Skip to main content

Whitham Lab Publications - Last 6 Years

For full list of publications see Steve Whitham's CV.

  1. Elmore, M. G., Groves, C. L., Hajimorad, M. R., Stewart, T. P., Gaskill, M. A., Wise, K. A., Sikora, E., Kleczewski, N. K., Smith, D. L., Mueller, D. S., Whitham, S. A. (2022) Detection and discovery of plant viruses in soybean by metagenomic sequencing. Virology J. 19:149. doi: 10.1186/s12985-022-01872-5.
  2. Bredow, M., Natukunda, M. I., Beernink, B. M., Chicowski, A.S, Salas-Fernandez, M. G., Whitham, S. A. (2022) Characterization of a foxtail mosaic virus vector for gene silencing and analysis of innate immune responses in Sorghum bicolor. Mol. Plant Pathol. In pressdoi: 10.1111/mpp.13270
  3. Yu, H., Ruan, H., Xia, X., Chicowski, A.S., Whitham, S.A., Li, Z., Wang, G., Liu, W. (2022) Maize FERONIA-like receptor genes are involved in the response of multiple disease resistance in maize. Mol. Plant Pathol. 23:9.
  4. Xu, R.*, Gao, M., Li, M., Whitham, S.A., Zhang, S., Xu, Y. (2022) Identification of MdGRF genes and the necessary role of MdGRF02 in apple root growth regulation. Scientia Horticulturae 295:110866. doi: 10.1016/j.scienta.2021.110866
  5. McCaghey, M., Shao, D., Kurcezewski, J., Lindstrom, A., Ranjan, A., Whitham, S. A., Conley, S. P., Williams, B., Smith, D. L., Kabbage, M.* (2021) Host-induced gene silencing of a Sclerotinia sclerotiorum oxaloacetate acetylhydrolase using bean pod mottle virus as a vehicle reduces disease on soybean. Front. Plant Sci. 12:677631. doi: 10.3389/fpls.2021.677631
  6. Gerber, M., Pillay, N.*, Holan, K., Whitham, S. A., Berger, D. K. (2021) Automated Hyper-Parameter Tuning of a Mask R-CNN for Quantifying Common Rust Severity in Maize, 2021 International Joint Conference on Neural Networks (IJCNN), pp. 1-7. doi: 10.1109/IJCNN52387.2021.9534417.
  7. Pillay N.*, Gerber M., Holan K., Whitham S. A., Berger D. K. (2021) Quantifying the Severity of Common Rust in Maize Using Mask R-CNN. In: Rutkowski L., Scherer R., Korytkowski M., Pedrycz W., Tadeusiewicz R., Zurada J.M. (eds) Artificial Intelligence and Soft Computing. ICAISC 2021. Lecture Notes in Computer Science, vol 12854. Springer, Cham. doi: 10.1007/978-3-030-87986-0_18
  8. O'Conner, S., Zheng, W., Qi, M., Kandel, Y., Fuller, R., Whitham, S. A., Li, L.*. (2021) GmNF-YC4-2 Increases Protein, Exhibits Broad Disease Resistance and Expedites Maturity. Int. J. Mol. Sci. 22: 3586;
  9. Chung, S. H., Bigham, M., Lappe, R., Chan, B., Nagalakshmi, U., Whitham, S. A., Dinesh-Kumar, S., Jander, G.* (2021) A sugarcane mosaic virus vector for rapid in planta screening of proteins that inhibit the growth of insect herbivores. Plant Biotechnol. J. doi: 10.1111/pbi.13585
  10. Beernink, B. M., Holan, K. L., Lappe, R. R., Whitham, S. A. Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones. J. Vis. Exp. (168), e62277, doi:10.3791/62277 (2021)
  11. Zheng, N., Li, T., Dittman, J. D., Su, J., Li, R., Gassmann, W., Peng, D., Whitham, S. A.*, Liu, S.*, Yang, B.* (2020) CRISPR/Cas9-based gene editing using egg cell-specific promoters in Arabidopsis and soybean. Front. Plant Sci. 11:800. doi: 10.3389/fpls.2020.00800
  12. Elmore, M. G.*, Banerjee, S., Pedley, K. F., Ruck, A., Whitham, S. A. (2020) De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection. Physiol. Mol. Plant Pathol. 110:101464. doi: 10.1016/j.pmpp.2020.101464
  13. Mei, Y., Beernink, B. M., Ellison, E. E., Konečná, E., Neelakandan, A. K., Voytas, D. F., Whitham, S. A.* (2019) Protein expression and gene editing in monocots using foxtail mosaic virus vectors. Plant Direct. 3:e00181. doi: 10.1002/pld3.181
