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Michael Purugganan

Silver Professor; Professor of Biology; Co-Principal Investigator

    1988 …2019
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    Research Output 1988 2019

    2019

    Copy Number Variation in Domestication

    Lye, Z. N. & Purugganan, M., Jan 1 2019, In : Trends in Plant Science.

    Research output: Contribution to journalReview article

    domestication
    mutation
    genetic variation
    animals
    genes

    Cross-species hybridization and the origin of North African date palms

    Flowers, J., Hazzouri, K. M., Gros-Balthazard, M., Mo, Z., Koutroumpa, K., Perrakis, A., Ferrand, S., Khierallah, H. S. M., Fuller, D. Q., Aberlenc, F., Fournaraki, C. & Purugganan, M., Jan 29 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 5, p. 1651-1658 8 p.

    Research output: Contribution to journalArticle

    Middle East
    Northern Africa
    Population
    Genome
    Phoeniceae

    Evolutionary Insights into the Nature of Plant Domestication

    Purugganan, M., Jul 22 2019, In : Current Biology. 29, 14, p. R705-R714

    Research output: Contribution to journalReview article

    Open Access
    domestication
    Crops
    crops
    Genomics
    genomics

    Genome-wide association mapping of date palm fruit traits

    Hazzouri, K. M., Gros-Balthazard, M., Flowers, J. M., Copetti, D., Lemansour, A., Lebrun, M., Masmoudi, K., Ferrand, S., Dhar, M. I., Fresquez, Z. A., Rosas, U., Zhang, J., Talag, J., Lee, S., Kudrna, D., Powell, R. F., Leitch, I. J., Krueger, R. R., Wing, R. A., Amiri, K. M. A. & 1 others, Purugganan, M. D., Dec 1 2019, In : Nature Communications. 10, 1, 4680.

    Research output: Contribution to journalArticle

    Open Access
    fruits
    genome
    Fruits
    Genome-Wide Association Study
    Fruit

    The bracteatus pineapple genome and domestication of clonally propagated crops

    Chen, L. Y., VanBuren, R., Paris, M., Zhou, H., Zhang, X., Wai, C. M., Yan, H., Chen, S., Alonge, M., Ramakrishnan, S., Liao, Z., Liu, J., Lin, J., Yue, J., Fatima, M., Lin, Z., Zhang, J., Huang, L., Wang, H., Hwa, T. Y. & 25 others, Kao, S. M., Choi, J. Y., Sharma, A., Song, J., Wang, L., Yim, W. C., Cushman, J. C., Paull, R. E., Matsumoto, T., Qin, Y., Wu, Q., Wang, J., Yu, Q., Wu, J., Zhang, S., Boches, P., Tung, C. W., Wang, M. L., Coppens d’Eeckenbrugge, G., Sanewski, G. M., Purugganan, M. D., Schatz, M. C., Bennetzen, J. L., Lexer, C. & Ming, R., Oct 1 2019, In : Nature Genetics. 51, 10, p. 1549-1558 10 p.

    Research output: Contribution to journalArticle

    Open Access
    Ananas
    Genome
    Bromelains
    Capsicum
    South America

    The complex geography of domestication of the African rice Oryza glaberrima

    Choi, J. Y., Zaidem, M., Gutaker, R., Dorph, K., Singh, R. K. & Purugganan, M., Mar 1 2019, In : PLoS genetics. 15, 3, p. e1007414

    Research output: Contribution to journalArticle

    Open Access
    Oryza glaberrima
    Geography
    domestication
    geography
    rice

    Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

    Dreissig, S., Mascher, M., Heckmann, S. & Purugganan, M., Sep 1 2019, In : Molecular Biology and Evolution. 36, 9, p. 2029-2039 11 p.

    Research output: Contribution to journalArticle

    Open Access
    domestication
    Hordeum
    barley
    Genetic Recombination
    recombination
    2018

    Evolutionary and ecological functional genomics, from lab to the wild

    Zaidem, M. L., Groen, S. C. & Purugganan, M., Jan 1 2018, (Accepted/In press) In : Plant Journal.

    Research output: Contribution to journalArticle

    Genomics
    genomics
    phenotypic variation
    Systems Biology
    plant response

    Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

    Choi, J. Y. & Purugganan, M. D., Feb 1 2018, In : Molecular Biology and Evolution. 35, 2, p. 365-382 18 p.

