Open Access Highly Accessed Research article

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves

Adrienne N Moran Lauter1, Gregory A Peiffer1, Tengfei Yin2, Steven A Whitham3, Dianne Cook2, Randy C Shoemaker14 and Michelle A Graham14*

Author Affiliations

1 USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 1565 Agronomy Hall, Ames, IA 50011, USA

2 Department of Statistics, Iowa State University, Ames, Iowa 50011, USA

3 Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA

4 Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA

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BMC Genomics 2014, 15:702  doi:10.1186/1471-2164-15-702

Published: 22 August 2014



Iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. A lack of bioavailable iron in soil leads to iron deficiency chlorosis (IDC), causing a reduction in photosynthesis and interveinal yellowing of leaves. Soybeans (Glycine max (L.) Merr.) grown in high pH soils often suffer from IDC, resulting in substantial yield losses. Iron efficient soybean cultivars maintain photosynthesis and have higher yields under IDC-promoting conditions than inefficient cultivars.


To capture signaling between roots and leaves and identify genes acting early in the iron efficient cultivar Clark, we conducted a RNA-Seq study at one and six hours after replacing iron sufficient hydroponic media (100 μM iron(III) nitrate nonahydrate) with iron deficient media (50 μM iron(III) nitrate nonahydrate). At one hour of iron stress, few genes were differentially expressed in leaves but many were already changing expression in roots. By six hours, more genes were differentially expressed in the leaves, and a massive shift was observed in the direction of gene expression in both roots and leaves. Further, there was little overlap in differentially expressed genes identified in each tissue and time point.


Genes involved in hormone signaling, regulation of DNA replication and iron uptake utilization are key aspects of the early iron-efficiency response. We observed dynamic gene expression differences between roots and leaves, suggesting the involvement of many transcription factors in eliciting rapid changes in gene expression. In roots, genes involved iron uptake and development of Casparian strips were induced one hour after iron stress. In leaves, genes involved in DNA replication and sugar signaling responded to iron deficiency. The differentially expressed genes (DEGs) and signaling components identified here represent new targets for soybean improvement.

Iron deficiency chlorosis; Soybean; Glycine max; RNA-Seq