF Ouwerkerk, AH Meijer, E Pe’, L Colombo, P Christou, E Guiderdoni & A Pereira (2005) EU-OSTID: A collection of transposon insertional mutants for functional genomics in rice. Plant Mol Biol. 59: 99-110.
  • van der Vossen EA, Gros J, Sikkema A, Muskens M, Wouters D, Wolters P, Pereira A, Allefs S. (2005) The Rpi-blb2 gene from Solanum bulbocastanum is an Mi-1 gene homolog conferring broad-spectrum late blight resistance in potato. Plant J. 44:208-22.
  • Chalfun-Junior A, Franken J, Mes JJ, Marsch-Martinez N, Pereira A, Angenent GC. (2005) ASYMMETRIC LEAVES2-LIKE1 gene, a member of the AS2/LOB family, controls proximal-distal patterning in Arabidopsis petals. Plant Mol Biol. 57: 559-75.
  • Aharoni A, S Dixit, R Jetter, E Thoenes, G van Arkel, A Pereira (2004) The SHINE Clade of AP2 domain transcription factors activate wax biosynthesis, alter cuticle properties and confer drought tolerance when overexpressed in Arabidopsis. Plant Cell 16: 2463-2480.
  • Hirochika H, E Guiderdoni, G An, Y Hsing, MY Eun, C-D Han, N Upadhyaya, S Ramachandran, Q Zhang, A Pereira, V Sundaresan and H Leung (2004) Rice mutant resources for gene discovery. Plant Mol Biol 54: 325-334.
  • Greco R, PBF Ouwerkerk, AJC Taal, C Sallaud, E Guiderdoni, AH Meijer, JHC Hoge and A Pereira (2004) Transcription and somatic transposition of the maize En/Spm transposon system in rice. Mol Genet Genomics 270: 514-523.
  • Kohli A, MQ Prynne, B Miro, A Pereira, RM Twyman, T Capell and P Christou (2004) Differentiation-mediated changes in transposition behavior make the Activator transposon an ideal tool for functional genomics in rice. Mol. Breed. 13: 177-191.
  • van der Vossen E, A Sikkema, B te Lintel Hekkert, J Gros, P Stevens, M Muskens, D Wouters, A Pereira, W Stiekema and S Allefs (2003) An ancient R ¬gene from the wild potato species Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans in cultivated potato and tomato. Plant J 36: 867-882.
  • Greco R, PB Ouwerkerk, RJ De Kam, C Sallaud, C Favalli, L Colombo, E Guiderdoni, AH Meijer, JH Hoge and A Pereira (2003) Transpositional behavior of an Ac/Ds system for reverse genetics in rice. Theor Appl Genet 108: 10-24.
  • Cotsaftis O, C Sallaud, JC Breitler, D Meynard, R Greco, A Pereira, E Guiderdoni (2002) Transposon-mediated generation of marker free rice plants containing a Bt endotoxin gene for insect resistance. Mol Breed. 10: 165-180.
  • Marsch-Martinez N, R Greco, G van Arkel, L Herrera-Estrella, A Pereira (2002) Activation Tagging using the En-I maize transposon system in Arabidopsis. Plant Physiol 129: 1544-1556.
  • Annadana S, Beekwilder MJ, Kuipers G, Visser PB, Outchkourov N, Pereira A, Udayakumar M, De Jong J, Jongsma MA. (2002) Cloning of the chrysanthemum UEP1 promoter and comparative expression in florets and leaves of Dendranthema grandiflora. Transgenic Res. 11: 437-445.
  • Enckevort LJG van, J Lasschuit, WJ Stiekema, E Jacobsen and A Pereira (2001) Development of Ac and Ds transposon tagging lines for gene isolation in diploid potato. Mol Breed. 7: 117-129.
  • Kohli A, J Xiong, R Greco, P Christou and A Pereira (2001) Tagged Transcriptome Display (TTD) in Indica Rice using Ac Transposition. Mol Gen Genet 266: 1-11.
  • Greco R, PBF Ouwerkerk, AJC Taal, C Favalli, T Beguiristain, P Puigdomènech, L Colombo, JHC Hoge and A Pereira (2001) Early and multiple Ac transpositions in rice generated by an adjacent strong enhancer. Plant Mol Biol 46: 215-227.
  • Greco R, PBF Ouwerkerk, C Sallaud, A Kohli, L Colombo, P Puigdomènech, E Guiderdoni, P Christou, JHC Hoge, and A Pereira A (2001) Transposon insertional mutagenesis in rice. Pl Physiol. 125: 1175-1177.
  • Enckevort LJG van, JEM Bergervoet, WJ Stiekema, A Pereira & E Jacobsen (2000) Selection of independent Ds transposon insertions in somatic tissue of potato by protoplast regeneration. Theor Appl Genet, 101: 503-510.
  • Pereira A (2000) A transgenic perspective on plant functional genomics. Transgenic Res. 9: 245-260.
  • Speulman E, R van Aspern, J van der Laak, WJ Stiekema & A Pereira (2000) Target selected insertional mutagenesis on chromosome IV of Arabidopsis using the En-I transposon system. J. Biotech. 78: 301-312.
  • Meissner RC, H Jin, E Cominelli, M Denekamp, A Fuertes, R Greco, HD Kranz, S Penfield, K Petroni, A Urzainqui, C Martin, J Paz-Ares, S Smeekens, C Tonelli, B Weisshaar, E Baumann, V Klimyuk, S Marillonnet, K Patel, E Speulman, AF Tissier, D Bouchez, JDJ Jones, A Pereira, E Wisman, and M Bevan (1999) Function Search in a Large Transcription Factor Gene Family in Arabidopsis: Assessing the Potential of Reverse Genetics to Identify Insertional Mutations in R2R3 MYB Genes. Plant Cell 11: 1827-1840.
