PUBLICATIONS

 

 

 

Preprints

In Press

Peer Reviewed Research

Papers from Baxter Lab Members

Review Articles

 

(All publications below are hyperlinks.)

To see how many times preprints from the Baxter lab have been downloaded, click here.

 

 

 

 

*Pre-Prints

5.  Shakoor N, Agnew E, Ziegler G, Lee S, Lizárraga C, Fahlgren N, Baxter I, Mockler TC.  Genome-wide association study reveals transient loci underlying the genetic architecture of biomass accumulation under cold stress in sorghum.  doi: https://doi.org/10.1101/760025.  Submitted to bioRxiv.

 

4.  Huang P, Mamidi S, Healey A, Grimwood J,  Jenkins J, Barry K, Sreedasyam A, Shu S, Feldman M, Wu J, Yu Y, Chen C, Johnson J, Sakakibara H, Kiba T, Sakurai T, Rokhsar D, Baxter I, Schmutz J, Brutnell TP, Kellogg EA.  The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene.  doi: https://doi.org/10.1101/744557.  

Submitted to bioRxiv.

 

3.  Whitt L, Ricachenevsky F, Ziegler G, Clemens S, Walker E, Maathuis FJM, Kear P, Baxter I.  A curated list of genes that control elemental accumulation in plants.  doi: https://doi.org/10.1101/456384.  Submitted to bioRxiv.

2.  Ellsworth P, Feldman M, Baxter I, Cousins A.  A genetic link between whole-plant water use efficiency and leaf carbon isotope composition in the C4 grass Setaria.  doi: https://doi.org/10.1101/285676.  Submitted to bioRxiv.

1.  Ziegler G, Kear P, Wu D, Ziyomo C, Lipka A, Gore M, Hoekenga O, Baxter I.  Elemental Accumulation in Kernels of the Maize Nested Association Mapping Panel Reveals Signals of Gene by Environment Interactions.  doi: https://doi.org/10.1101/164962.  Submitted to bioRxiv.

*In Press

 

 

*Peer-Reviewed Research

55.  Asaro A, Dilkes B, Baxter I.  Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome.  Plant Direct.  Published May 2019.  doi: https://doi.org/10.1002/pld3.139.

54.  Schaefer R J, Michno J-M, Jeffers J, Hoekenga O, Dilkes B, Baxter I, Myers C.  Integrating co-expression networks with GWAS to prioritize causal genes in maize.  The Plant Cell.  Published December 2018. DOI: https://doi.org/10.1105/tpc.18.00299.

53.  Feldman M J, Ellsworth P Z, Fahlgren N, Gehan M A, Cousins A B, Baxter I.  Components of water use efficiency have unique genetic signatures in the model C4 grass Setaria.  Plant Physiology.  Published October 2018. DOI: https://doi.org/10.1104/pp.18.00146.

52.  Kohler I, Huber S, Bernacchi C, Baxter I.  Increased temperatures may safeguard the nutritional quality of crops under future elevated CO2 concentrations.  The Plant Journal.  Published November 17, 2018.  https://doi.org/10.1111/tpj.14166.

51.  Pauli D, Ziegler G, Ren M, Jens M A, Hunsaker D J, Zhang M, Baxter I, Gore M A.  Multivariate analysis of the cotton seed ionome reveals integrated genetic signatures of abiotic stress response.  G3: GENES, GENOMES, GENETICS.  Published April 1, 2018; doi: https://doi.org/10.1534/g3.117.300479.

50.  Banan D, Paul R, Feldman M J, Holmes M, Schlake H, Baxter I, Leakey A D B.  High fidelity detection of crop biomass QTL from low-cost imaging in the field.  Plant Direct.  Published February 22, 2018.  doi: https://doi.org/10.1002/pld3.41.

49.  Ziegler G, Nelson R, Granada S, Krishnan HB, Gillman JD, Baxter I. Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections.  Plant Direct.  2018;2:1–14; https://doi.org/10.1002/pld3.33.

48.  Veley K M, Berry J C, Fentress S J, Schachtman D P, Baxter I, Bart R.  High-thoroughput profiling identifies resource use efficient and abiotic stress tolerant sorghum varieties.  Plant Direct. 2017;00:1–13; https://doi.org/10.1002/pld3.23.