    Research output: Contribution to journalArticle

    Retroelements
    terminal repeat sequences
    Terminal Repeat Sequences
    retrotransposons
    methylation

    Mapping of HKT1;5 gene in barley using gwas approach and its implication in salt tolerance mechanism

    Hazzouri, K. M., Khraiwesh, B., Amiri, K. M. A., Pauli, D., Blake, T., Shahid, M., Mullath, S. K., Nelson, D., Mansour, A. L., Salehi-Ashtiani, K., Purugganan, M. & Masmoudi, K., Feb 19 2018, In : Frontiers in Plant Science. 9, 156.

    Research output: Contribution to journalArticle

    salt tolerance
    barley
    sodium
    genes
    leaves

    Multiple origin but single domestication led to Oryza sativa

    Choi, J. Y. & Purugganan, M. D., Mar 1 2018, In : G3: Genes, Genomes, Genetics. 8, 3, p. 797-803 7 p.

    Research output: Contribution to journalArticle

    Alleles
    Oryza
    Domestication
    Datasets

    The rice genome revolution: from an ancient grain to Green Super Rice

    Wing, R. A., Purugganan, M. & Zhang, Q., Jun 5 2018, (Accepted/In press) In : Nature Reviews Genetics. p. 1-13 13 p.

    Research output: Contribution to journalArticle

    Genome
    Genomics
    Agriculture
    Population
    Food
    2017

    Seed plant-specific gene lineages involved in carpel development

    Pfannebecker, K. C., Lange, M., Rupp, O., Becker, A. & Purugganan, M., Apr 1 2017, In : Molecular Biology and Evolution. 34, 4, p. 925-942 18 p.

    Research output: Contribution to journalArticle

    Plant Genes
    carpels
    Spermatophytina
    Gene Regulatory Networks
    Seeds

    The rice paradox: Multiple origins but single domestication in Asian Rice

    Choi, J. Y., Platts, A. E., Fuller, D. Q., Hsing, Y. I., Wing, R. A., Purugganan, M. D. & Kim, Y., Apr 1 2017, In : Molecular Biology and Evolution. 34, 4, p. 969-979 11 p.

    Research output: Contribution to journalArticle

    domestication
    rice
    Oryza sativa
    wild rice
    archaeological evidence
    2016

    Cryptic genetic variation for arabidopsis thaliana seed germination speed in a novel salt stress environment

    Yuan, W., Flowers, J., Sahraie, D. J. & Purugganan, M., 2016, In : G3: Genes, Genomes, Genetics. 6, 10, p. 3129-3138 10 p.

    Research output: Contribution to journalArticle

    Germination
    Arabidopsis
    Seeds
    Salts
    Chromosomes, Human, Pair 4

    Developing maps of fitness consequences for plant genomes

    Joly-Lopez, Z., Flowers, J. & Purugganan, M., Apr 1 2016, In : Current Opinion in Plant Biology. 30, p. 101-107 7 p.

    Research output: Contribution to journalArticle

    mutation
    genome
    regulatory sequences
    physical chromosome mapping
    intergenic DNA

    Domestication history and geographical adaptation inferred from a SNP map of African rice

    Meyer, R. S., Choi, J. Y., Sanches, M., Plessis, A., Flowers, J., Amas, J., Dorph, K., Barretto, A., Gross, B., Fuller, D. Q., Bimpong, I. K., Ndjiondjop, M. N., Hazzouri, K. M., Gregorio, G. B. & Purugganan, M., Aug 8 2016, (Accepted/In press) In : Nature Genetics.

    Research output: Contribution to journalArticle

    Single Nucleotide Polymorphism
    Salt-Tolerance
    Population Density
    Metagenomics
    Western Africa

    EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments

    Wilkins, O., Hafemeister, C., Plessis, A., Holloway-Phillips, M. M., Pham, G. M., Nicotra, A. B., Gregorio, G. B., Krishna Jagadish, S. V., Septiningsih, E. M., Bonneau, R. & Purugganan, M., Oct 1 2016, In : Plant Cell. 28, 10, p. 2365-2384 20 p.

    Research output: Contribution to journalArticle

    Gene Regulatory Networks
    regulator genes
    Transcription Factors
    transcription factors
    rice

    Evolution of plant phenotypes, from genomes to traits

    Casacuberta, J. M., Jackson, S., Panaud, O., Purugganan, M. & Wendel, J., 2016, In : G3: Genes, Genomes, Genetics. 6, 4, p. 775-778 4 p.

