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

Authors: Moran Lauter, Adrienne; Peiffer, Gregory; YIN, TENGFEI - Iowa State University; COOK, DIANNE - Iowa State University; Shoemaker, Randy; Graham, Michelle

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2014
Publication Date: 8/22/2014
Citation: Moran Lauter, A., Peiffer, G.A., Yin, T., Cook, D., Shoemaker, R.C., Graham, M.A. 2014. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. Biomed Central (BMC) Genomics. 15:702 DOI: 10.1186/1471-2164-15-702.

Interpretive Summary: Iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. In plants, 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. In previous work it was determined that iron deficiency is sensed in the leaves, and that an unknown leaf signal regulates the expression of iron uptake genes in the root. In order 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 with iron deficient media. We observed dynamic gene expression differences between times points and between roots and leaves, suggesting the involvement of many transcription factors in eliciting rapid changes in gene expression. Genes involved in hormone signaling, regulation of DNA replication and iron uptake utilization are key aspects of the iron-efficiency response. While our analysis identified hundreds of genes responding to iron stress, identifying those genes responsible for greater stress tolerance that have little or no impact on yield is an important challenge for the future.

Technical Abstract: 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. In order 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. The differentially expressed genes (DEGs) and signaling components identified here represent new targets for soybean improvement.