  14. Bao, Y., Zarecor, S., Shah, D., Tuel, T., Campbell, D. A., Chapman, A. V. E., Imberti, D., Kiekhaefer, D., Imberti, H., Lübberstedt, T., Yin, Y., Nettleton, D., Lawrence-Dill, C. J., Whitham, S. A., Tang, L., Howell, S. H.* (2019) Assessing plant performance in the enviratron. Plant Methods. 15:117. doi: 10.1186/s13007-019-0504-y
  15. Qi, M., Yu, M., Grayczyk, J. P., Darben, L. M., Rieker, M. E. G., Seitz, J., Voegele, R. T., Whitham, S. A., Link, T. I.* (2019) Candidate effectors from Uromyces appendiculatus, the causal agent of rust on common bean, can be discriminated based on suppression of immune responses. Front. Plant Sci. 10:1182doi: 10.3389/fpls.2019.01182
  16. Mei, Y., Liu, G., Zhang, C., Hill, J. H., Whitham, S. A.* (2019) A sugarcane mosaic virus vector for gene expression in maize. Plant Direct. 3:e00158. doi: 10.1002/pld3.158
  17. Chang, H. X., Tan, R., Hartman, G. L., Wen, Z., Sang, H., Domier, L. L., Whitham, S. A., Wang, D., Chilvers, M. I.* (2019) Characterization of soybean STAY-GREEN genes in susceptibility to foliar chlorosis of sudden death syndrome. Plant Physiol. 180:711-717. doi: 10.1104/pp.19.00046
  18. Helm, M., Qi, M., Sarkar, S., Yu, H., Whitham, S. A., Innes, R. W.* (2019). Engineering a decoy substrate in soybean to enable recognition of the Soybean mosaic virus NIa protease. Mol. Plant Microbe Interact. 32:760-769. doi: 10.1094/MPMI-12-18-0324-R
  19. Pedley, K. F.*, Pandey, A. K., Ruck, A., Lincoln, L. M., Whitham, S. A., Graham, M. A.* (2019) Rpp1 encodes a ULP1-NBS-LRR protein that controls immunity to Phakopsora pachyrhizi in soybean. Mol. Plant Microbe Interact. 32:120-133doi: 10.1094/MPMI-07-18-0198-FI
  20. Qi, M., Zheng, W., Zhao, X., Hohenstein, J., Kandel, Y., O'Conner, S., Wang, Y., Du, C., Nettleton, D., Macintosh, G., Tylka, G., Wurtele, E., Whitham, S. A., Li, L.* (2019) QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnol. J. 17:252-263. doi: 10.1111/pbi.12961
  21. Xu,H.-Y., Zhang, C., Li, Z.-C., Wang, Z.-R., Jiang, X.-X., Shi, Y.-F., Fang, Y., Braun, E., Mei, Y., Qiu, W.-L., Li, S., Wang, B., Xu, J., Navarre, D., Ren, D., Cheng, N., Nakata, P. A., Graham, M. A., Whitham, S. A., Liu, J.-Z.* (2018) GmMEKK1 is a key regulator of cell death and defense responses in soybean. Plant Physiol. 178:907-922. doi: 10.1104/pp.18.00903
  22. Irizarry, M. D., Elmore, M. G., Batzer, J. C., Whitham, S. A., Mueller, D. S.* (2018). Alternative hosts for Soybean vein necrosis virus and feeding preferences of its vector soybean thrips. Plant Health Progress. 19:176-181. doi: 10.1094/PHP-11-17-0071-RS
  23. Hajimorad, M. R.*, Domier, L. L., Tolin, S. A., Whitham, S. A., Saghai Maroof, M. A. (2018) Soybean mosaic virus: A successful potyvirus with a wide distribution but restricted natural host range. Mol. Plant Pathol. 19:1563-1579. doi: 10.1111/mpp.12644
  24. Burkhow, S. J., Stephens, N. M., Mei, Y., Duenas, M. E., Freppon, D. J., Ding, G., Smith, S. C., Lee, Y.-J., Nikolau, B. J., Whitham, S. A., Smith, E. A.* (2018) Characterizing virus-induced gene silencing at the cellular level with in situ multimodal imaging. Plant Methods. 14:37doi: 10.1186/s13007-018-0306-7
  25. Ranjan, A., Jayaraman, D., Grau, C., Hill, J. H., Whitham, S. A., Ané, J.-M., Kabbage, M.* (2018) The pathogenic development of Sclerotinia sclerotiorum in soybean requires specific host NADPH oxidases. Mol. Plant Pathol. 19:700-713doi: 10.1111/mpp.12555
