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Carbonic Anhydrase Mutants in Zea mays Have Altered Stomatal Responses to Environmental Signals.

Kolbe AR, Brutnell TP, Cousins AB, Studer AJ.

Plant Physiol. 2018 Jul;177(3):980-989. doi: 10.1104/pp.18.00176. Epub 2018 May 24.


Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses.

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2018 May 2;8(1):7120. doi: 10.1038/s41598-018-25620-4.


Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing.

Zhang Y, Giuliani R, Zhang Y, Zhang Y, Araujo WL, Wang B, Liu P, Sun Q, Cousins A, Edwards G, Fernie A, Brutnell TP, Li P.

J Integr Plant Biol. 2018 Apr 17. doi: 10.1111/jipb.12656. [Epub ahead of print]


Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants.

Coelho CP, Huang P, Lee DY, Brutnell TP.

Trends Plant Sci. 2018 Jan;23(1):66-78. doi: 10.1016/j.tplants.2017.09.008. Epub 2017 Oct 19. Review.


Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2017 Oct 19;7(1):13528. doi: 10.1038/s41598-017-13236-z. Erratum in: Sci Rep. 2018 May 2;8(1):7120.


Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases.

Begemann MB, Gray BN, January E, Gordon GC, He Y, Liu H, Wu X, Brutnell TP, Mockler TC, Oufattole M.

Sci Rep. 2017 Sep 14;7(1):11606. doi: 10.1038/s41598-017-11760-6.


Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria.

Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee MC, Jiang H, Lipka AE, Brutnell TP, Dinneny JR, Leakey ADB, Baxter I.

PLoS Genet. 2017 Jun 23;13(6):e1006841. doi: 10.1371/journal.pgen.1006841. eCollection 2017 Jun.


An N-acetylglucosamine transporter required for arbuscular mycorrhizal symbioses in rice and maize.

Nadal M, Sawers R, Naseem S, Bassin B, Kulicke C, Sharman A, An G, An K, Ahern KR, Romag A, Brutnell TP, Gutjahr C, Geldner N, Roux C, Martinoia E, Konopka JB, Paszkowski U.

Nat Plants. 2017 May 26;3:17073. doi: 10.1038/nplants.2017.73.


Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.

Huang P, Jiang H, Zhu C, Barry K, Jenkins J, Sandor L, Schmutz J, Box MS, Kellogg EA, Brutnell TP.

Nat Plants. 2017 Apr 18;3:17054. doi: 10.1038/nplants.2017.54.


Setaria viridis as a Model System to Advance Millet Genetics and Genomics.

Huang P, Shyu C, Coelho CP, Cao Y, Brutnell TP.

Front Plant Sci. 2016 Nov 28;7:1781. eCollection 2016. Review.


The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes.

Studer AJ, Schnable JC, Weissmann S, Kolbe AR, McKain MR, Shao Y, Cousins AB, Kellogg EA, Brutnell TP.

Genome Biol. 2016 Oct 28;17(1):223.


Characterization and Transposon Mutagenesis of the Maize (Zea mays) Pho1 Gene Family.

Salazar-Vidal MN, Acosta-Segovia E, Sánchez-León N, Ahern KR, Brutnell TP, Sawers RJ.

PLoS One. 2016 Sep 20;11(9):e0161882. doi: 10.1371/journal.pone.0161882. eCollection 2016.


Transcriptome response of cassava leaves under natural shade.

Ding Z, Zhang Y, Xiao Y, Liu F, Wang M, Zhu X, Liu P, Sun Q, Wang W, Peng M, Brutnell T, Li P.

Sci Rep. 2016 Aug 19;6:31673. doi: 10.1038/srep31673.


Cross species selection scans identify components of C4 photosynthesis in the grasses.

Huang P, Studer AJ, Schnable JC, Kellogg EA, Brutnell TP.

J Exp Bot. 2017 Jan;68(2):127-135. doi: 10.1093/jxb/erw256. Epub 2016 Jul 19.


Grasses suppress shoot-borne roots to conserve water during drought.

Sebastian J, Yee MC, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP, Dinneny JR.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):8861-6. doi: 10.1073/pnas.1604021113. Epub 2016 Jul 15.


Advancing Crop Transformation in the Era of Genome Editing.

Altpeter F, Springer NM, Bartley LE, Blechl AE, Brutnell TP, Citovsky V, Conrad LJ, Gelvin SB, Jackson DP, Kausch AP, Lemaux PG, Medford JI, Orozco-Cárdenas ML, Tricoli DM, Van Eck J, Voytas DF, Walbot V, Wang K, Zhang ZJ, Stewart CN Jr.

