Genome-wide identification and expression analyses of the Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in onion (Allium cepa L.)

ABSTRACT

RNA silencing is a highly conserved gene expression regulatory mechanism participating in plant development and stress responses. Dicer-like protein (DCL), Argonaute protein (AGO) and RNA-dependent RNA polymerase (RDR) are directly involved in RNA silencing. So far, the characterisation and expression analysis of RDR, AGO and DCL proteins have not been performed in onion. A genome-wide analysis identified eight AcAGO, four AcDCL and four AcRDR putative genes in onion. Their cis-acting elements were investigated. The transcript levels of genes in different onion tissues and response to abiotic stress were studied. The results demonstrated that AcAGOs, AcDCLs and AcRDRs showed various tissue expression patterns. AcAGO2 and AcAGO4b were highly expressed in onion bulbs. AcDCLs and AcRDRs showed the highest transcript levels in inflorescence. AcAGO1, AcAGO5 and AcDCL1 were constitutively expressed in leaf and bulb during onion bulb expansion. AcRDR1 and AcRDR6 were upregulated during bulb expansion. AcAGOs were upregulated with salinity treatment, whereas AcDCLs and AcRDRs showed different expression patterns in abiotic stress response. Our results provided a basis for further clarification of RNA silencing-mediated environment stimulation response and development in onion.

KEYWORDS:

• Onion
• AGO
• DCL
• RDR
• tissues
• expression profile
• stress response

Acknowledgements

The authors thank Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, China, Key Laboratory of Vegetable Biology in Cold Region of Heilongjiang Province and Key Laboratory of Genetic Improvement and Facility Cultivation of Horticultural Crops in Northern Cold Region of Heilongjiang Province for their help with the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Author contributions

Conceptualisation: L. Q., Y. W.; Methodology: L. Q., Y. W.; Formal analysis and investigation: L. Q., X. L., Y. W.; Resources and Data Curation: L. Q., X. L., X. Z.; Writing–original draft preparation: L. Q.; Writing–review and editing: L. Q., Y. W.; Funding acquisition: L. Q., Y. W.

Additional information

Funding

This study was funded by University Innovative Talents Programs for Youth of Heilongjiang Province of China [UNPYSCT-2020113]; R&D Projects in Heilongjiang Province [GA21B012]; Natural Science Foundation of Heilongjiang Province of China [LH2020C012]; Dongnong Scholar Program of Northeast Agricultural University of China [19QC08]. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.