  26. Qi, M., Grayczyk, J. P., Seitz, J. M., Lee, Y., Link, T. I., Choi, D., Pedley, K. F., Voegele, R. T., Baum, T. J., Whitham, S. A.* (2018) Suppression or activation of immune responses by predicted secreted proteins of the soybean rust pathogen Phakopsora pachyrhizi. Mol. Plant Microbe Interact. 31:163-174. doi: 10.1094/MPMI-07-17-0173-FI
  27. Mei, Y., Whitham, S. A.* (2018) Virus-induced gene silencing in maize with a Foxtail mosaic virus vector. Methods Mol. Biol. 1676:129-139. doi: 10.1007/978-1-4939-7315-6_7
  28. Liu, J. Z.*, Duan, J., Ni, M., Liu, Z., Qiu, W.-L., Whitham, Steven A., Qian, W.-J. (2017) S-nitrosylation inhibits the kinase activity of tomato phosphoinositide-dependent kinase 1 (PDK1). J. Biol. Chem. 292:19743-19751. doi: 10.1074/jbc.M117.803882
  29. Lu, H., Tang, L.*, Whitham, S. A., Mei, Y. (2017) An automated platform for maize seedling morphological traits characterization. Sensors. 17:2082. doi:10.3390/s17092082
  30. Rajamaki, M.-L.*, Xi, D., Sikorskaite, S., Valkonen, J. P. T., Whitham, S. A. (2017) Differential requirement of the ribosomal protein S6 and ribosomal protein S6 kinase for plant-virus accumulation and interaction of S6 kinase with potyviral VPg. Mol. Plant Microbe Interact. 30:374-384. doi: 10.1094/MPMI-06-16-0122-R
  31. Bak, A., Cheung, A., Yang, C., Whitham, S. A., Casteel, C. L.* (2017) A viral protease relocalizes in the presence of the vector to promote vector performance. Nat. Comm. 8:14493doi: 10.1038/ncomms14493
  32. De Carvalho, M. C. C. G, Nascimento, L. C., Darben, L. M., Polizel-Podanosqui, A. M., Lopes-Caitar, V. S., Rocha, C. S., Qi, M., Carazzolle, M. F., Kuwahara, M. K., Pereira, G. A. G., Abdelnoor, R. V., Whitham, S. A., Marcelino-Guimarães, F. C.* (2017) Prediction of P. pachyrhizi secretome expressed in planta and potential effector families. Mol. Plant Pathol. 18:363-377. doi: 10.1111/mpp.12405
  33. Qi, M., Link, T. I., Müller, M., Hirschburger, D., Pudake, R. N., Pedley, K. F., Braun, E., Voegele, R. T., Baum, T. J., Whitham, S. A.* (2016) A small cysteine-rich protein from the Asian soybean rust fungus, Phakopsora pachyrhizi, suppresses plant immunity. PLoS Pathog. 12:e1005827. doi: 10.1371/journal.ppat.1005827
  34. Martin, K. M., Singh, J., Hill, J. H., Whitham, S. A., Cannon, S.* (2016) Dynamic transcriptome profiling of Bean common mosaic virus (BCMV) infection in common bean (Phaseolus vulgaris L.). BMC Genomics 17:613 doi: 10.1186/s12864-016-2976-8
  35. Whitham, S. A.*, Qi, M., Innes, R. W., Ma, W., Lopes-Caitar, V., Hewezi, T. (2016) Molecular soybean-pathogen interactions. Annu. Rev. Phytopathol. 54:19.1-19.26 doi: 10.1146/annurev-phyto-080615-100156
  36. Mei, Y., Zhang, C., Kernodle, B. M., Hill, J. H., Whitham, S. A.* (2016) A Foxtail mosaic virus vector for virus-induced gene silencing in maize. Plant Physiol. 171:760-772 doi: 10.1104/pp.16.00172
  37. Irizarry, M. D.*, Groves, C. L., Elmore, M. G., Bradley, C. A., Dasgupta, R., German, T., Jardine, D. J., Saalau-Rojas, E., Smith, D. L., Tenuta, A. U., Whitham, S. A., Mueller, D. S. (2016) Re-emergence of Tobacco streak virus infecting soybean in the United States and Canada. Plant Health Progress 17:92-94 doi: 10.1094/PHP-BR-15-0052
  38. Whitham, S. A.*, Lincoln, L. M., Chowda-Reddy, R. V., Dittman, J. D., O’Rourke, J. A., Graham, M. A.* (2016) Virus-induced gene silencing and transient gene expression in soybean using Bean pod mottle virus infectious clones. Curr. Protoc. Plant Biol. 1:263-283. doi: 10.1002/cppb.20012