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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #339616

Research Project: Functional and Structural Genetic Analysis of Soybean and Other Legumes

Location: Corn Insects and Crop Genetics Research

Title: Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches

Author
item ASSEFA, TESHALE - Iowa State University
item ZHANG, JIAOPING - Iowa State University
item CHOWDA-REDDY, R.V. - Iowa State University
item Moran Lauter, Adrienne
item SINGH, ARTI - Iowa State University
item O`Rourke, Jamie
item Graham, Michelle
item SINGH, ASHEESH - Iowa State University

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2020
Publication Date: 1/28/2020
Citation: 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. https://doi.org/10.1186/s12870-020-2237-5.
DOI: https://doi.org/10.1186/s12870-020-2237-5

Interpretive Summary: Soybean is a major agricultural export and has uses in food, feed, and industry. Soil conditions can limit iron availability resulting in yield loss. Unlike model species, crops have undergone selection for thousands of years, altering their ability to respond to stress. This study leverages genome wide association and epistatic studies with previous gene expression studies to identify regions of the soybean genome important in iron deficiency tolerance. The results not only identified new regions of interest for future breeding programs, but also revealed that a major QTL for iron tolerance is actually four independent regions each of which plays an important role in soybean’s iron deficiency response.

Technical Abstract: Iron (Fe) is an essential micronutrient for plant growth and development. Iron deficiency chlorosis (IDC), caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean (Glycine max) yield. A genome-wide association study (GWAS) and a genome-wide epistatic study (GWES) were performed using 460 diverse soybean PI lines from more than 25 countries, in field and hydroponic iron stress conditions, using more than 36,000 single nucleotide polymorphism (SNP) markers. Combining this approach with available RNA-sequencing data identified significant markers, genomic regions, and novel genes associated with or responding to iron deficiency. Sixty-nine genomic regions associated with IDC tolerance were identified across 19 chromosomes via the GWAS, including the major-effect quantitative trait locus (QTL) on chromosome Gm03. Cluster analysis of significant SNPs in this region deconstructed this historically prominent QTL into four distinct linkage blocks, enabling the identification of multiple candidate genes for iron chlorosis tolerance. The complementary GWES identified SNPs in this region interacting with nine other genomic regions, providing the first evidence of epistatic interactions impacting iron deficiency tolerance. This study demonstrates that integrating cutting edge GWA, GWE, and gene expression studies is a powerful strategy to identify novel iron tolerance QTL and candidate loci from diverse germplasm. Crops, unlike model species, have undergone selection for thousands of years, constraining and/or enhancing stress responses. Leveraging genomics-enabled approaches to study these adaptations is essential for future crop improvement.