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Items: 1 to 50 of 110

1.

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

Wing RA, Purugganan MD, Zhang Q.

Nat Rev Genet. 2018 Jun 5. doi: 10.1038/s41576-018-0024-z. [Epub ahead of print] Review.

PMID:
29872215
2.

Multiple Origin but Single Domestication Led to Oryza sativa.

Choi JY, Purugganan MD.

G3 (Bethesda). 2018 Mar 2;8(3):797-803. doi: 10.1534/g3.117.300334.

3.

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice.

Choi JY, Purugganan MD.

Mol Biol Evol. 2018 Feb 1;35(2):365-382. doi: 10.1093/molbev/msx284.

4.

The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.

Choi JY, Platts AE, Fuller DQ, Hsing YI, Wing RA, Purugganan MD.

Mol Biol Evol. 2017 Apr 1;34(4):969-979. doi: 10.1093/molbev/msx049.

5.

Systems genetics of plant adaptation to environmental stresses.

Groen SC, Purugganan MD.

Am J Bot. 2016 Dec;103(12):2019-2021. doi: 10.3732/ajb.1600340. Epub 2016 Nov 18. No abstract available.

6.

Tracing ancestor rice of Suriname Maroons back to its African origin.

van Andel TR, Meyer RS, Aflitos SA, Carney JA, Veltman MA, Copetti D, Flowers JM, Havinga RM, Maat H, Purugganan MD, Wing RA, Schranz ME.

Nat Plants. 2016 Oct 3;2:16149. doi: 10.1038/nplants.2016.149.

PMID:
27694825
7.

Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment.

Yuan W, Flowers JM, Sahraie DJ, Purugganan MD.

G3 (Bethesda). 2016 Oct 13;6(10):3129-3138. doi: 10.1534/g3.116.033944.

8.

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

Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, Dorph K, Barretto A, Gross B, Fuller DQ, Bimpong IK, Ndjiondjop MN, Hazzouri KM, Gregorio GB, Purugganan MD.

Nat Genet. 2016 Sep;48(9):1083-8. doi: 10.1038/ng.3633. Epub 2016 Aug 8.

PMID:
27500524
9.

Extreme QTL mapping of germination speed in Arabidopsis thaliana.

Yuan W, Flowers JM, Sahraie DJ, Ehrenreich IM, Purugganan MD.

Mol Ecol. 2016 Sep;25(17):4177-96. doi: 10.1111/mec.13768.

PMID:
27454560
10.

Developing maps of fitness consequences for plant genomes.

Joly-Lopez Z, Flowers JM, Purugganan MD.

Curr Opin Plant Biol. 2016 Apr;30:101-7. doi: 10.1016/j.pbi.2016.02.008. Epub 2016 Mar 4. Review.

11.

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

Rest JS, Wilkins O, Yuan W, Purugganan MD, Gurevitch J.

Plant J. 2016 Feb;85(4):548-60. doi: 10.1111/tpj.13124.

12.

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

Hazzouri KM, Flowers JM, Visser HJ, Khierallah HS, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD.

Nat Commun. 2015 Nov 9;6:8824. doi: 10.1038/ncomms9824.

13.

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.

Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EF, Salehi-Ashtiani K, Purugganan MD.

Plant Cell. 2015 Sep;27(9):2353-69. doi: 10.1105/tpc.15.00492. Epub 2015 Sep 21.

14.

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

Pires IS, Negrão S, Oliveira MM, Purugganan MD.

Physiol Plant. 2015 Sep;155(1):43-54. doi: 10.1111/ppl.12356. Epub 2015 Jul 22.

PMID:
26082319
15.

An evolutionary genomic tale of two rice species.

Purugganan MD.

Nat Genet. 2014 Sep;46(9):931-2. doi: 10.1038/ng.3071.

PMID:
25162803
16.

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

Li SI, Buttery NJ, Thompson CR, Purugganan MD.

BMC Genomics. 2014 Jul 21;15:616. doi: 10.1186/1471-2164-15-616.

17.

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.

18.

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

Fuller DQ, Denham T, Arroyo-Kalin M, Lucas L, Stevens CJ, Qin L, Allaby RG, Purugganan MD.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6147-52. doi: 10.1073/pnas.1308937110. Epub 2014 Apr 21.

19.

Storytelling and story testing in domestication.

Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MT, Larson G, Thomas MG.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6159-64. doi: 10.1073/pnas.1400425111. Epub 2014 Apr 21.

20.

Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS.

Rosas U, Mei Y, Xie Q, Banta JA, Zhou RW, Seufferheld G, Gerard S, Chou L, Bhambhra N, Parks JD, Flowers JM, McClung CR, Hanzawa Y, Purugganan MD.

Nat Commun. 2014 Apr 16;5:3651. doi: 10.1038/ncomms4651.

21.

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

Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, Uy I, Yuan W, Wilkins O, Michel CI, Locklear S, Concepcion GP, Purugganan MD.

Mol Biol Evol. 2014 Apr;31(4):793-803. doi: 10.1093/molbev/msu051. Epub 2014 Jan 23.

22.

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 JM, Purugganan MD, Nakamura I, Sato Y, Sato T, Crayn D, Simon B, Waters DL, Henry RJ, Ishikawa R.

Rice (N Y). 2013 Oct 28;6(1):26. doi: 10.1186/1939-8433-6-26.

23.

Evolution of crop species: genetics of domestication and diversification.

Meyer RS, Purugganan MD.

Nat Rev Genet. 2013 Dec;14(12):840-52. doi: 10.1038/nrg3605. Review.

PMID:
24240513
24.

Plasticity regulators modulate specific root traits in discrete nitrogen environments.

Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD.

PLoS Genet. 2013;9(9):e1003760. doi: 10.1371/journal.pgen.1003760. Epub 2013 Sep 5.

25.

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

Rosas U, Cibrian-Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM.

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):15133-8. doi: 10.1073/pnas.1305883110. Epub 2013 Aug 26. Erratum in: Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2555.

26.

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

Pires IS, Negrão S, Pentony MM, Abreu IA, Oliveira MM, Purugganan MD.

BMC Plant Biol. 2013 Jul 4;13:97. doi: 10.1186/1471-2229-13-97.

27.

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

Thanawala SU, Rister J, Goldberg GW, Zuskov A, Olesnicky EC, Flowers JM, Jukam D, Purugganan MD, Gavis ER, Desplan C, Johnston RJ Jr.

Dev Cell. 2013 Apr 15;25(1):93-105. doi: 10.1016/j.devcel.2013.02.016.

28.

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.

Samis KE, Murren CJ, Bossdorf O, Donohue K, Fenster CB, Malmberg RL, Purugganan MD, Stinchcombe JR.

Ecol Evol. 2012 Jun;2(6):1162-80. doi: 10.1002/ece3.262.

29.

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

Huang P, Molina J, Flowers JM, Rubinstein S, Jackson SA, Purugganan MD, Schaal BA.

Mol Ecol. 2012 Sep;21(18):4593-604. doi: 10.1111/j.1365-294X.2012.05625.x. Epub 2012 May 30.

PMID:
22646149
30.

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

Banta JA, Ehrenreich IM, Gerard S, Chou L, Wilczek A, Schmitt J, Kover PX, Purugganan MD.

Ecol Lett. 2012 Aug;15(8):769-77. doi: 10.1111/j.1461-0248.2012.01796.x. Epub 2012 May 15.

PMID:
22583905
31.

Genome-wide patterns of Arabidopsis gene expression in nature.

Richards CL, Rosas U, Banta J, Bhambhra N, Purugganan MD.

PLoS Genet. 2012;8(4):e1002662. doi: 10.1371/journal.pgen.1002662. Epub 2012 Apr 19.

32.

The plant proteome folding project: structure and positive selection in plant protein families.

Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD.

Genome Biol Evol. 2012;4(3):360-71. doi: 10.1093/gbe/evs015. Epub 2012 Feb 16.

33.

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

Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD.

Mol Biol Evol. 2012 Feb;29(2):675-87. doi: 10.1093/molbev/msr225. Epub 2011 Sep 13.

PMID:
21917724
34.

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD.

PLoS One. 2011;6(6):e20670. doi: 10.1371/journal.pone.0020670. Epub 2011 Jun 6.

35.

Molecular evidence for a single evolutionary origin of domesticated rice.

Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD.

Proc Natl Acad Sci U S A. 2011 May 17;108(20):8351-6. doi: 10.1073/pnas.1104686108. Epub 2011 May 2.

36.

The cooperative amoeba: Dictyostelium as a model for social evolution.