47.  Flores-Ramirez M R, Rellan-Alvarez R, Wozniak B, Gebreselassie M-N, Jakobsen I, Olalde-Portugal V, Baxter I, Paszkowski U, Sawers R.  Coordinated changes in the accumulation of metal ions in Maize (Zea mays ssp. may L.) in response to inoculation with the arbuscular mycorrhizal fungus Funneliformis mosseae.  Plant and Cell Physiology, Volume 58, Issue 10, 1 October 2017, Pages 1689–1699; https://doi.org/10.1093/pcp/pcx100.

 

46.  Feldman M J, Paul R E, Banan D, Barrett J F, Sebastian J, Yee  M, Jiang H, Lipka A E , Brutnell T P, Dinneny J R, Leakey A D B, Baxter I.  Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria.  PLOS Genetics 13(6)e1006841; https://doi.org/10.1371/journal.pgen.1006841.

45.  Sawers R J H, Svane S F, Quan C, Grønlund M, Wozniak B, Gebrselassie M-N, González-Muñoz E, Chávez Montes R A, Baxter I, Goudet J, Jakobsen I and Paszkowski U. (2017), Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters. New Phytol. doi:10.1111/nph.14403.

 

44.  Addo-Quaye C, Buescher E, Chaikam V, Best N, Baxter I, Dilkes B.  Forward genetics by sequencing EMS variation induced inbred lines.  G3: GENES, GENOMES, GENETICS February 1, 2017 vol. 7 no. 2 413-425; https://doi.org/10.1534/g3.116.029660.

43.  Asaro, A B, Ziegler G R, Ziyomo C, Hoekenga, O A, Dilkes B P, Baxter I. The interaction of genotype and environment determines variation in the Maize kernel ionome.  G3: GENES, GENOMES, GENETICS December 1, 2016 vol. 6 no. 12 4175-4183; https://doi.org/10.1534/g3.116.034827.

42.  Huber S, Li K, Nelson R, Ulyanov A, DeMuro C, Baxter I.  Canopy position has a profound effect on soybean seed composition.  PeerJ 4:e2452; doi:10.7717/peerj.2452.

 

41.  Sebastian J, Yee M, Viana WG, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP and Dinneny JR.  Grasses suppress shoot-borne roots to conserve water during drought.  PNAS 2016 ; published ahead of print July 15, 2016, doi:10.1073/pnas.1604021113.

 

40.  Shakoor N, Ziegler G R, Dilkes BP, Brenton Z, Boyles R, Connolly EL, Kresovich S and Baxter I.  Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition.  Plant Physiology, Vol 170, Issue 4.  First published on February 19, 2016.  doi: 10.1104/pp.15.01971.

 

39.  Noah Fahlgren*, Maximilian Feldman*, Malia A. Gehan*, Melinda S. Wilson, Christine Shyu, Douglas W. Bryant, Steven T. Hill, Colton J. McEntee, Sankalpi N. Warnasooriya, Indrajit Kumar, Tracy Ficor, Stephanie Turnipseed, Kerrigan B. Gilbert, Thomas P. Brutnell, James C. Carrington, Todd C. Mockler, Ivan Baxter, Donald Danforth Plant Science Center, United States (NF, MF, MAG, MSW, CS, DWB, STH, CJM, SW, IK, TF, ST, KBG, TPB, JCC, and TCM); USDA-ARS, Donald Danforth Plant Science Center, United States (IB).  A versatile phenotyping system and analytics platform reveals diverse temporal responses to water limitation in Setaria.  MolecularPlant, Vol 8, Issue 10.  doi: 10.1016/j.molp.2015.06.005.

 

38.  Ziegler G R, Hartsock RH, Baxter I. (2015) Zbrowse: an interactive GWAS results browser.  PeerJ Computer Science 1:e3 https://doi.org/10.7717/peerj-cs.3.

