Location: Corn Insects and Crop Genetics Research
2019 Annual Report
Accomplishments
1. Characterizing the speed and diversity of the soybean iron stress response. Iron deficiency chlorosis (IDC) is a global crop production problem, significantly impacting yield. Since IDC-prone fields are not uniform and IDC tolerant lines tend to have low yield on non-IDC prone soil, farmers prefer to run the risk of using high yielding, IDC susceptible lines. However, in the North Central United States IDC yield loss estimates exceed $150 million per year. While various genetic approaches have been used to identify genes involved in iron stress tolerance from model species, few studies have focused on agronomically important crop species. Therefore, ARS researchers in Ames, Iowa designed a whole genome expression study to explore the speed and diversity of the soybean iron stress response and find new avenues for crop improvement. The researchers identified over 10,000 genes whose activity was changed in response to iron stress at 30, 60 or 120 minutes after the onset of iron stress. These analyses revealed that unlike model species, the genes involved in iron uptake, defense and regulation of cell replication are hallmarks of the soybean iron stress response. Further, the findings suggest soybean uses a novel root to shoot signal to initiate the iron stress response. These findings suggest a novel approach for soybean improvement and highlight the need for conducting additional IDC studies in diverse, agronomically important crop species.
2. Deconstructing the genetic architecture of iron deficiency chlorosis (IDC) in soybean. Iron is an essential micronutrient for plant growth and development. IDC, caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean yield. ARS researchers in Ames, Iowa with collaborators from Iowa State University used a genome-wide study of 460 diverse soybean plant introduction lines to identify significant markers, genomic regions, and novel genes associated with or responding to tolerance to iron deficiency. Sixty-nine genomic regions associated with IDC tolerance were identified including the historical quantitative trait locus on chromosome Gm03. Cluster analysis of significant markers in this region revealed four distinct linkage blocks, enabling the identification of multiple candidate genes for iron chlorosis tolerance. This study demonstrates that integrating cutting edge genomic approaches is a powerful strategy to identify novel iron tolerance genes and networks from diverse germplasm. Our results suggest that crops, unlike model species, have undergone selection for thousands of years, constraining and/or enhancing stress responses. This emphasizes the need to understand stress responses in economically valuable crop species, highlighting an important gap in research.
Review Publications
Xu, H., Zhang, C., Li, Z., Wang, Z., Jiang, X., Shi, Y., Braun, E., Mei, Y., Qiu, W., Li, S., Wang, B., Xu, J., Navarre, D.A., Ren, D., Cheng, N., Nakata, P.A., Graham, M.A., Whitman, S., Liu, J. 2018. The MAPK kinase kinase GmMEKK1 regulates cell death and defense responses. Plant Physiology. doi:10.1104/pp.18.00903.
Pedley, K.F., Pandey, A.K., Ruck, A.L., Lincoln, L.M., Whitham, S.A., Graham, M.A. 2018. Rpp1 encodes a ULP1-NBS-LRR protein that controls immunity to Phakopsora pachyrhizi in soybean. Molecular Plant-Microbe Interactions. 32:120-133.
Rutter, L., Vanderplas, S., Cook, D., Graham, M.A. 2019. ggenealogy: An R package for visualizing genealogical data. Journal of Statistical Software. 89(13)1-31. https://doi.org/10.18637/jss.v089.i13.
McCabe, C.E., Cianzio, S.R., O'Rourke, J.A., Graham, M.A. 2018. Leveraging RNA-Seq to characterize resistance to brown stem rot and the Rbs3 locus in soybean. Molecular Plant-Microbe Interactions. 31(10):1083-1094. https://doi.org/10.1094/MPMI-01-18-0009-R.
