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Comparative transcriptome analysis provides key insights into gene expression pattern during the formation of nodule-like structures in Brachypodium

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Abstract

Auxins can induce the formation of nodule-like structures (NLS) in plant roots even in the absence of rhizobia and nitrogen-fixing bacteria can colonize these structures. Interestingly, NLS can be induced in roots of both legumes and non-legumes. However, our understanding of NLS formation in non-legumes at a molecular level is limited. This study aims to investigate NLS formation at a developmental and molecular level in Brachypodium distachyon. We treated Brachypodium roots with the synthetic auxin, 2,4-D, to induce NLS at a high frequency (> 80%) under controlled conditions. A broad base and a diffuse meristem characterized these structures. Next, we performed a comprehensive RNA-sequencing experiment to identify differentially expressed genes (DEGs) in Brachypodium roots during NLS formation. We identified 618 DEGs; several of which are promising candidates for control of NLS based on their biological and molecular functions. We validated the expression pattern of several genes via RT-PCR. Next, we compared the expression profile of Brachypodium roots with rice roots during NLS formation. We identified 76 single-copy ortholog pairs in rice and Brachypodium that are both differentially expressed during this process. Some of these genes are involved in auxin signaling, root development, and legume-rhizobia symbiosis. We established an experimental system to study NLS formation in Brachypodium at a developmental and genetic level, and used RNA-sequencing analysis to understand the molecular mechanisms controlling this root organogenesis program. Furthermore, our comparative transcriptome analysis in Brachypodium and rice identified a key set of genes for further investigating this genetic pathway in grasses.

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Abbreviations

NLS:

nodule-like structures

RNS:

root nodule symbiosis

LHK1:

Lotus histidine kinase 1

CRE1:

cytokinin response 1

2,4-D:

2,4-dichlorophenoxyacetic acid

dpt:

days post treatment

DEGs:

differentially expressed genes

FDR:

false discovery rate

FC:

fold change

GO:

gene ontology

SEA:

singular enrichment analysis

TFs:

transcription factors

AP2/ERF:

APETALA2/ethylene responsive factor

NAC:

NAM (for no apical meristem), ATAF1 and -2, and CUC2 (for cup-shaped cotyledon)

ARFs:

auxin response factors

bHLH:

basic helix-loop-helix

GRAS:

gibberellic-acid insensitive (GAI), REPRESSOR of GAI (RGA), and SCARECROW (SCR)

LOB:

lateral organ boundaries

WUS:

WUSCHEL

RLKs:

receptor-like kinases

LRR:

leucine-rich repeat

ABC:

ATP-binding cassette

MATE:

multi-antimicrobial extrusion protein

SAUR:

small auxin upregulated RNA

RT-PCR:

reverse transcriptase polymerase chain reaction

PLT:

PLETHORA

WOX11:

WUSCHEL-RELATED HOMEOBOX 11

BRX:

BREVIS RADIX

SCR:

SCARECROW

SHR:

SHORT ROOT

NSP1:

NODULATION SIGNALING PATHWAY1

NSP2:

NODULATION SIGNALING PATHWAY2

PIN:

PIN-FORMED

LAX:

LIKE AUXIN1

CLV:

CLAVATA

CLE:

CLAVAT3 (CLV3)/ENDOSPERM SURROUNDING REGION (ESR)

FON:

FLORAL ORGAN NUMBER

FOS1:

FON2 SPARE1

CPM:

counts per million

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Acknowledgements

This work was supported by the Arkansas Center for Plant-Powered Production, as part of the National Science Foundation’s Research Infrastructure Improvement Award EPS-1003970; the Arkansas Science & Technology Authority basic research award (Project No. 15-B-07); the Arkansas INBRE program supported by a grant from the National Institute of General Medical Sciences (NIGMS), P20 GM103429 from the National Institutes of Health and a University Research Council award, University of Central Arkansas, AR. The authors would like to thank Dr. Rahul Mehta, University of Central Arkansas, for his help with the SEM images. The authors would also like to thank Ryan Hiltenbrand, Ashley Spurr, Hannah McCarthy, David Zimulinda, and Raj Singh for their assistance with the experiments.

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Authors and Affiliations

  1. Department of Biology, University of Central Arkansas, Conway, AR, 72035, USA

    Jacklyn Thomas, Andres Vega, Ha Ram Kim & Arijit Mukherjee

  2. Bioinformatics & Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA

    Megan J. Bowman

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Contributions

AM received grant support and contributed reagents/materials/analysis tools. AM conceived and designed the experiments. JT, AV, and HRK performed the experiments. JT, HRK, MJB, and AM analyzed the data. AM, JT, and MJB prepared the manuscript. All authors reviewed and approved the manuscript.

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Correspondence to Arijit Mukherjee.

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Supplementary Fig. 1

Lateral root numbers in Brachypodium roots during 2,4-D treatment. A) shows that lateral root numbers are decreased in Brachypodium roots upon 2,4-D treatment when compared to controls at 7dpt. Data represents the average of 3 experimental replications (n = 15–20) ± SE. The asterisk (*) shows a significant difference between the two conditions by t test (P < 0.001). B) shows that lateral root numbers are decreased in Brachypodium roots upon 2,4-D treatment when compared to controls at 14dpt. Data represents the average of 3 experimental replications (n = 15–20) ± SE. The asterisk (*) shows a significant difference between the two conditions by t test (P < 0.01). (JPEG 34 kb)

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Thomas, J., Bowman, M.J., Vega, A. et al. Comparative transcriptome analysis provides key insights into gene expression pattern during the formation of nodule-like structures in Brachypodium. Funct Integr Genomics 18, 315–326 (2018). https://doi.org/10.1007/s10142-018-0594-z

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