 

37.  Krishnan H, Kim W, Oehrle N, Alaswad A, Baxter I, Wiebold W, Nelson R. (2015) Introgression of Leginsulin, a Cysteine-Rich Protein, and High-Protein Trait from an Asian Soybean Plant Introduction Genotype into a North American Experimental Soybean Line. J. Agric. Food Chem., 63(11), pp 2862-2869. doi: 10.1021/j505202z.

 

36.  Huang P, Feldman M, Schroder S, Bahri B A, Diao X, Zhi H, Estep M, Baxter I, Devos K M and Kellogg E A (2014), Population genetics of Setaria viridis, a new model system. Molecular Ecology, 23: 4912–4925. doi: 10.1111/mec.12907

 

35.  Kusano M, Baxter I*, Fukushima A, Oikawa A, Okazaki Y, Nakabayashi R, Bouvrette D, Achard F, Jacubowski A, Ballam J, Harrigan GG, Saito K. (2014).  Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding. *co-corresponding author.  Metabolomics.  doi: 10.1007/s11306-014-0702-6.

 

34.  Baxter I*, Ziegler G, Lahner B, Mickelbart MV, Foley R, Danku J, Armstrong P, Salt DE and Hoekenga OA. (2014) Single-kernel ionomic profiles are highly heritable indicators of genetic and environmental influences on elemental accumulation in maize grain (Zea mays).   PLoS One 9(1): e87628.  doi: 10.1371/journal.pone.0087628.  *corresponding author

 

33.  Zhang M, Pinson S, Tarpley L, Huang XY, Lahner B, Yakubova E, Baxter I, Guerinot M, Salt DE. (2014) Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain. Theor. Appl. Genet. 127: 137-165.  doi: 10.1007/s00122-013-2207-5.

 

32.  Gillman JD, Baxter I, Bilyeu K.  (2013) Phosphorus partitioning of soybean lines containing different mutant alleles of two soybean seed-specific (Glycine max (L.) Merr) ATP-binding cassette phytic acid transporter homeologs. Plant Genome 6(1): 1-10.  doi:10.3835/plantgenome2012.06.0010. 

 

31.  Shen M, Broeckling CD, Chu EY, Ziegler G, Baxter IR, Prenni JE, and Hoekenga OA.  (2013). Leveraging non-targeted metabolite profiling via statistical genomics. PLoS One 8(2): e57667.  doi:10.1371/journal.pone.0057667.

 

30.  McDowell SC, Akmakjian G, Sladek C, Mendoza-Cozatl D, Morrissey JB, Saini N, Mittler R, Baxter I, Salt DE, Ward JM, Schroeder JI, Guerinot ML, and Harper JF.  (2013). Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions. PLoS One 8(5): e63014.  doi: 10.1371/journal.pone.0063014.  

 

29.  Baxter I*, Gustin J, Settles AM, Hoekenga OA. (2012) Ionomic characterization of maize kernels in the intermated B73 x Mo17 (IBM) population. Crop Sci. 53(1): 208-220. *co-corresponding author

 

28.  Ziegler G, Terauchi A, Becker A, Armstrong P, Hudson K, Baxter I. (2012) Ionomic screening of field-grown soybeans identifies mutants with altered seed elemental composition. Plant Genome doi: 10.3835/plantgenome2012.07.0012.

 

27. Yu D*, Danku J*, Baxter I*, Kim S, Vatamaniuk OK, Vitek O, Ouzzani M, Salt DE. (2012) High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome. BMC Genomics 13(1): 623 *Contributed equally.

 

26.  Chao DY, Silva A, Baxter I, Huang YS, Nordborg M, Danku J, Lahner B, Yakubova E, Salt DE. (2012) Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana. PLoS Genet. 8(9): e1002923. doi: 10.1371/journal.pgen.1002923. 

 

25.  Muhlemann JK, Maeda H, Chang CY, San Miguel P,  Baxter I,  Cooper B, Perera MA, Nikolau BJ, Vitek O, Morgan JA, Dudareva N. (2012) Developmental changes in the metabolic network of snapdragon flowers.  PLoS ONE 7(7): e40381. doi: 10.1371/journal.pone.0040381.

