Location: Corn Insects and Crop Genetics Research
2021 Annual Report
Accomplishments
1. Iron deficiency followed by phosphate deficiency induces novel gene expression changes in soybean. Plants grown in the field experience many abiotic stresses throughout the growing season. The cumulative effect of these stresses is a loss of yield. To understand the genes and networks underlying stress tolerance, ARS scientists in Ames, Iowa, measured gene expression in soybean in response to iron deficiency stress followed by exposure to phosphate deficiency stress (sequential stresses), to more closely mimic field grown plant stress exposure. These analyses determined that sequential stress induces a unique suite of genes not differentially expressed under repeated stress conditions. These novel genes are usually involved in highly specialized processes such as pollen development. However, after sequential stress exposure these same genes are recruited to function in novel tissues, performing basic processes such as cell wall modifications. These findings improve our understanding of soybean response to complex nutrient deficiency stress exposure and will improve our understanding of the genes and networks underlying plant stress tolerance which can be leveraged by researchers to improve stress tolerance in soybean and other important crop species.
2. Molecular responses to iron stress are conserved across time and tissues. Iron is a micronutrient essential for the proper growth and development of all organisms. In plants, lack of usable iron can result in iron deficiency chlorosis (IDC), which is characterized by yellowing of the leaves, reduced plant growth and lower yield. To understand the molecular mechanisms contributing to iron stress responses, ARS scientists in Ames, Iowa, studied two nearly genetically identical lines, one line was iron stress tolerant, while the other line was susceptible to iron stress. The two lines were then grown in three different conditions: normal growth conditions for ten days (no stress control), normal growth conditions for eight days followed by two days of iron stress, or for ten days in iron stress conditions. We compared gene expression differences between the different growing conditions and between lines. Whole genome analyses of root and shoot tissue identified thousands of genes with altered expression patterns, with functions related to the cell cycle, gene silencing, iron acquisition and defense. Comparing these results with previous studies from our group suggest early gene expression changes are initiated in the root, then extend to the leaves. In this study, with later timepoints, the leaves signal back to the roots when iron needs have been met or if additional iron is needed. These novel signaling mechanisms have not been described in model species. These findings improve our understanding of the genes and networks underlying plant stress tolerance which can be leveraged by researchers to improve iron stress tolerance in soybean and other important crop species.
3. Utilizing the whole plant to understand disease resistance signaling from root to shoot. Brown stem rot (BSR) reduces soybean yield by up to 38%. The causal agent of BSR is Phialophora gregata, a slow growing necrotrophic fungus whose life-cycle includes inactive and active disease causing phases, each lasting several weeks and spreading from root to shoot. BSR leaf symptoms are often misdiagnosed as other soybean diseases or nutrient stress, making BSR resistance especially difficult to phenotype and utilize in breeding programs. To shed light on the genes and networks contributing to resistance, ARS scientists in Ames, Iowa, funded by the National Institute of Food and Agriculture, conducted whole genome expression analyses of infected and mock-infected root, stem, and leaf tissues of a BSR resistant soybean at 12, 24 and 36 hours. Comparing infected and mock-infected plants revealed that leaves, stems and roots use the same defense pathways. Gene networks associated with defense, photosynthesis, nutrient regulation, DNA replication and growth are the hallmarks of BSR resistance. These same resistance pathways were identified in an earlier study comparing resistant and susceptible responses seven days after infection. Since P. gregata is a slow growing pathogen, with disease symptoms taking several weeks to appear, breeders must wait for five weeks to score plants for resistance or susceptibility, in largely destructive assays. Our data suggests resistance and susceptibility can be detected molecularly, hours after infection. The genes and networks described here will be used to develop novel diagnostic tools to facilitate expedited breeding and screening for BSR resistance. In addition, candidate disease resistance genes can be used for introducing resistance to elite soybean lines using traditional breeding or transgenic approaches.
4. Genotypic characterization of the U.S. peanut core collection. Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. In work funded by the National Institute of Food and Agriculture, ARS scientist in Ames, Iowa, and a broad team of scientists collected tissue and extracted and sequenced DNA from 812 select peanut lines representing differences in phenotype and country of origin in the U.S. peanut collection. Analyses identified 14,430 high-quality, informative markers across the collection. Analysis of the data divided 812 lines into five distinct genotypic clusters, largely corresponding with botanical variety and market type, but not country of origin. A genetic cluster, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest lines cultivated by ancient farmers. Comparing these lines with their predicted parents, suggests subgenome exchanges are an important source of diversity. These diverse regions are likely novel sources of resistance and phenotypic variation. Markers associated with these regions can be used by peanut breeders and growers to develop improved peanut varieties.
Review Publications
O'Rourke, J.A., Graham, M.A. 2021. Gene expression responses to sequential nutrient deficiency stresses in soybean. International Journal of Molecular Sciences. 22(3). Article 1252. https://doi.org/10.3390/ijms22031252.
Atencio, L., Salazar, J., Moran Lauter, A., Gonzales, M.D., O'Rourke, J.A., Graham, M.A. 2021. Characterizing short and long term iron stress responses in iron deficiency tolerant and susceptible soybean (Glycine max L. Merr.). Plant Stress. 2.Article 100012. https://doi.org/10.1016/j.stress.2021.100012.
Brown, A.V., Connors, S., Huang, W., Wilkey, A., Grant, D.M., Weeks, N.T., Cannon, S.B., Graham, M.A., Nelson, R. 2020. A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research. 49(D1):D1496-D1501. https://doi.org/10.1093/nar/gkaa1107.
Otyama, P.I., Kulkarni, R., Chamberlin, K., Ozias-Akins, P., Chu, Y., Lincoln, L.M., MacDonald, G.E., Anglin, N.L., Dash, S., Bertioli, D.J., Fernandez-Baca, D., Graham, M.A., Cannon, S.B., Cannon, E.K.S. 2020. Genotypic characterization of the U.S. peanut core collection. G3, Genes/Genomes/Genetics. 10(11):4013-4026. https://doi.org/10.1534/g3.120.401306.
McCabe, C.E., Graham, M.A. 2020. New tools for characterizing early brown stem rot disease resistance signaling in soybean. The Plant Genome. 13(3). Article e20037. https://doi.org/10.1002/tpg2.20037.