Plant Cell. 2016 Jul;28(7):1510-20. doi: 10.1105/tpc.16.00196. Epub 2016 Jun 22. Review.


A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis.

Huang P, Brutnell TP.

Curr Opin Plant Biol. 2016 Jun;31:91-9. doi: 10.1016/j.pbi.2016.03.014. Epub 2016 Apr 11. Review.


Interactions of C4 Subtype Metabolic Activities and Transport in Maize Are Revealed through the Characterization of DCT2 Mutants.

Weissmann S, Ma F, Furuyama K, Gierse J, Berg H, Shao Y, Taniguchi M, Allen DK, Brutnell TP.

Plant Cell. 2016 Feb;28(2):466-84. doi: 10.1105/tpc.15.00497. Epub 2016 Jan 26.


Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species.

Ding Z, Weissmann S, Wang M, Du B, Huang L, Wang L, Tu X, Zhong S, Myers C, Brutnell TP, Sun Q, Li P.

PLoS One. 2015 Oct 14;10(10):e0140629. doi: 10.1371/journal.pone.0140629. eCollection 2015.


Tillering in the sugary1 sweet corn is maintained by overriding the teosinte branched1 repressive signal.

Kebrom TH, Brutnell TP.

Plant Signal Behav. 2015;10(12):e1078954. doi: 10.1080/15592324.2015.1078954.


Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AA, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JD, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JA, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J.

New Phytol. 2015 Oct;208(1):13-9. doi: 10.1111/nph.13532. Epub 2015 Jul 14. Erratum in: New Phytol. 2016 Jan;209(2):885.


A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I, Ficor T, Turnipseed S, Gilbert KB, Brutnell TP, Carrington JC, Mockler TC, Baxter I.

Mol Plant. 2015 Oct 5;8(10):1520-35. doi: 10.1016/j.molp.2015.06.005. Epub 2015 Jun 20.


Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population.

Zhang N, Gibon Y, Wallace JG, Lepak N, Li P, Dedow L, Chen C, So YS, Kremling K, Bradbury PJ, Brutnell T, Stitt M, Buckler ES.

Plant Physiol. 2015 Jun;168(2):575-83. doi: 10.1104/pp.15.00025. Epub 2015 Apr 27.


Growth-defence balance in grass biomass production: the role of jasmonates.

Shyu C, Brutnell TP.

J Exp Bot. 2015 Jul;66(14):4165-76. doi: 10.1093/jxb/erv011. Epub 2015 Feb 22. Review.


Transcriptional response to petiole heat girdling in cassava.

Zhang Y, Ding Z, Ma F, Chauhan RD, Allen DK, Brutnell TP, Wang W, Peng M, Li P.

Sci Rep. 2015 Feb 12;5:8414. doi: 10.1038/srep08414.


Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses.

Brutnell TP, Bennetzen JL, Vogel JP.

Annu Rev Plant Biol. 2015;66:465-85. doi: 10.1146/annurev-arplant-042811-105528. Epub 2015 Jan 22. Review.


Comparative analyses of C₄ and C₃ photosynthesis in developing leaves of maize and rice.

Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W, Xu J, Weissmann S, Studer A, Li P, Zhang C, LaRue T, Shao Y, Ding Z, Sun Q, Patel RV, Turgeon R, Zhu X, Provart NJ, Mockler TC, Fernie AR, Stitt M, Liu P, Brutnell TP.

Nat Biotechnol. 2014 Nov;32(11):1158-65. doi: 10.1038/nbt.3019. Epub 2014 Oct 12.


Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks.

Warnasooriya SN, Brutnell TP.

J Exp Bot. 2014 Jun;65(11):2825-34. doi: 10.1093/jxb/eru221. Epub 2014 May 27. Review.


Editorial overview: Growing the future: synthetic biology in plants.

O'Connor SE, Brutnell TP.

Curr Opin Plant Biol. 2014 Jun;19:iv-v. doi: 10.1016/j.pbi.2014.05.005. Epub 2014 May 24. No abstract available.


Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes.

Tausta SL, Li P, Si Y, Gandotra N, Liu P, Sun Q, Brutnell TP, Nelson T.

J Exp Bot. 2014 Jul;65(13):3543-55. doi: 10.1093/jxb/eru152. Epub 2014 Apr 30.


A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize.

Studer AJ, Gandin A, Kolbe AR, Wang L, Cousins AB, Brutnell TP.

Plant Physiol. 2014 Jun;165(2):608-617. Epub 2014 Apr 4.


Bundle sheath suberization in grass leaves: multiple barriers to characterization.

