Whitham Lab Publications - Last 5 Years

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

  1. Kim, S.-B.*, Kim, K.-T., In, S., Jaiswal, N., Lee, G. W., Jung, S., Rogers, A., Gautam, S., Gómez-Trejo, L. F., Helm, M., Ahn, H.-K., Lee, H.-Y., Read, Q. D., Woo, J., Holan, K. L., Whitham, S. A., Jones, J. D. G., Choi, D., Dean, R., Park, E., Balint-Kurti, P. (2024) Use of the Puccinia sorghi haustorial transcriptome to identify and characterize AvrRp1-D recognized by the maize Rp1-D resistance protein. Accepted.  PLoS Pathogens.
  2. Lan, H.-J., Ran, J., Wang, W.-X., Zhang, L., Wu, N.-N., Zhao, Y.-T., Huang, M.-J., Ni., M., Liu, F., Cheng, N., Nakata, P. A., Pan, J., Whitham, S. A., Baker, B. J., Liu, J.-Z*. (2024) Clathrin light chains negatively regulate plant immunity by hijacking the autophagy pathway. Plant Comm. 5: 100937. doi: 10.1016/j.xplc.2024.100937
  3. Bish, M. D., Ramachandran, S. R., Wright, A., Lincoln, L. M., Whitham, S. A., Graham, M. A.*, Pedley, K. F.* (2024) The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi. Mol. Plant Microbe Interact. 37: 561-570. doi: 10.1094/MPMI-01-24-0007-R
  4. Holan, K. L., White, C. H., Whitham, S. A.* (2024) Application of a U-NET neural network to the Puccinia sorghi-maize pathosystem. Phytopathol. 114: 990-999. doi: 10.1094/PHYTO-09-23-0313-KC
  5. Normantovich, M., Amitzur, A., Offri, S., Pashkovsky, K., Shnaider, Y., Nizan, S., Yogev, O., Jacob, A., Taylor, C. G., Desbiez, C., Whitham, S. A., Bar-Ziv, A., Perl-Treves, R.* (2024) The melon Fom-1-Prv resistance gene pair: correlated spatial expression and interaction with a viral protein. Plant Direct. 8:e565. doi: 10.1002/pld3.565.
  6. Qi, M., Yu, H., Bredow, M., Chicowski, A. S., Fields, L. D., Whitham, S. A.* (2024) Insights into Phakopsora pachyrhizi effector-effector interactions. Mol. Plant Microbe Interact. 37: 227-231. doi: 10.1094/MPMI-08-23-0120-FI
  7. Chicowski, A. S., Bredow, M., Utiyama, A. S., Marcelino-Guimarães, F. C.*, Whitham, S. A.* (2024) Soybean-Phakopsora pachyrhizi interactions: toward the development of next-generation disease-resistant plants. Plant Biotechnol. J. 22: 296–315. doi: 10.1111/pbi.14206
  8. 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. ACS Sens. 8: 3902-3913. doi: 10.1021/acssensors.3c01478.
  9. 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.
  10. Bredow, M., Natukunda, M. I., Beernink, B. M., Sartor-Chicowski, A., 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Yu,H., Ruan, H., Xia, X., Sartor Chicowski, A., 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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
  21. 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
  22. 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. 19(9):1713-1724. doi: 10.1111/pbi.13585
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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. 10:1182. doi: 10.3389/fpls.2019.01182
  29. 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
  30. 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
  31. 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
  32. 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. 32:120-133. doi: 10.1094/MPMI-07-18-0198-FI
  33. 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