  • Speulman E, PLJ Metz, G van Arkel, B te Lintel Hekkert, WJ Stiekema, and A Pereira (1999) A Two-Component Enhancer-Inhibitor Transposon Mutagenesis System for Functional Analysis of the Arabidopsis Genome. Plant Cell 11: 1853-1866.
  • Kubo H, AJM Peeters, MGM Aarts, A Pereira, and M Koornneef (1999) ANTHOCYANINLESS2, A Homeobox Gene Affecting Anthocyanin and Root development in Arabidopsis. Plant Cell 11: 1217-1226.
  • Aarts MGM, B te Lintel Hekkert, EB Holub, JL Beynon, WJ Stiekema & A Pereira (1998) Identification of R-Gene Homologous DNA Fragments Genetically Linked to Disease Resistance Loci in Arabidopsis thaliana. MPMI 11: 251-258.
  • Aarts MGM , R Hodge, K Kalantidis, D Florack, Z Wilson BJ Mulligan, WJ Stiekema, R Scott & A Pereira (1997) The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes. Plant J. 12: 615-623.
  • Metz PLJ, E Jacobsen, JP Nap, A Pereira, WJ Stiekema (1997) The impact on biosafety of the phosphinothricin-tolerance transgene in inter-specific B. rapa X B. napus hybrids and their successive backcrosses. Theor. Appl. Genet. 95: 442-450.
  • El-Kharbotly A, A Pereira, WJ Stiekema & E Jacobsen (1996) Race specific resistance against Phytophthora infestans in potato is controlled by more genetic factors than only R-genes. Euphytica 90: 331-336.
  • Jacobs JME, HJ van Eck, K Horsman, PFP Arens, B Verkerk-Bakker. E Jacobsen, A Pereira, WJ Stiekema (1996) Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei. Mol Breeding 2: 51-60.
  • El-Kharbotly A, JME Jacobs, B te Lintel Hekkert, E Jacobsen, MS Ramana, WJ Stiekema & A Pereira (1996) Localization of Ds-transposon containing T-DNA inserts in the diploid transgenic potato: linkage to the R1 resistance gene against Phytophthora infestans. Genome 39: 249-257.
  • El-Kharbotly A, E Jacobsen, WJ Stiekema & A Pereira (1995) Genetic localization of transformation competence in diploid potato. Theor. Appl. Genet. 91: 553-706.
  • Jacobs JME, HJ van Eck, PFP Arens, B Verkerk-Bakker, B te Lintel Hekkert, H Bastiaanssen, A El-Kharbotly, A Pereira, E Jacobsen & WJ Stiekema (1995) Agenetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. Theor. Appl. Genet. 91: 289-300.
  • van Engelen FA, JW Molthoff, AJ Conner, JP Nap, A Pereira, WJ Stiekema (1995) pBINPLUS: an improved plant transformation vector based on pBIN19. Transgenic Res. 4: 288-290.
  • Aarts MGM, CJ Keizer, WJ Stiekema & A Pereira (1995) Molecular characterization of the CER1 gene of Arabidopsis involved in epicuticular wax biosynthesis and pollen fertility. Plant Cell 7: 2115-2127.
  • Aarts MG, Corzaan P, Stiekema WJ, Pereira A. (1995) A two-element Enhancer-Inhibitor transposon system in Arabidopsis thaliana. Mol Gen Genet. 247: 555-64.
  • El-Kharbotly A, C Leonards-Schippers, DJ Huigen, E Jacobsen, A Pereira, WJ Stiekema, F Salamini & C Gebhardt (1994) Segregation analysis and RFLP mapping of the R1 and R3 alleles conferring race-specific resistance to Phytophthora infestans in progeny of dihaploid potato parents. Mol. Gen. Genet. 242: 749-754.
  • Aarts MGM, W Dirkse, WJ Stiekema & A Pereira (1993) Transposon tagging of a male sterility gene in Arabidopsis. Nature 363: 715-717.
  • Pereira A, JME Jacobs, W te Lintel Hekkert, E Rutgers, E Jacobsen & WJ Stiekema (1992) Towards the isolation of resistance genes by transposon tagging in potato. Neth. J. Pl. Path. 98: 215-221.
  • Pereira A, M Aarts, S van Agtmaal, WJ Stiekema & E Jacobsen (1991) Waxy variegation in transgenic potato. Maydica 36: 323-327.
  • Pereira A & H Saedler (1989) Transpositional behaviour of the maize En/Spm element in transgenic tobacco. EMBO J. 8: 1315-1321.
  • Pereira A, H Cuypers, A Gierl, Zs Schwarz-Sommer & H Saedler (1986) Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J. 5: 835-841.
  • O'Reilly, C, NS Shepherd, A Pereira, Zs Schwarz-Sommer, I Bertram, DS Robertson, PA Peterson & H Saedler (1985) Molecular cloning of the a1 locus of Zea mays using the transposable elements En and Mu1. EMBO J. 4: 877-882.
  • Pereira A, Zs Schwarz-Sommer, A Gierl, I Bertram, PA Peterson & H Saedler (1985) Genetic and molecular analysis of the Enhancer (En) transposable element system of Zea mays. EMBO J. 4: 17-23.
  • Pereira A, PA Peterson (1985) Origin and diversity of mutants controlled by the Uq transposable element system in maize. Genet Res Camb. 46: 219-236.

