Whitham Lab Publications - Last 5 Years

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

  1. Qi, M., Yu, H., Bredow, M., Chicowski, A. S., Fields, L. D., Whitham, S. A. (2023) Insights into Phakopsora pachyrhizi effector-effector interactions. Mol. Plant Microbe Interact. Accepted. doi: 10.1101/2023.08.30.555440.
  2. Chicowski, A. S., Bredow, M., Utiyama, A. S., Marcelino-Guimarães, F. C.*, Whitham, S. A. (2023) Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants. Plant Biotechnol. J. Accepted
  3. N., Singh, Khan, R. R., Xu, W., Whitham, S. A., Dong, L. (2023) Plant virus sensor for rapid detection of bean pod mottle virus using virus-specific nanocavities. ACS Sensors. Accepted 09/13/2023. doi: 10.1021/acssensors.3c01478.
  4. Beernink, B. M., Whitham, S. A. (2023) Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots. Mol. Plant Pathol. 24:811-822.  doi: 10.1111/mpp.13330.
  5. Bredow, M., Natukunda, M. I., Beernink, B. M., Chicowski, A.S., Salas-Fernandez, M. G., Whitham, S. A. (2023) Characterization of a foxtail mosaic virus vector for gene silencing and analysis of innate immune responses in Sorghum bicolor. Mol. Plant Pathol. 24:71-79. doi: 10.1111/mpp.13270.
  6. Lappe, R. R., Elmore, M. G., Lozier, Z. R., Jander, G., Miller, W. A., Whitham, S. A. (2022) Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics. 23:767. doi: 10.1186/s12864-022-09001-w.
  7. 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.
  8. Beernink, B. M., Lappe, R. L., Bredow, M., Whitham, S. A. (2022) Impacts of RNA mobility signals on virus induced somatic and heritable gene editing. Front. Genome Ed. 4:925088. doi: 10.3389/fgeed.2022.925088.
  9. Chung, S. H., Zhang, S., Song, H., Whitham, S. A., Jander, G. (2022) Maize resistance to insect herbivory is enhanced by silencing expression of genes for jasmonate-isoleucine degradation using sugarcane mosaic virus. Plant Direct. 6:e407. doi: 10.1002/pld3.407.
  10. Bueno, T. V., Fontes, P. P., Abe, V. Y., Satiko, A. U., Senra, R. L., Oliveira, L. S., dos Santos, A. B., Capote Ferreira, E. G., Darben, L. M., de Oliveira, A. B., Abdelnoor, R. V., Whitham, S. A., Fietto, L. G., Marcelino-Guimarães, F. C. (2022) A Phakopsora pachyrhizi effector suppresses PAMP-triggered immunity and interacts with a soybean glucan endo-1,3- β -glucosidase to promote virulence. Mol. Plant Microbe Interact. 35:779-790. doi: 10.1094/MPMI-12-21-0301-R.
  11. 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. 23:1331-1345. doi: 10.1111/mpp.13232.
  12. 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.
  13. 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.
  14. 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.
  15. 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
  16. 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; https://doi.org/10.3390/ijms22073586
  17. 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
  18. Beernink, B. M., Holan, K. L., Lappe, R. R., Whitham, S. A. (2021) 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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