    Research output: Contribution to journalArticle

    Plant Genome
    Phenotype

    Extreme QTL mapping of germination speed in Arabidopsis thaliana

    Yuan, W., Flowers, J., Sahraie, D. J., Ehrenreich, I. M. & Purugganan, M., Sep 1 2016, In : Molecular Ecology. 25, 17, p. 4177-4196 20 p.

    Research output: Contribution to journalArticle

    Germination
    Arabidopsis
    quantitative trait loci
    Seeds
    germination

    Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis

    Rest, J. S., Wilkins, O., Yuan, W., Purugganan, M. D. & Gurevitch, J., Feb 1 2016, In : Plant Journal. 85, 4, p. 548-560 13 p.

    Research output: Contribution to journalArticle

    transcriptomics
    Dehydration
    Arabidopsis
    meta-analysis
    Meta-Analysis

    Systems genetics of plant adaptation to environmental stresses

    Groen, S. C. & Purugganan, M. D., Dec 1 2016, In : American Journal of Botany. 103, 12, p. 2019-2021 3 p.

    Research output: Contribution to journalArticle

    Plant Physiological Phenomena
    Physiological Adaptation
    Gene-Environment Interaction
    Systems Biology
    plant adaptation

    Tracing ancestor rice of Suriname Maroons back to its African origin

    Van Andel, T. R., Meyer, R. S., Aflitos, S. A., Carney, J. A., Veltman, M. A., Copetti, D., Flowers, J., Havinga, R. M., Maat, H., Purugganan, M., Wing, R. A. & Schranz, M. E., Oct 3 2016, In : Nature Plants. 2, 16149.

    Research output: Contribution to journalLetter

    Oryza glaberrima
    Suriname
    ancestry
    rice
    landraces
    2015

    Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress

    Pires, I. S., Negrão, S., Oliveira, M. M. & Purugganan, M. D., Sep 1 2015, In : Physiologia Plantarum. 155, 1, p. 43-54 12 p.

    Research output: Contribution to journalArticle

    Salinity
    salt stress
    Oryza sativa
    rice
    salinity

    Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

    Plessis, A., Hafemeister, C., Wilkins, O., Gonzaga, Z. J., Meyer, R. S., Pires, I., Müller, C., Septiningsih, E. M., Bonneau, R. & Purugganan, M., Nov 26 2015, In : eLife. 4, NOVEMBER2015, e08411.

    Research output: Contribution to journalArticle

    Gene Expression Regulation
    Gene expression
    Genes
    Gene Expression
    Plant Genes

    Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

    Hazzouri, K. M., Flowers, J., Visser, H. J., Khierallah, H. S. M., Rosas, U., Pham, G. M., Meyer, R. S., Johansen, C. K., Fresquez, Z. A., Masmoudi, K., Haider, N., El Kadri, N., Idaghdhour, Y., Malek, J. A., Thirkhill, D., Markhand, G. S., Krueger, R. R., Zaid, A. & Purugganan, M., Nov 9 2015, In : Nature Communications. 6, 8824.

    Research output: Contribution to journalArticle

    sequencing
    fruits
    genome
    crops
    polymorphism

    Whole-genome resequencing reveals extensive natural variation in the model green alga chlamydomonas reinhardtii

    Flowers, J., Hazzouri, K. M., Pham, G. M., Rosas, U., Bahmani, T., Khraiwesh, B., Nelson, D., Jijakli, K., Abdrabu, R., Harris, E. H., Lefebvre, P. A., Hom, E. F. Y., Salehi-Ashtiani, K. & Purugganan, M., 2015, In : Plant Cell. 27, 9, p. 2353-2369 17 p.

    Research output: Contribution to journalArticle

    Chlamydomonas reinhardtii
    Chlorophyta
    Genome
    genome
    Genes
    2014

    An evolutionary genomic tale of two rice species

    Purugganan, M. D., 2014, In : Nature Genetics. 46, 9, p. 931-932 2 p.

    Research output: Contribution to journalArticle

    Plant Genome
    Oryza

    Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

    Fuller, D. Q., Denham, T., Arroyo-Kalin, M., Lucas, L., Stevens, C. J., Qin, L., Allaby, R. G. & Purugganan, M. D., Apr 29 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6147-6152 6 p.

    Research output: Contribution to journalArticle

    Seeds
    Proxy
    Population Density
    Domestication
    Ear

    Current perspectives and the future of domestication studies

    Larson, G., Piperno, D. R., Allaby, R. G., Purugganan, M. D., Andersson, L., Arroyo-Kalin, M., Barton, L., Vigueira, C. C., Denham, T., Dobney, K., Doust, A. N., Gepts, P., Gilbert, M. T. P., Gremillion, K. J., Lucas, L., Lukens, L., Marshall, F. B., Olsen, K. M., Pires, J. C., Richerson, P. J. & 4 others, De Casas, R. R., Sanjur, O. I., Thomas, M. G. & Fuller, D. Q., Apr 29 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6139-6146 8 p.

