Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

This article is part of a special issue on plant genomics.

Open Access Highly Accessed Open Badges Research

Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization

Sara Schaarschmidt12*, Peter M Gresshoff3 and Bettina Hause1

Author affiliations

1 Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany

2 Humboldt-Universit├Ąt zu Berlin, Faculty of Agriculture and Horticulture, Division Urban Plant Ecophysiology, Lentzeallee 55-57, 14195 Berlin, Germany

3 ARC Centre of Excellence for Integrative Legume Research (CILR), The University of Queensland, St. Lucia, Queensland 4072, Australia

For all author emails, please log on.

Citation and License

Genome Biology 2013, 14:R62  doi:10.1186/gb-2013-14-6-r62

Published: 18 June 2013



Similarly to the legume-rhizobia symbiosis, the arbuscular mycorrhiza interaction is controlled by autoregulation representing a feedback inhibition involving the CLAVATA1-like receptor kinase NARK in shoots. However, little is known about signals and targets down-stream of NARK. To find NARK-related transcriptional changes in mycorrhizal soybean (Glycine max) plants, we analyzed wild-type and two nark mutant lines interacting with the arbuscular mycorrhiza fungus Rhizophagus irregularis.


Affymetrix GeneChip analysis of non-inoculated and partially inoculated plants in a split-root system identified genes with potential regulation by arbuscular mycorrhiza or NARK. Most transcriptional changes occur locally during arbuscular mycorrhiza symbiosis and independently of NARK. RT-qPCR analysis verified nine genes as NARK-dependently regulated. Most of them have lower expression in roots or shoots of wild type compared to nark mutants, including genes encoding the receptor kinase GmSIK1, proteins with putative function as ornithine acetyl transferase, and a DEAD box RNA helicase. A predicted annexin named GmAnnx1a is differentially regulated by NARK and arbuscular mycorrhiza in distinct plant organs. Two putative CCAAT-binding transcription factor genes named GmNF-YA1a and GmNF-YA1b are down-regulated NARK-dependently in non-infected roots of mycorrhizal wild-type plants and functional gene analysis confirmed a positive role for these genes in the development of an arbuscular mycorrhiza symbiosis.


Our results indicate GmNF-YA1a/b as positive regulators in arbuscular mycorrhiza establishment, whose expression is down-regulated by NARK in the autoregulated root tissue thereby diminishing subsequent infections. Genes regulated independently of arbuscular mycorrhization by NARK support an additional function of NARK in symbioses-independent mechanisms.

Affymetrix annexin; GeneChip; autoregulation; arbuscular mycorrhiza; CCAAT-binding transcription factor NF-Y; Rhizophagus irregularis; Glycine max (soybean); quantitative RT-PCR; split-root system