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Items: 1 to 50 of 59

1.

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture.

Han Z, Crisp PA, Stelpflug S, Kaeppler SM, Li Q, Springer NM.

Genetics. 2018 May 30. pii: genetics.300987.2018. doi: 10.1534/genetics.118.300987. [Epub ahead of print]

2.

Extensive Genetic Diversity is Present within North American Switchgrass Germplasm.

Evans J, Sanciangco MD, Lau KH, Crisovan E, Barry K, Daum C, Hundley H, Jenkins J, Kennedy M, Kunde-Ramamoorthy G, Vaillancourt B, Acharya A, Schmutz J, Saha M, Kaeppler SM, Brummer EC, Casler MD, Buell CR.

Plant Genome. 2018 Mar;11(1). doi: 10.3835/plantgenome2017.06.0055.

3.

Genotype-by-environment interactions affecting heterosis in maize.

Li Z, Coffey L, Garfin J, Miller ND, White MR, Spalding EP, de Leon N, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN.

PLoS One. 2018 Jan 17;13(1):e0191321. doi: 10.1371/journal.pone.0191321. eCollection 2018.

4.

Suppression of CINNAMOYL-CoA REDUCTASE increases the level of monolignol ferulates incorporated into maize lignins.

Smith RA, Cass CL, Mazaheri M, Sekhon RS, Heckwolf M, Kaeppler H, de Leon N, Mansfield SD, Kaeppler SM, Sedbrook JC, Karlen SD, Ralph J.

Biotechnol Biofuels. 2017 May 2;10:109. doi: 10.1186/s13068-017-0793-1. eCollection 2017.

5.

TIPS: a system for automated image-based phenotyping of maize tassels.

Gage JL, Miller ND, Spalding EP, Kaeppler SM, de Leon N.

Plant Methods. 2017 Mar 31;13:21. doi: 10.1186/s13007-017-0172-8. eCollection 2017.

6.

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development.

Stelpflug SC, Sekhon RS, Vaillancourt B, Hirsch CN, Buell CR, de Leon N, Kaeppler SM.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.04.0025.

7.

Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility.

Chen S, Kaeppler SM, Vogel KP, Casler MD.

PLoS One. 2016 Nov 28;11(11):e0167005. doi: 10.1371/journal.pone.0167005. eCollection 2016.

8.

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize.

Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA.

Plant Cell. 2016 Nov;28(11):2700-2714. Epub 2016 Nov 1.

9.

A robust, high-throughput method for computing maize ear, cob, and kernel attributes automatically from images.

Miller ND, Haase NJ, Lee J, Kaeppler SM, de Leon N, Spalding EP.

Plant J. 2017 Jan;89(1):169-178. doi: 10.1111/tpj.13320. Epub 2016 Nov 19.

10.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data.

Grabowski PP, Evans J, Daum C, Deshpande S, Barry KW, Kennedy M, Ramstein G, Kaeppler SM, Buell CR, Jiang Y, Casler MD.

New Phytol. 2017 Jan;213(1):154-169. doi: 10.1111/nph.14101. Epub 2016 Jul 22.

11.

Stover Composition in Maize and Sorghum Reveals Remarkable Genetic Variation and Plasticity for Carbohydrate Accumulation.

Sekhon RS, Breitzman MW, Silva RR, Santoro N, Rooney WL, de Leon N, Kaeppler SM.

Front Plant Sci. 2016 Jun 8;7:822. doi: 10.3389/fpls.2016.00822. eCollection 2016.

12.

Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium.

Ramstein GP, Evans J, Kaeppler SM, Mitchell RB, Vogel KP, Buell CR, Casler MD.

G3 (Bethesda). 2016 Apr 7;6(4):1049-62. doi: 10.1534/g3.115.024950.

13.

Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis.

Zhang X, Hirsch CN, Sekhon RS, de Leon N, Kaeppler SM.

J Exp Bot. 2016 Mar;67(6):1907-17. doi: 10.1093/jxb/erw006. Epub 2016 Jan 29.

14.

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.

Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2015 Nov;84(4):800-15. doi: 10.1111/tpj.13041.

15.

Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis.

Haase NJ, Beissinger T, Hirsch CN, Vaillancourt B, Deshpande S, Barry K, Buell CR, Kaeppler SM, de Leon N.

G3 (Bethesda). 2015 Jun 1;5(8):1593-602. doi: 10.1534/g3.115.017665.

16.

Autophagic recycling plays a central role in maize nitrogen remobilization.

Li F, Chung T, Pennington JG, Federico ML, Kaeppler HF, Kaeppler SM, Otegui MS, Vierstra RD.