    Research output: Contribution to journalArticle

    Archaeology
    Genetic Techniques
    Domestication
    Research

    Population Genomics of Plant Species

    Hazzouri, K. M., Purugganan, M. & Flowers, J., 2014, In : Advances in Botanical Research. 69, p. 311-334 24 p.

    Research output: Contribution to journalArticle

    genome
    mating systems
    population size
    genetic variation

    Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)

    Molina, J., Hazzouri, K. M., Nickrent, D., Geisler, M., Meyer, R. S., Pentony, M. M., Flowers, J., Pelser, P., Barcelona, J., Inovejas, S. A., Uy, I., Yuan, W., Wilkins, O., Michel, C. I., Locklear, S., Concepcion, G. P. & Purugganan, M., Apr 2014, In : Molecular Biology and Evolution. 31, 4, p. 793-803 11 p.

    Research output: Contribution to journalArticle

    Rafflesia
    Rafflesiaceae
    Chloroplast Genome
    chloroplast
    angiosperm

    Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum

    Li, S. I., Buttery, N. J., Thompson, C. R. L. & Purugganan, M. D., Jul 21 2014, In : BMC Genomics. 15, 1, 616.

    Research output: Contribution to journalArticle

    Dictyostelium
    Chimerism
    Genes
    Clone Cells
    Interpersonal Relations

    Storytelling and story testing in domestication

    Gerbault, P., Allaby, R. G., Boivin, N., Rudzinski, A., Grimaldi, I. M., Pires, J. C., Climer Vigueira, C., Dobney, K., Gremillion, K. J., Barton, L., Arroyo-Kalin, M., Purugganan, M. D., De Casas, R. R., Bollongino, R., Burger, J., Fuller, D. Q., Bradley, D. G., Balding, D. J., Richerson, P. J., Gilbert, M. T. P. & 2 others, Larson, G. & Thomas, M. G., Apr 29 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6159-6164 6 p.

    Research output: Contribution to journalArticle

    Population Genetics
    History
    Research Personnel
    Domestication
    Research

    Variation in arabidopsis flowering time associated with cis-regulatory variation in CONSTANS

    Rosas, U., Mei, Y., Xie, Q., Banta, J. A., Zhou, R. W., Seufferheld, G., Gerard, S., Chou, L., Bhambhra, N., Parks, J. D., Flowers, J. M., McClung, C. R., Hanzawa, Y. & Purugganan, M. D., Apr 16 2014, In : Nature Communications. 5, 3651.

    Research output: Contribution to journalArticle

    mutations
    Arabidopsis
    Transcription Factors
    Genes
    Mutation
    2013

    Different evolutionary histories of two cation/proton exchanger gene families in plants

    Pires, I. S., Negrão, S., Pentony, M. M., Abreu, I. A., Oliveira, M. M. & Purugganan, M. D., Jul 4 2013, In : BMC Plant Biology. 13, 1, 97.

    Research output: Contribution to journalArticle

    protons
    cations
    antiporters
    gene duplication
    history

    Evolution of crop species: Genetics of domestication and diversification

    Meyer, R. S. & Purugganan, M. D., Dec 2013, In : Nature Reviews Genetics. 14, 12, p. 840-852 13 p.

    Research output: Contribution to journalArticle

    Mutation
    Quantitative Trait Loci
    Genome-Wide Association Study
    Genes
    Genome

    Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture

    Rosas, U., Cibrian-Jaramillo, A., Ristova, D., Banta, J. A., Gifford, M. L., Fan, A. H., Zhou, R. W., Kim, G. J., Krouk, G., Birnbaum, K. D., Purugganan, M. D. & Coruzzi, G. M., Sep 10 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 37, p. 15133-15138 6 p.

    Research output: Contribution to journalArticle

    Arabidopsis
    Genes
    Abscisic Acid
    Indoleacetic Acids
    Nitrates

    Introduction to theme "genomics in ecology, evolution, and systematics"

    Shaffer, H. B. & Purugganan, M. D., 2013, In : Annual Review of Ecology, Evolution, and Systematics. 44, p. 1-4 4 p.