Book Editor

  • “Plant Reverse Genetics”, 2011, in series Methods in Molecular Biology, Humana Press, USA, Volume 678, DOI: 10.1007/978-1-60761-682-5

Invited Articles/Book Chapters

  • Ambavaram MM, Pereira A (2011) Setting up reverse transcription quantitative-PCR experiments. Methods Mol Biol. 2011; 678:45-54.
  • Harb A, Pereira A (2011) Screening Arabidopsis genotypes for drought stress resistance. Methods Mol Biol. 2011; 678:191-8.
  • Marsch-Martínez N, Pereira A (2011) Activation tagging with En/Spm-I /dSpm transposons in Arabidopsis. Methods Mol Biol. 678: 91-105.
  • Krishnan A, Ambavaram MMR, Harb A, Batlang U, Wittich PE, Pereira A (2009) Genetic networks underlying plant abiotic stress responses. n: Genes for Plant Abiotic Stress (Jenks MA and Wood AJ eds.) John Wiley & Sons, Inc., Ames IA, USA
  • Marsch-Martinez N, Pereira A (2009) Activation tagging for gain-in-function mutants. In Plant Developmental Biology – Biotechnological Perspectives, Pua EC, Davey MR (eds) Springer Publishing Company, Berlin, Germany.
  • Pereira A (2002) Transposon Tagging Methods in Heterologous Plants. In: Molecular Plant Biology; A Practical Approach Volume I (P. Gilmartin & C. Bowler eds.), Oxford University Press, Oxford, UK, pp 53-81.
  • Pereira A (2001) Mutagenesis and genetic dissection of plant stress responses. In: Molecular tools for the assessment of plant adaptation to the environment. (M.J. Hawkesford & P. Buchner eds.), Kluwer publishers, pp 17-42.
  • Greco R, PBF Ouwerkerk, C Sallaud, A Kohli, C Favalli, T Beguiristain, L Colombo, E Pè, P Puigdomènech, E Guiderdoni, P Christou, JHC Hoge, and A Pereira (2001) Transposons and functional genomics in rice. In: Rice Genetics IV. Proceedings of the Fourth International Rice Genetics Symposium (Khush, GS, Brar DS, Hardy B, eds.), 22-27 October 2000. Los Banos, Philippines. pp 263-277.
  • Aarts MGM, C Koncz, & A Pereira (2000) Transposon and T-DNA Mutagenesis. In: Arabidopsis: A Practical Approach (Z.A. Wilson ed.), Oxford University Press, NY, pp 143-166.
  • Kohli A., Xiong J, Greco R, Christou P and Pereira A (2000) Tagged Transcriptome Display (TTD): using Ac elements to identify transcribed sequences in indica rice. Rice Genetics Newsletter 17: 119-121
  • Pereira, A (1999) Plant genomics revolutionizing agricultural research. Biotechnology and Development Monitor. 40: 2-7.
    Nap, J-P and A Pereira (1999) Meeting Report: From high throughput genomics to useful transgenic crops. Molecular Breeding 5: 481–483.
  • Pereira A (1998) Heterologous transposon tagging systems. In: Transgenic Plant Research (K.Lindsey ed.) Harwood Academic Publishers, UK., pp 91-108.
  • Pereira, A & MGM Aarts (1998) Transposon Tagging with the En-I System. In: Methods in Molecular Biology, Vol 82: Arabidopsis Protocols (J. Martinez-Zapater, J Salinas eds.), Humana Press Inc., Totowa, NJ, USA, pp 329-338.
  • Stiekema WJ and A Pereira (1998) Unravelling the genome by genome sequencing and gene function analysis. In: Arabidopsis, (eds. J.A. Roberts and M. Anderson), Annual Plant Reviews, Volume 1, Sheffield Academic Press, UK., pp 31-32.
  • Ramulu, KS, P Dijkhuis, A Pereira, GC Angenent, Ch.H. Hanisch ten Cate, MM van Lookeren Campagne (1998) EMS Mutagenesis and Transposon Tagging for the Isolation of Apomixis Mutants and Genes in Arabidopsis and Petunia. In: Proc. Symp. Current Topics in Plant Cytogenetics Related to Plant Improvement, (T. Lelley ed.), Tulln, Austria, WUW-Universitatsverslag, pp. 258-267.
  • Ramulu, KS, P Dijkhuis, A Pereira, GC Angenent, MM van Lookeren Campagne and JJM Dons (1998) EMS and Transposon Mutagenesis for the Isolation of Apomictic Mutants in Plants. In: Somaclonal Variation and Induced Mutations in Crop Improvement, (S.M. Jain et al eds.) Kluwers Academic Publishers, Dordrecht, pp. 379-400.
  • Jacobs, J.M.E., B. te Lintel Hekkert, A. El-Kharbotly, E. Jacobsen, W.J. Stiekema & A. Pereira (1994) Ac-Ds transposons mapped near disease resistance loci for targeted tagging in potato. In: The Molecular and Cellular Biology of the Potato. (WR Belknap, ME Vayda & WD Park, eds.) CAB International, Wallingford, UK., pp 21-30.
  • Jacobsen, E, E Flipse, AJ Kuipers, A Pereira, RGF Visser (1992) Manipulation of starch biosynthesis in potato and its implications for breeding. In: Proc. Joint Conf. EAPR Breeding & Varietal Assessment Section & EUCARPIA Potato Section. pp 68-71.

