Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Soybean Seed Improvement Through Quantitative Analysis of Phenotypic Diversity in Response to Environmental Fluctuations

Location: Plant Genetics Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Coordinated changes in the accumulation of metal ions in maize (Zea mays ssp. mays L.) in response to inoculation with the arbuscular mycorrhizal fungus Funneliformis mosseae - (Peer Reviewed Journal)

Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13C metabolic flux analysis - (Peer Reviewed Journal)
Hendry, J.I., Prasannan, C., Ma, F., Mollers, B., Jaiswal, D., Digmurti, M., Allen, D.K., Frigaard, N., Dasgupta, S., Wangikar, P.P. 2017. Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13C metabolic flux analysis. Biotechnology and Bioengineering. doi: 10.1002/bit.26350.

BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana - (Peer Reviewed Journal)
Hindt, M.N., Akmakjian, G.Z., Pivarski, K.L., Punshon, T., Baxter, I.R., Salt, D., Guerinot, M. 2017. BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana. Metallomics. doi: 10.1039/c7mt00152e.

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria - (Peer Reviewed Journal)
Feldman, M., Paul, R., Banan, D., Barrett, J., Sebastian, J., Yee, M., Jiang, H., Lipka, A., Brutnell, T., Dinneny, J., Leakey, A., Baxter, I.R. 2017. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genetics. doi: 10.1371/journal.pgen.1006841.

Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform - (Review Article)
Marshall-Colon, A., Long, S.P., Allen, D.K., Allen, G.D., Beard, D., Benes, B., Caemmerer, S., Christensen, A., Cox, D.J., Hart, J., Hirst, P., Kannan, K., Katz, D.S., Lynch, J., Millar, A., Panneerselvan, B., Price, N., Prusinkiewicz, P., Raila, D., Shekar, R.G., Shrivastava, S., Shukla, D., Srinivasan, V., Stitt, M., Turk, M.J., Voit, E.O., Wang, Y., Yin, X., Zhu, X. 2017. Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform. Frontiers in Plant Science. 8:786. doi: 10.3389/fpls.2017.00786.

Phospholipase D¿ enhances diacylglycerol flux into triacylglycerol - (Peer Reviewed Journal)
Yang, W., Wang, G., Li, J., Bates, P.D., Wang, X., Allen, D.K. 2017. Phospholipase D¿ enhances diacylglycerol flux into triacylglycerol. Plant Physiology. 174(1):110-123. doi: 10.1104/pp.17.00026.

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 - (Peer Reviewed Journal)
Sawers, R., Svane, S., Quan, C., Gronlund, M., Wozniak, B., Gebreselassie, M.N., Gonzalez-Munoz, E., Chavez Montes, R., Baxter, I.R., Goudet, J., Jakobsen, I., 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 Phytologist. 214(2):632-643. doi:10.1111/nph.14403.

Forward genetics by sequencing EMS variation-induced inbred lines - (Peer Reviewed Journal)
Addo-Quaye, C., Buescher, E., Best, N., Chaikam, V., Baxter, I.R., Dilkes, B. 2017. Forward genetics by sequencing EMS variation-induced inbred lines. G3, Genes/Genomes/Genetics. 7(2):413-425. doi: 10.1534/g3.116.029660.

Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition Reprint Icon - (Peer Reviewed Journal)
Shakoor, N., Ziegler, G.R., Dilkes, B., Brenton, Z., Boyles, R., Connolly, E., Kresovich, S., Baxter, I.R. 2016. Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition. Plant Physiology. 170:1989-1998.

The interaction of genotype and environment determines variation in the maize kernal ionome - (Peer Reviewed Journal)
Asaro, A., Ziegler, G.R., Ziyomo, C., Hoekenga, O., Dilkes, B.P., Baxter, I.R. 2016. The interaction of genotype and environment determines variation in the maize kernal ionome. G3, Genes/Genomes/Genetics. 6(12):4175-4183. doi: 10.1534/g3.116.034827.

Synergism between inositol polyphosphates and TOR kinase signaling in nutrient sensing, growth control, and lipid metabolism in Chlamydomonas - (Peer Reviewed Journal)
Couso, I., Evans, B., Li, J., Liu, Y., Ma, F., Diamond, S., Allen, D.K., Umen, J.G. 2016. Synergism between inositol polyphosphates and TOR kinase signaling in nutrient sensing, growth control, and lipid metabolism in Chlamydomonas. The Plant Cell. 28(5):2026-2042. doi: 10.1105/tpc.16.00351.

