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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