Mertz RA, Brutnell TP.

J Exp Bot. 2014 Jul;65(13):3371-80. doi: 10.1093/jxb/eru108. Epub 2014 Mar 22. Review.


Model-based clustering for RNA-seq data.

Si Y, Liu P, Li P, Brutnell TP.

Bioinformatics. 2014 Jan 15;30(2):197-205. doi: 10.1093/bioinformatics/btt632. Epub 2013 Nov 4.


Methods for performing crosses in Setaria viridis, a new model system for the grasses.

Jiang H, Barbier H, Brutnell T.

J Vis Exp. 2013 Oct 1;(80). doi: 10.3791/50527.


Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species.

Petti C, Shearer A, Tateno M, Ruwaya M, Nokes S, Brutnell T, Debolt S.

Front Plant Sci. 2013 Jun 19;4:181. doi: 10.3389/fpls.2013.00181. eCollection 2013.


Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae).

Mauro-Herrera M, Wang X, Barbier H, Brutnell TP, Devos KM, Doust AN.

G3 (Bethesda). 2013 Feb;3(2):283-95. doi: 10.1534/g3.112.005207. Epub 2013 Feb 1.


Reference genome sequence of the model plant Setaria.

Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM.

Nat Biotechnol. 2012 May 13;30(6):555-61. doi: 10.1038/nbt.2196.


Engineering C4 photosynthetic regulatory networks.

Weissmann S, Brutnell TP.

Curr Opin Biotechnol. 2012 Jun;23(3):298-304. doi: 10.1016/j.copbio.2011.12.018. Epub 2012 Jan 17. Review.


A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq.

Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP.

PLoS One. 2011;6(10):e26426. doi: 10.1371/journal.pone.0026426. Epub 2011 Oct 19. Erratum in: PLoS One. 2011;6(11). doi: 10.1371/annotation/e5ef7afc-7e81-4053-8670-1bb3402f63fd.


grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses.

Whipple CJ, Kebrom TH, Weber AL, Yang F, Hall D, Meeley R, Schmidt R, Doebley J, Brutnell TP, Jackson DP.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):E506-12. doi: 10.1073/pnas.1102819108. Epub 2011 Aug 1.


Brachypodium as a model for the grasses: today and the future.

Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt BF 3rd, Hong SY, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LA, Park CM, Sedbrook J, Watt M, Zheng SJ, Vogel JP.

Plant Physiol. 2011 Sep;157(1):3-13. doi: 10.1104/pp.111.179531. Epub 2011 Jul 19. No abstract available.


Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses.

Li P, Brutnell TP.

J Exp Bot. 2011 May;62(9):3031-7. doi: 10.1093/jxb/err096. Epub 2011 Mar 31. Review.


Identification of the pr1 gene product completes the anthocyanin biosynthesis pathway of maize.

Sharma M, Cortes-Cruz M, Ahern KR, McMullen M, Brutnell TP, Chopra S.

Genetics. 2011 May;188(1):69-79. doi: 10.1534/genetics.110.126136. Epub 2011 Mar 8.


Regulatory mechanisms underlying C4 photosynthesis.

Wang L, Peterson RB, Brutnell TP.

New Phytol. 2011 Apr;190(1):9-20. doi: 10.1111/j.1469-8137.2011.03649.x. Epub 2011 Feb 8. Review.


The activator/dissociation transposable elements comprise a two-component gene regulatory switch that controls endogenous gene expression in maize.

Bai L, Brutnell TP.

Genetics. 2011 Mar;187(3):749-59. doi: 10.1534/genetics.110.124149. Epub 2010 Dec 31.


The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D.

Front Plant Sci. 2011 Jul 25;2:34. doi: 10.3389/fpls.2011.00034. eCollection 2011.


The developmental dynamics of the maize leaf transcriptome.

Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP.

Nat Genet. 2010 Dec;42(12):1060-7. doi: 10.1038/ng.703. Epub 2010 Oct 31.


Setaria viridis: a model for C4 photosynthesis.

Brutnell TP, Wang L, Swartwood K, Goldschmidt A, Jackson D, Zhu XG, Kellogg E, Van Eck J.

Plant Cell. 2010 Aug;22(8):2537-44. doi: 10.1105/tpc.110.075309. Epub 2010 Aug 6.


Physiological and genetic characterization of end-of-day far-red light response in maize seedlings.

Dubois PG, Olsefski GT, Flint-Garcia S, Setter TL, Hoekenga OA, Brutnell TP.

Plant Physiol. 2010 Sep;154(1):173-86. doi: 10.1104/pp.110.159830. Epub 2010 Jul 28.

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