Location: Corn Insects and Crop Genetics Research
2022 Annual Report
Accomplishments
1. Characterizing responses to iron deficiency chlorosis in the soybean germplasm collection. In plants, iron deficiency causes interveinal leaf yellowing, and a reduction in photosynthesis and yield. However, much or our knowledge of iron deficiency response mechanisms is from model species. Studies suggest important differences in iron stress responses between soybean and model species. Since crops have been adapted to multiple climates around the world, there are likely multiple mechanisms for responding to iron stress. In collaboration with researchers from Iowa State University, ARS scientists in Ames, Iowa, selected 18 unique soybean lines from the USDA soybean germplasm collection, with a range of iron stress tolerance. The lines were grown in both iron sufficient and deficient conditions and responses were compared. These analyses confirmed that multiple lines responded to iron stress within 60 minutes, much faster than observed in model species. Across all lines, iron stress responses were first detected in the roots, suggesting soybean uses novel root to shoot signaling mechanisms. Also, results suggested there are multiple novel mechanisms for conferring iron stress tolerance in the soybean germplasm collection. These findings highlight the need for conducting research in diverse, agronomically important crop species. Such studies will aid plant breeders in developing soybean lines with improved stress tolerance and greater yield, benefitting both farmers and growers.
2. Using genomics to determine the molecular effects of combining multiple resistance genes to combat Aphids in soybean. Throughout history, plant breeders have incorporated multiple resistance genes targeting specific pathogens or pests within a single line. Lines with multiple resistance genes offer a more robust and durable resistance response compared to lines with individual resistance genes. In soybean, aphid resistance is conferred by Rag genes. Plants containing the Rag1 and Rag2 genes are significantly more resistant to aphid attack than plants containing either Rag1 or Rag2 alone. To understand how combining resistance genes enhances resistance, researchers from Iowa State University and ARS scientists in Ames, Iowa, conducted whole genome expression analyses of four soybean lines (aphid-susceptible, Rag1, Rag2 and a line containing Rag1 and Rag2), collecting samples after infestation with soybean aphids. Approximately 1,000 genes were specifically expressed in response to aphids in the line containing Rag1 and Rag2, but not in either of the single resistance lines. Many of the genes unique to the Rag1 and Rag2 line had functions related to defense including modification of cell walls, detection of pests and pathogens and defense signaling. Understanding how combining multiple resistance genes results in enhanced resistance is essential for future crop improvement, helping preserve yield for farmers and growers.
3. Characterizing novel regions of the soybean genome for tolerance to iron deficiency. Yield loss due to iron deficiency stress is a problem throughout the major soybean growing regions of the U.S. Fiskeby III is a soybean cultivar with a high level of resistance to multiple abiotic stresses, including iron deficiency. Conversely, Mandarin (Ottawa) suffers severe yield loss when exposed to iron stress. In a project funded by the United Soybean Board, and working with collaborators at the University of Minnesota, ARS scientists in Ames, Iowa, used whole genome expression analyses to compare the Fiskeby III and Mandarin (Ottawa) responses to normal and iron deficient conditions. Researchers then combined previous genome mapping with the whole genome expression analyses to identify 15 candidate genes for a genomic region associated with iron stress tolerance on Fiskeby III chromosome 5. Using virus induced gene silencing (VIGS), all 15 candidate genes were assessed for their roles in iron stress tolerance. Silencing of a multidrug and toxic compound extrusion (MATE) transporter gene resulted in iron stress symptoms, even though plants were grown in iron sufficient conditions. To further evaluate this gene, whole genome expression analyses were conducted on MATE silenced plant grown in iron sufficient and deficient conditions. These analyses confirmed the identify of a new iron stress response gene. These findings can be leveraged by plant breeders to improve abiotic stress tolerance in soybean and other crop species.
4. Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing. Leaf angle is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. Ideally, more vertical leaves in the top layers and more horizontal leaves in the lower canopy would maximize overall light conversion efficiency and photosynthesis. Leaf arrangement in sorghum is reversed, suggesting room for improvement. The Dwarf3 (Dw3) auxin transporter has a validated role in controlling leaf angle in sorghum. Iowa State University researchers in collaboration with ARS scientists in Ames, Iowa, used whole genome expression analyses to monitor gene activity across the plant canopy in five sorghum genotypes, each having different versions of the Dw3 gene and with significant leaf angle differences. The researchers identified 284 genes whose activity differed across the canopy in all five genotypes, nine genes were associated with previously identified genomic regions associated with leaf angle. The majority of these genes are involved in transmembrane transport, hormone regulation, response to stimuli, lipid metabolism, and photosynthesis. Further characterization of these genes will allow sorghum researchers to alter leaf angle to the ideal state for sorghum and consequently improve yield, benefitting farmers and growers around the world.
5. Identification of candidate genes for a major quantitative disease resistance locus for Phytophthora root rot. Phytophthora root rot is the second most damaging disease of soybean. Historically, breeders have relied on single resistance genes to combat this disease, however, widespread use of these genes has allowed the pathogen to evolve to evade plant resistance responses. Unlike qualitative resistance, which is controlled by single resistance genes, partial resistance, also known as quantitative resistance, is more durable as it is controlled by several genes distributed across the genome. In work funded by the United Soybean Board, researchers from The Ohio State University, Chungnam National University and ARS scientists (Ames, Iowa and Raleigh, North Carolina) have identified a region on soybean chromosome 18 that contributes up to 45% to quantitative resistance to the pathogen. The researchers combined high resolution mapping with whole genome expression analyses to identify a single gene of interest within this region. This research is an important step in identifying genes conferring durable resistance, however further work is needed to understand how this gene contributes to resistance to protect plan yield for farmers and growers.
Review Publications
Natukunda, M.I., Hohenstein, J.D., McCabe, C.E., Graham, M.A., Qi, Y., Singh, A.K., MacIntosh, G.C. 2021. Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids. BMC Genomics. 22. Article 887. https://doi.org/10.1186/s12864-021-08147-3.
Natukunda, M.I., Mantilla-Perez, M.B., Graham, M.A., Liu, P., Salas-Fernandez, M.G. 2022. Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing. BMC Genomics. 23. Article 95. https://doi.org/10.1186/s12864-021-08251-4.
O'Rourke, J.A., Morrisey, M.J., Merry, R., Espina, M.J., Lorenz, A.J., Stupar, R.M., Graham, M.A. 2021. Mining Fiskeby III and Mandarin (Ottawa) expression profiles to understand iron stress tolerant responses in soybean. International Journal of Molecular Sciences. 22(20). Article 11032. https://doi.org/10.3390/ijms222011032.
Kohlhase, D.R., Mccabe, C.E., Singh, A.K., O'Rourke, J.A., Graham, M.A. 2021. Comparing early transcriptomic responses of 18 soybean (Glycine max) genotypes to iron stress. International Journal of Molecular Sciences. 22(21). Article 11643. https://doi.org/10.3390/ijms222111643.