Li SI, Purugganan MD.

Trends Genet. 2011 Feb;27(2):48-54. doi: 10.1016/j.tig.2010.11.003. Epub 2010 Dec 16. Review.

PMID:
21167620
37.

Plant phenotypic plasticity in a changing climate.

Nicotra AB, Atkin OK, Bonser SP, Davidson AM, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, van Kleunen M.

Trends Plant Sci. 2010 Dec;15(12):684-92. doi: 10.1016/j.tplants.2010.09.008. Epub 2010 Oct 21. Review.

PMID:
20970368
38.

Migration, isolation and hybridization in island crop populations: the case of Madagascar rice.

Mather KA, Molina J, Flowers JM, Rubinstein S, Rauh BL, Lawton-Rauh A, Caicedo AL, McNally KL, Purugganan MD.

Mol Ecol. 2010 Nov;19(22):4892-905. doi: 10.1111/j.1365-294X.2010.04845.x. Epub 2010 Oct 21.

PMID:
20964753
39.

Archaeological data reveal slow rates of evolution during plant domestication.

Purugganan MD, Fuller DQ.

Evolution. 2011 Jan;65(1):171-83. doi: 10.1111/j.1558-5646.2010.01093.x.

PMID:
20666839
40.

Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum.

Flowers JM, Li SI, Stathos A, Saxer G, Ostrowski EA, Queller DC, Strassmann JE, Purugganan MD.

PLoS Genet. 2010 Jul 1;6(7):e1001013. doi: 10.1371/journal.pgen.1001013.

41.

Population genomics of the Arabidopsis thaliana flowering time gene network.

Flowers JM, Hanzawa Y, Hall MC, Moore RC, Purugganan MD.

Mol Biol Evol. 2009 Nov;26(11):2475-86. doi: 10.1093/molbev/msp161. Epub 2009 Jul 22.

PMID:
19625391
42.

A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana.

Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R.

PLoS Genet. 2009 Jul;5(7):e1000551. doi: 10.1371/journal.pgen.1000551. Epub 2009 Jul 10.

43.

Candidate gene association mapping of Arabidopsis flowering time.

Ehrenreich IM, Hanzawa Y, Chou L, Roe JL, Kover PX, Purugganan MD.

Genetics. 2009 Sep;183(1):325-35. doi: 10.1534/genetics.109.105189. Epub 2009 Jul 6.

44.

Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana.

Reininga JM, Nielsen D, Purugganan MD.

Mol Ecol. 2009 Jul;18(13):2844-55. doi: 10.1111/j.1365-294X.2009.04206.x. Epub 2009 Apr 24.

PMID:
19457201
45.

The nature of selection during plant domestication.

Purugganan MD, Fuller DQ.

Nature. 2009 Feb 12;457(7231):843-8. doi: 10.1038/nature07895. Review.

PMID:
19212403
46.

Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis thaliana MAF2-5 flowering time gene cluster.

Caicedo AL, Richards C, Ehrenreich IM, Purugganan MD.

Mol Biol Evol. 2009 Mar;26(3):699-711. doi: 10.1093/molbev/msn300. Epub 2009 Jan 12.

PMID:
19139056
47.

The evolution of plant genomes: scaling up from a population perspective.

Flowers JM, Purugganan MD.

Curr Opin Genet Dev. 2008 Dec;18(6):565-70. doi: 10.1016/j.gde.2008.11.005. Epub 2009 Jan 7. Review.

PMID:
19131240
48.

A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons.

Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H, Sari MA, Collin F, Flowers JM, Pitrat M, Purugganan MD, Dogimont C, Bendahmane A.

Science. 2008 Aug 8;321(5890):836-8. doi: 10.1126/science.1159023.

49.

Retraction.

Shimizu KK, Reininga JM, Caicedo AL, Mays CA, Moore RC, Olsen KM, Ruzsa S, Coop G, Bustamante CD, Purugganan MD.

Science. 2008 Apr 11;320(5873):176. doi: 10.1126/science.320.5873.176a. No abstract available.

PMID:
18403691
50.

Sequence variation of MicroRNAs and their binding sites in Arabidopsis.

Ehrenreich IM, Purugganan MD.

Plant Physiol. 2008 Apr;146(4):1974-82. doi: 10.1104/pp.108.116582. Epub 2008 Feb 27.

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