Professional Background

  • 2011- present Professor, Departments of Crop, Soil and Environmental Sciences, and Plant Pathology, University of Arkansas, Fayetteville, AR, USA
  • 2006 –2010 Research Professor, Stress Systems Biology, Virginia Bioinformatics Institute, Virginia Tech, USA
  • 2004 – 2006 Theme Coordinator Stress Biology, Plant Research International, Wageningen University & Research Centre (WUR), The Netherlands
  • 2000 – 2004 Cluster Leader: Functional Genomic Analysis, Business unit Genomics/Bioscience, Plant Research International (PRI), Wageningen University and Research Center (WUR), Wageningen, The Netherlands (NL).
  • 1996 – 2000 Section Leader: Gene Isolation, Department Molecular Biology, Plant Research International (formerly CPRO-DLO), NL
  • 1991 – 1996 Senior Scientist CPRO, CPRO-DLO in the Department Molecular Biology, NL
  • 1989 – 1991 Junior Scientist at ITAL in Wageningen, working for Ministry of Agriculture and Fisheries (DLO), The Netherlands (NL).
  • 1986 – 1988 Post-Doctoral fellow, Max-Planck Institute für Züchtungsforschung, Cologne, Germany. Research involved the study of the transposons in heterologous hosts.
  • 1985 – 1986 Teaching assistant at Iowa State University, USA on course ‘Cytogenetics and Plant Breeding’
  • 1984 – 1985 Ph.D. research at Max-Planck Institute für Züchtungsforschung, Cologne, Germany. This involved the molecular characterization of the autonomous maize Enhancer (also called Spm) transposable element, leading to a burst in the isolation of maize genes (A1, C1, C2), including the first plant regulatory gene C1 which is a myb homolog.

Honors and Awards

  • 2008 ‘Scholar of the Week’ at Virginia Tech, for period November 17-28, selected by Vice President for Research, Virginia Tech.
  • 1999: ‘Excellent Scientist’ Award from the Dutch Ministry of Agriculture and Fisheries, for period 1999-2005, provided Professor level salary scale.
  • 1986: ISU Research Excellence award
  • 1985: ‘Otto Hahn Medal’ from the Max-Planck Society for Excellent Young Scientist, included a 2 year open international fellowship