Grasses suppress shoot-borne roots to conserve water during drought - (Peer Reviewed Journal)
Sebastian, J., Yee, M., Viana, W.G., Rellan-Alvarez, R., Feldman, M., Priest, H., Trontin, C., Lee, T., Jiang, H., Baxter, I.R., Mockler, T., Hochholdinger, F., Brutnell, T.P., Dinneny, J.R. 2016. Grasses suppress shoot-borne roots to conserve water during drought. Proceedings of the National Academy of Sciences. 113(31):8861-8866. doi: 10.1073/pnas.1604021113.

Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network Reprint Icon - (Review Article)
Hodges, M., Dellero, Y., Keech, O., Betti, M., Raghavendra, A.S., Sage, R., Zhu, X., Allen, D.K., Weber, A.P. 2016. Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network. Journal of Experimental Botany. 67(10):3015-3026. doi:10.1093/jxb/erw145.

Assessing compartmentalized flux in lipid metabolism with isotopes Reprint Icon - (Review Article)
Allen, D.K. 2016. Assessing compartmentalized flux in lipid metabolism with isotopes. Biochimica et Biophysica Acta. doi:10.1016/j.bbalip.2016.03.017.

Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of DCT2 mutants Reprint Icon - (Peer Reviewed Journal)
Weissmann, S., Ma, F., Furuyama, K., Gierse, J.K., Berg, H., Shao, Y., Taniguchi, M., Allen, D.K., Brutnell, T.P. 2016. Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of DCT2 mutants. The Plant Cell. 28:466-484.

Quantifying plant phenotypes with isotopic labeling and metabolic flux analysis Reprint Icon - (Review Article)
Allen, D.K. 2016. Quantifying plant phenotypes with isotopic labeling and metabolic flux analysis. Current Opinion in Biotechnology. 37:45-52. doi:10.1016/j.copbio.2015.10.002.

A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria Reprint Icon - (Peer Reviewed Journal)
Fahlgren, N., Feldman, M., Gehan, M.A., Wilson, M., Shyu, C., Bryant, D.W., Hill, S.T., McEntee, C.J., Warnasooriya, S.N., Kumar, I., Ficor, T., Turnipseed, S., Gilbert, K.B., Brutnell, T.P., Carrington, J.C., Mockler, T.C., Baxter, I.R. 2015. A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant. 8:1520-1535.

Zbrowse: An interactive GWAS results browser Reprint Icon - (Peer Reviewed Journal)
Ziegler, G.R., Hartsock, R.H., Baxter, I.R. 2015. Zbrowse: An interactive GWAS results browser. Peer J Computer Science. 1:e3. https://dx.doi.org/10.7717/peerj-cs.3.

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up Reprint Icon - (Review Article)
Fahlgren, N., Gehan, M., Baxter, I.R. 2015. Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Current Opinion in Plant Biology. 24:93-99.

Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future Reprint Icon - (Peer Reviewed Journal)
Allen, D.K., Bates, P.D., Tjellstrom, H. 2015. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Progress in Lipid Research. 58:97-120.

Transcriptional response to petiole heat girdling in cassava Reprint Icon - (Peer Reviewed Journal)
Zhang, Y., Ding, Z., Ma, F., Chauhan, R.D., Allen, D.K., Brutnell, T., Wang, W., Peng, M., Li, P. 2015. Transcriptional response to petiole heat girdling in cassava. Scientific Reports. 5:8414.

Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits? Reprint Icon - (Review Article)
Baxter, I.R. 2015. Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits? Journal of Experimental Botany. 66(8):2127-2131.

Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation Reprint Icon - (Peer Reviewed Journal)
Ma, F., Jazmin, L.J., Young, J.D., Allen, D.K. 2014. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. Proceedings of the National Academy of Sciences. 111(47):16967-16972.

Population genetics of Setaria viridis, a new model system Reprint Icon - (Peer Reviewed Journal)
Huang, P., Feldman, M., Schroder, S., Bahri, B.A., Diao, X., Zhi, H., Estep, M., Baxter, I.R., Devos, K.M., Kellogg, E.A. 2014. Population genetics of Setaria viridis, a new model system. Molecular Ecology. 23(20):4912-4925.

Single kernel ionomic profiles are highly heritable indicators of genetic and environmental influences on elemental accumulation in maize grain (Zea mays) - (Peer Reviewed Journal)

Last Modified: 07/24/2017
Footer Content Back to Top of Page