 

24.  Baxter I*, Hermans C, Lahner B, Yakubova E, Tikhonova M, Verbruggen N, Chao DY, Salt DE. (2012) Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thalianaPLoS One 7(4): e35121. PMCID: PMC3338729. doi:10.1371/journal.pone.0035121 *corresponding author 

 

23.  Krishnan H, Jang S, Baxter I, and Weiebold W. (2012). Growing location has a pronounced effect on the accumulation of cancer chemopreventive agent Bowman-Birk inhibitor in soybean seeds. Crop Science 52: 1786-1794. 

 

22.  Yu D, Danku J, Baxter I, Kim S, Vatamaniuk OK, Salt DE, and Vitek O (2011). Noise reduction in genome-wide perturbation screens using linear mixed-effect models. Bioinformatics 27, 2173-2180. 

 

21.  Chao DY, Gable K, Chen M, Baxter I, Dietrich CR, Cahoon EB, Guerinot ML, Lahner B, Lu S, Markham JE, Morrissey J, Han G, Gupta SD, Harmon JM, Jaworski JG, Dunn TM, and Salt DE (2011). Sphingolipids in the root play an important role in regulating the leaf ionome in Arabidopsis thaliana. Plant Cell 23, 1061-1081.

 

20.  Becker A, Chao DY, Zhang X, Salt DE, and Baxter I (2011). Bulk segregant analysis using single nucleotide polymorphism microarrays. PLoS One 6, e15993. 

 

19.  Tian H, Baxter IR, Lahner B, Reinders A, Salt DE, and Ward JM (2010). Arabidopsis NPCC6/NaKR1 is a phloem mobile metal binding protein necessary for phloem function and root meristem maintenance. Plant Cell 22, 3963-3979.

 

18.  Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M, Vitek O, and Salt DE (2010).  A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet 6, e1001193.

 

17.  Buescher E, Achberger T, Amusan I, Giannini A, Ochsenfeld C, Rus A, Lahner B, Hoekenga O, Yakubova E, Harper JF, Guerinot ML, Zhang M, Salt DE, and Baxter IR (2010).  Natural genetic variation in selected populations of Arabidopsis thaliana is associated with ionomic differences. PLoS One 5, e11081.

 

16.  Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, and Nordborg M (2010).  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627-631.

 

15.  Vogel JP, et al (132 authors including Baxter, I.)  The International Brachypodium Initiative (2009). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763-768.

 

14.  Morrissey J, Baxter IR, Lee J, Li L, Lahner B, Grotz N, Kaplan J, Salt DE, and Guerinot ML (2009). The ferroportin metal efflux proteins function in iron and cobalt homeostasis in Arabidopsis. Plant Cell 21, 3326-3338.

 

13.  Baxter I, Hosmani PS, Rus A, Lahner B, Borevitz JO, Muthukumar B, Mickelbart MV, Schreiber L, Franke RB, and Salt DE (2009). Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis. PLoS Genet 5, e1000492.

 

12.  Danku J, Gumaelius L, Baxter I, and Salt DE (2008). A high-throughput method for Saccharomyces cerevisiae (yeast) ionomics. Journal of Analytical Atomic Spectrometry 24, 103-107.

 

11.  Baxter IR, Vitek O, Lahner B, Muthukumar B, Borghi M, Morrissey J, Guerinot ML, and Salt DE (2008). The leaf ionome as a multivariable system to detect a plant's physiological status. Proc Natl Acad Sci USA 105, 12081-12086.

 

10.  Baxter I, Muthukumar B, Park HC, Buchner P, Lahner B, Danku J, Zhao K, Lee J, Hawkesford MJ, Guerinot ML, and Salt DE (2008). Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a mitochondrial molybdenum transporter (MOT1). PLoS Genet 4, e1000004.

 

9.  Eltabakh MY, Ouzzani M, Aref WG, Elmagarmid AK, Laura-Silva Y, Arshad MU, Salt DE, and Baxter I (2008). Managing biological data using bdbms. In IEEE 24th International Conference on Data Engineering pp.1600-1603. (Cancún, México).

 

8.  Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, Weigel D, Jones JD, and Ecker JR (2007). Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci USA 104, 12057-12062.