Plant Cell. 2015 May;27(5):1389-408. doi: 10.1105/tpc.15.00158. Epub 2015 May 5.

17.

Defining window-boundaries for genomic analyses using smoothing spline techniques.

Beissinger TM, Rosa GJ, Kaeppler SM, Gianola D, de Leon N.

Genet Sel Evol. 2015 Apr 17;47:30. doi: 10.1186/s12711-015-0105-9.

18.

Image analysis of anatomical traits in stalk transections of maize and other grasses.

Heckwolf S, Heckwolf M, Kaeppler SM, de Leon N, Spalding EP.

Plant Methods. 2015 Apr 9;11:26. doi: 10.1186/s13007-015-0070-x. eCollection 2015.

19.

Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize (Zea mays L.) lines.

Li M, Heckwolf M, Crowe JD, Williams DL, Magee TD, Kaeppler SM, de Leon N, Hodge DB.

J Exp Bot. 2015 Jul;66(14):4305-15. doi: 10.1093/jxb/erv016. Epub 2015 Feb 20.

20.

Genome-wide association analysis reveals new targets for carotenoid biofortification in maize.

Suwarno WB, Pixley KV, Palacios-Rojas N, Kaeppler SM, Babu R.

Theor Appl Genet. 2015 May;128(5):851-64. doi: 10.1007/s00122-015-2475-3. Epub 2015 Feb 18.

21.

Genetic perturbation of the maize methylome.

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM.

Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.

22.

Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

Salvo SA, Hirsch CN, Buell CR, Kaeppler SM, Kaeppler HF.

PLoS One. 2014 Oct 30;9(10):e111407. doi: 10.1371/journal.pone.0111407. eCollection 2014.

23.

QTL mapping and phenotypic variation of root anatomical traits in maize (Zea mays L.).

Burton AL, Johnson J, Foerster J, Hanlon MT, Kaeppler SM, Lynch JP, Brown KM.

Theor Appl Genet. 2015 Jan;128(1):93-106. doi: 10.1007/s00122-014-2414-8. Epub 2014 Oct 19.

PMID:
25326723
24.

QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.).

Burton AL, Johnson JM, Foerster JM, Hirsch CN, Buell CR, Hanlon MT, Kaeppler SM, Brown KM, Lynch JP.

Theor Appl Genet. 2014 Nov;127(11):2293-311. doi: 10.1007/s00122-014-2353-4. Epub 2014 Sep 18.

PMID:
25230896
25.

Insights into the effects of long-term artificial selection on seed size in maize.

Hirsch CN, Flint-Garcia SA, Beissinger TM, Eichten SR, Deshpande S, Barry K, McMullen MD, Holland JB, Buckler ES, Springer N, Buell CR, de Leon N, Kaeppler SM.

Genetics. 2014 Sep;198(1):409-21. doi: 10.1534/genetics.114.167155. Epub 2014 Jul 17.

26.

Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize.

Stelpflug SC, Eichten SR, Hermanson PJ, Springer NM, Kaeppler SM.

Genetics. 2014 Sep;198(1):209-18. doi: 10.1534/genetics.114.165480. Epub 2014 Jul 14.

27.

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2014 Sep;79(6):993-1008. doi: 10.1111/tpj.12601. Epub 2014 Aug 11.

28.

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination.

Sekhon RS, Hirsch CN, Childs KL, Breitzman MW, Kell P, Duvick S, Spalding EP, Buell CR, de Leon N, Kaeppler SM.

Plant Physiol. 2014 Jun;165(2):658-669. Epub 2014 Apr 7.

29.

Insights into the maize pan-genome and pan-transcriptome.

Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR.

Plant Cell. 2014 Jan;26(1):121-35. doi: 10.1105/tpc.113.119982. Epub 2014 Jan 31.

30.

A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number.

Beissinger TM, Hirsch CN, Vaillancourt B, Deshpande S, Barry K, Buell CR, Kaeppler SM, Gianola D, de Leon N.

Genetics. 2014 Mar;196(3):829-40. doi: 10.1534/genetics.113.160655. Epub 2013 Dec 30.

31.

The genetic architecture of maize stalk strength.

Peiffer JA, Flint-Garcia SA, De Leon N, McMullen MD, Kaeppler SM, Buckler ES.

PLoS One. 2013 Jun 20;8(6):e67066. doi: 10.1371/journal.pone.0067066. Print 2013.

32.

Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays.

Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM.

PLoS One. 2013 Apr 23;8(4):e61005. doi: 10.1371/journal.pone.0061005. Print 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/0444d495-9231-4097-abe0-4750b9045971.

33.

Marker density and read depth for genotyping populations using genotyping-by-sequencing.

