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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Research Project #434493

Research Project: Genetic and Genomic Characterization of Soybean and Other Legumes

Location: Corn Insects and Crop Genetics Research

2020 Annual Report

1. Identifying gene expression changes in response to micro- and macro- nutrient deficiencies in soybean. Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by non-crop model species such as Arabidopsis. This selection likely resulted in novel stress adaptations unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the US and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. ARS scientists in Ames, Iowa, directly compared whole-genome expression responses of leaves and roots to iron (a micronutrient) and phosphate (a macronutrient) deficiency. Conducting experiments side by side allowed direct comparison of nutrient stress responses, examined 24 hours after the onset of stress. While soybean responds largely to iron deficiency and not resupply, it responds strongly to phosphate resupply and not deficiency. Though the timing of responses was different, both nutrient stress signals used the same molecular pathways. The study was also used to examine gene expression changes in response to multiple stress events. It identified 865 genes whose gene expression changed between first and second stress exposure and 3,375 genes only differentially expressed after a second stress event. This study demonstrates the speed and diversity of the soybean stress response to multiple nutrient deficiencies. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.

2. Using genotypic, phenotypic and shape based clusters to understand soybean root system architecture. Root system architecture is difficult to phenotype and past studies suffer from limited scale and scope, as well as variability in measuring techniques. In collaboration with researchers at Iowa State University, a ARS scientist in Ames, Iowa, studied the root system architecture of 292 soybean lines from the soybean germplasm collection. This phenotypic data was combined with the soybean genotyping chip to explore the genetic diversity of soybean root system architecture traits. Genomic locations of interest were identified for traits such as root shape, length, number, mass, angle. Phenotypic and genotypic data were used to group lines into eight genotype- and phenotype-based clusters. Genotype-based clusters correlated with geographic origins and demonstrated that much of US elite germplasm lacks genetic diversity for root system architecture traits. Combining genetic and phenotypic analyses results provides opportunities for targeted breeding efforts to maximize the beneficial genetic diversity for future genetic gains.

Review Publications
O'Rourke, J.A., Mccabe, C.E., Graham, M.A. 2020. Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Functional and Integrative Genomics. 20:321-341.
Assefa, T., Zhang, J., Chowda-Reddy, R.V., Moran Lauter, A.N., Singh, A., O'Rourke, J.A., Graham, M.A., Singh, A.K. 2020. Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches. Biomed Central (BMC) Plant Biology. 20:42.
Falk, K.G., Juberi, T.Z., O'Rourke, J.A., Singh, A., Sarkar, S., Ganapathysubramanian, B., Singh, A.K. 2020. Soybean root system architecture trait study through genotypic, phenotypic and shape-based clusters. Plant Phenomics.
Moran Lauter, A., Rutter, L., Cook, D., O'Rourke, J.A., Graham, M.A. 2020. Examining short-term responses to a long-term problem: RNA-seq analyses of iron deficiency chlorosis tolerant soybean. International Journal of Molecular Sciences. 21:3591.