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Genome-wide in silico identification of LysM-RLK genes in potato (Solanum tuberosum L.)

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Abstract

The receptor like kinases (RLKs) belong to the RLK/Pelle superfamily, one of the largest gene families in plants. RLKs play an important role in plant development, as well as in response to biotic and abiotic stresses. The lysine motif receptor like kinases (LysM-RLKs) are a subfamily of RLKs containing at least one lysine motif (LysM) that are involved in the perception of elicitors or pathogen-associated molecular patterns (PAMPs). In the present study, 77 putative RLKs genes and three receptor like proteins were identified in potato (Solanum tuberosum) genome, following a genome-wide search. The 77 potato RLK proteins are classified into two major phylogenetic groups based on their kinase domain amino acid sequence similarities. Out of 77 RLKs, 10 proteins had at least one LysM. Among them three RLP proteins were found in potato genome with either 2 or three tandem LysM but these lacked a cytoplasmic kinase domain. Expression analyses of a potato LysM-RLKs (StLysM-RLK05) was carried out by a Real time RT-PCR, following inoculation of potato leaves and immature tubers with late blight and common scab pathogens, respectively. The expression was significantly higher in resistant than in susceptible following S. scabies inoculation. The StLysM-RLK05 sequence was verified and it was polymorphic in scab susceptible cultivar. The present study provides an overview of the StLysM-RLKs gene family in potato genome. This information is helpful for future functional analysis of such an important protein family, in Solanaceae species.

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Abbreviations

MAPK:

Mitogen activated protein kinases

PAMPs:

Pathogen-associated molecular patterns

RKs:

Receptor kinases

RLKs:

Receptor-like kinases

CEBiP:

Chitin-elicitor binding protein

AUDPC:

Area under the disease progress curve

PDB:

Protein Data Bank

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Funding

This work was carried out with the aid of a grant from The Natural Sciences and Engineering Research Council of Canada (NSERC). SJ acknowledges MITACS for funding and Progest2001 Inc. for providing the genotype AG704.10.

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Author notes

  1. Farhad Nazarian-Firouzabadi

    Present address: Agronomy and Plant Breeding Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran

  2. Huali Xue

    Present address: College of Science, Gansu Agricultural University, Lanzhou, 730070, People’s Republic of China

Authors and Affiliations

  1. Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X3V9, Canada

    Farhad Nazarian-Firouzabadi, Sripad Joshi, Huali Xue & Ajjamada C. Kushalappa

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  1. Farhad Nazarian-Firouzabadi
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  2. Sripad Joshi
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Contributions

FN conducted the experiments, bioinformatics analyses and wrote the manuscript; SJ conducted inoculation studies and edited the manuscript; HX conducted scab inoculation studies; AK conceived the idea and edited the manuscript.

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Correspondence to Ajjamada C. Kushalappa.

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Nazarian-Firouzabadi, F., Joshi, S., Xue, H. et al. Genome-wide in silico identification of LysM-RLK genes in potato (Solanum tuberosum L.). Mol Biol Rep 46, 5005–5017 (2019). https://doi.org/10.1007/s11033-019-04951-z

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