Beissinger TM, Hirsch CN, Sekhon RS, Foerster JM, Johnson JM, Muttoni G, Vaillancourt B, Buell CR, Kaeppler SM, de Leon N.

Genetics. 2013 Apr;193(4):1073-81. doi: 10.1534/genetics.112.147710. Epub 2013 Feb 14.

34.

Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize.

Sekhon RS, Childs KL, Santoro N, Foster CE, Buell CR, de Leon N, Kaeppler SM.

Plant Physiol. 2012 Aug;159(4):1730-44. doi: 10.1104/pp.112.199224. Epub 2012 Jun 25.

35.

Comparative population genomics of maize domestication and improvement.

Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J.

Nat Genet. 2012 Jun 3;44(7):808-11. doi: 10.1038/ng.2309.

36.

Maize HapMap2 identifies extant variation from a genome in flux.

Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D.

Nat Genet. 2012 Jun 3;44(7):803-7. doi: 10.1038/ng.2313.

PMID:
22660545
37.

TCUP: A Novel hAT Transposon Active in Maize Tissue Culture.

Smith AM, Hansey CN, Kaeppler SM.

Front Plant Sci. 2012 Jan 26;3:6. doi: 10.3389/fpls.2012.00006. eCollection 2012.

38.

A high-throughput core sampling device for the evaluation of maize stalk composition.

Muttoni G, Johnson JM, Santoro N, Rhiner CJ, von Mogel KJ, Kaeppler SM, de Leon N.

Biotechnol Biofuels. 2012 May 1;5(1):27. doi: 10.1186/1754-6834-5-27.

39.

Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing.

Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Buell CR.

PLoS One. 2012;7(3):e33071. doi: 10.1371/journal.pone.0033071. Epub 2012 Mar 16.

40.

Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences.

Zhang Y, Zalapa JE, Jakubowski AR, Price DL, Acharya A, Wei Y, Brummer EC, Kaeppler SM, Casler MD.

Genetica. 2011 Jul;139(7):933-48. doi: 10.1007/s10709-011-9597-6. Epub 2011 Jul 23.

PMID:
21786028
41.

B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize.

Eichten SR, Foerster JM, de Leon N, Kai Y, Yeh CT, Liu S, Jeddeloh JA, Schnable PS, Kaeppler SM, Springer NM.

Plant Physiol. 2011 Aug;156(4):1679-90. doi: 10.1104/pp.111.174748. Epub 2011 Jun 24.

42.

Genome-wide atlas of transcription during maize development.

Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM.

Plant J. 2011 May;66(4):553-63. doi: 10.1111/j.1365-313X.2011.04527.x. Epub 2011 Mar 9.

43.

Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars.

Zalapa JE, Price DL, Kaeppler SM, Tobias CM, Okada M, Casler MD.

Theor Appl Genet. 2011 Mar;122(4):805-17. doi: 10.1007/s00122-010-1488-1. Epub 2010 Nov 23.

PMID:
21104398
44.

Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2.

Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM, Springer NM.

Genetics. 2007 Oct;177(2):749-60. Epub 2007 Jul 29.

45.

Assessing the efficiency of RNA interference for maize functional genomics.

McGinnis K, Murphy N, Carlson AR, Akula A, Akula C, Basinger H, Carlson M, Hermanson P, Kovacevic N, McGill MA, Seshadri V, Yoyokie J, Cone K, Kaeppler HF, Kaeppler SM, Springer NM.

Plant Physiol. 2007 Apr;143(4):1441-51. Epub 2007 Feb 16.

46.

Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs.

Haun WJ, Laoueillé-Duprat S, O'connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM.

Plant J. 2007 Jan;49(2):325-37. Epub 2006 Dec 20.

47.

Detection of quantitative trait loci for seminal root traits in maize (Zea mays L.) seedlings grown under differential phosphorus levels.

Zhu J, Mickelson SM, Kaeppler SM, Lynch JP.

Theor Appl Genet. 2006 Jun;113(1):1-10. Epub 2006 May 3.

PMID:
16783587
48.

Mapping of QTLs for lateral root branching and length in maize (Zea mays L.) under differential phosphorus supply.

Zhu J, Kaeppler SM, Lynch JP.

Theor Appl Genet. 2005 Aug;111(4):688-95. Epub 2005 Jul 15.

PMID:
16021413
49.

Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins.

Springer NM, Kaeppler SM.

Plant Physiol. 2005 May;138(1):92-104.

50.

Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots.

Springer NM, Napoli CA, Selinger DA, Pandey R, Cone KC, Chandler VL, Kaeppler HF, Kaeppler SM.

Plant Physiol. 2003 Jun;132(2):907-25. Epub 2003 May 1.

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