 

7.  Baxter I, Ouzzani M, Orcun S, Kennedy B, Jandhyala SS, Salt DE. (2007) Purdue Ionomics Information Management System (PIIMS). An integrated functional genomics platform. Plant Physiol. 143: 600–611.

 

6.  Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, Yakubova E, and Salt DE (2006). Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. PLoS Genet 2, e210.

 

5.  Baxter IR, Young JC, Armstrong G, Foster N, Bogenschutz N, Cordova T, Peer WA, Hazen SP, Murphy AS, and Harper JF (2005). A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thalianaProc Natl Acad Sci USA 102, 2649-2654.

 

4.  Hazen SP, Pathan MS, Sanchez A, Baxter I, Dunn M, Estes B, Chang HS, Zhu  T, Kreps JA, and Nguyen HT (2005). Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Funct Integr Genomics 5,104-116.

 

3.  Baxter I, Tchieu J, Sussman MR, Boutry M, Palmgren MG, Gribskov M, Harper JF, and Axelsen KB (2003). Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiol 132, 618-628.

 

2.  Vitart V, Baxter I, Doerner P, and Harper JF (2001). Evidence for a role in growth and salt resistance of a plasma membrane H+-ATPase in the root endodermis. The Plant Journal 27, 191-201.

 

1.  Hegmans A, Sabat M, Baxter I, Freisinger E, and Lippert B (1998). Synthetic Ways to Tris(nucleobase) Complexes Derived from cis-Diammineplatinum(II) and a Platinum(II) Complex Containing Four Different Ligands, Three of Which Are Nucleobases. Inorg Chem 37, 4921-4928.

 

*Papers from Baxter Lab Members

1.  Gehan MA, Fahlgren N, Abbasi A, Berry JC, Callen ST, Chavez L, Doust AN, Feldman MJ, Gilbert KB, Hodge JG, Hoyer JS, Lin A, Liu S, Lizárraga C, Lorence A, Miller M, Platon E, Tessman M, Sax T (2017).  PlantCV v2: Image analysis software for high-throughput plant phenotyping.  PeerJ5:e4088 https://doi.org/10.7717/peerj.4088.

*Reviews

 

9.  Fahlgren N, Gehan MA & Baxter I (2015). Lights, camera, action: high-throughput plant phenotyping is ready for a close-up.  Curr Opin Plant Biol, 24:93-99  doi:  10.1016/j.pbi.2015.02.006

 

8.  Baxter I (2015). Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits?  Journal of Experimental Botany doi:  10.1093/jxb/erv040

 

7.  Baxter I and Dilkes BP (2012). Elemental profiles reflect plant adaptations to the environment. Science 36, 1661. 

 

6.  Baxter I (2010). Ionomics: The functional genomics of elements. Brief Funct Genomic Proteomic 9, 149-156.

 

5.  Baxter I (2009). Ionomics: studying the social network of mineral nutrients. Curr Opin Plant Biol 12, 381-386.

 

4.  Guerinot ML, Baxter I, Salt DE (2009). From the ionome to the genome: Identifying gene networks that control the mineral content of plants. In Plant Systems Biology. Coruzzi G and Gutierrez R, eds. Wiley-Blackwell.

3.  Lahner B, Baxter I, Salt DE. Ionomics and the study of the plant ionome. Annu. Rev. Plant Biol. 59:709–733. 2008.

2.  Baxter IR, and Borevitz JO (2006). Mapping a plant's chemical vocabulary. Nat Genet 38, 737-738.

1.  Peer W, Baxter I, Richards E, Freeman J, and Murphy A (2005). Phytoremediation and hyperacumulator plants. In Molecular Biology of Metal Homeostasis and Detoxification, M. Tamas and E. Martinoia, eds (Dordrecht, The Netherlands: Springer), pp. 299-340.

 

 

 

 
 
 
 

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© 2014 By Melissa Jurkowski, using WIX

 

*Corn picture = http://capl.washjeff.edu/browseresults.php?langID=2&photoID=5107&size=l

*Soybean picture = http://en.wikipedia.org/wiki/Soybean

*Setaria picture = http://pl.wikipedia.org/wiki/Włośnica_zielona

*Plasma picture = http://plaza.ufl.edu/kamenov/kamenov.htm

 

 

 

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