    Research output: Contribution to journalArticle

    genomics
    ecology
    taxonomy
    Biological Sciences
    demography

    Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

    Li, Y. H., Zhao, S. C., Ma, J. X., Li, D., Yan, L., Li, J., Qi, X. T., Guo, X. S., Zhang, L., He, W. M., Chang, R. Z., Liang, Q. S., Guo, Y., Ye, C., Wang, X. B., Tao, Y., Guan, R. X., Wang, J. Y., Liu, Y. L., Jin, L. G. & 15 others, Zhang, X. Q., Liu, Z. X., Zhang, L. J., Chen, J., Wang, K. J., Nielsen, R., Li, R. Q., Chen, P. Y., Li, W. B., Reif, J. C., Purugganan, M., Wang, J., Zhang, M. C., Wang, J. & Qiu, L. J., Aug 28 2013, In : BMC Genomics. 14, 1, 579.

    Research output: Contribution to journalArticle

    Soybeans
    Genome
    Single Nucleotide Polymorphism
    Domestication
    Genetic Association Studies

    Molecular relationships between australian annual wild rice, Oryza meridionalis, and two related perennial forms

    Sotowa, M., Ootsuka, K., Kobayashi, Y., Hao, Y., Tanaka, K., Ichitani, K., Flowers, J., Purugganan, M., Nakamura, I., Sato, Y. I., Sato, T., Crayn, D., Simon, B., Waters, D. L. E., Henry, R. J. & Ishikawa, R., 2013, In : Rice. 6, 26

    Research output: Contribution to journalArticle

    wild rice
    Oryza rufipogon
    rice
    genome
    nuclear genome

    Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

    Gifford, M. L., Banta, J. A., Katari, M. S., Hulsmans, J., Chen, L., Ristova, D., Tranchina, D., Purugganan, M. D., Coruzzi, G. M. & Birnbaum, K. D., Sep 2013, In : PLoS Genetics. 9, 9, e1003760.

    Research output: Contribution to journalArticle

    plasticity
    Nitrogen
    nitrogen
    Plant Development
    crop plant

    Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the drosophila retina

    Thanawala, S. U., Rister, J., Goldberg, G. W., Zuskov, A., Olesnicky, E. C., Flowers, J., Jukam, D., Purugganan, M., Gavis, E. R., Desplan, C. & Johnston, R. J., Apr 15 2013, In : Developmental Cell. 25, 1, p. 93-105 13 p.

    Research output: Contribution to journalArticle

    Drosophila
    Retina
    Modulation
    Basic Helix-Loop-Helix Transcription Factors
    Neurology
    2012

    Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana

    Banta, J. A., Ehrenreich, I. M., Gerard, S., Chou, L., Wilczek, A., Schmitt, J., Kover, P. X. & Purugganan, M. D., Aug 2012, In : Ecology Letters. 15, 8, p. 769-777 9 p.

    Research output: Contribution to journalArticle

    niche breadth
    phenology
    range size
    flowering
    climate modeling

    Cultivation as slow evolutionary entanglement: Comparative data on rate and sequence of domestication

    Fuller, D. Q., Asouti, E. & Purugganan, M. D., Mar 2012, In : Vegetation History and Archaeobotany. 21, 2, p. 131-145 15 p.

    Research output: Contribution to journalArticle

    domestication
    crop
    crops
    cereal
    Iva
    domestication
    rate
    Evolutionary
    Domestication
    Entanglement

    Genome-wide patterns of Arabidopsis gene expression in nature

    Richards, C. L., Rosas, U., Banta, J., Bhambhra, N. & Purugganan, M. D., Apr 2012, In : PLoS Genetics. 8, 4, e1002662.

    Research output: Contribution to journalArticle

    Arabidopsis
    gene expression
    genome
    Genome
    Gene Expression

    Longitudinal trends in climate drive flowering time clines in north american arabidopsis thaliana

    Samis, K. E., Murren, C. J., Bossdorf, O., Donohue, K., Fenster, C. B., Malmberg, R. L., Purugganan, M. D. & Stinchcombe, J. R., 2012, In : Ecology and Evolution. 2, 6, p. 1162-1180 19 p.

    Research output: Contribution to journalArticle

    cline
    flowering
    Arabidopsis thaliana
    climate
    quantitative traits

    Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice

    Flowers, J. M., Molina, J., Rubinstein, S., Huang, P., Schaal, B. A. & Purugganan, M. D., Feb 2012, In : Molecular Biology and Evolution. 29, 2, p. 675-687 13 p.

    Research output: Contribution to journalArticle

    Genetic Selection
    natural selection
    genomics
    polymorphism
    rice