Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

Abstract

BackgroundDicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven’t been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress.ResultsAs main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven’t been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation.ConclusionsAlmost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.

Genome Wide Identification of Key Components of RNA Silencing in Two <em>Phaseolus vulgaris</em> Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

“…Concerning the role of Dicer proteins in plant defense, little is known about DCL2, except that it is involved in the processing of viral dsRNA. However, it has also been observed that the quantity of DCL2 transcripts increases at the local site of infection by the CLRDV (Cotton leafroll dwarf virus) in a resistant genotype cotton Gossypium hirsutum [82]. This is in agreement with our results were up-regulation of both PvA_DCL2a and Pv_DCL2b is observed in incompatible interaction with C. lindemuthianum.…”

Genome-Wide Identification and Coexpression Network Analysis of DNA Methylation Pathway Genes and Their Differentiated Functions in Ginkgo biloba L.

“…DCL2 is responsible for producing 22-nt siRNA, and DCL4 is related to the generation of trans-acting small interfering RNAs (ta-siRNAs) and 21-nt siRNAs [55]. DCL3 generates 24-nt siRNAs which participate in RdDM [56,57]. However, the functions of various DCLs in G. biloba still need to be studied.…”

Core RNA Interference Genes Involved in miRNA and Ta-siRNA Biogenesis in Hops and Their Expression Analysis after Challenging with Verticillium nonalfalfae

“…Altered expression of DCL1 was observed in Fibermax (virus-susceptible) and Delta Opal (virusresistant) cotton plants after infection with Cotton leafroll dwarf virus (CLRDV). At 1 dpi, the susceptible cultivar Fibermax showed significantly lower expression of DCL1 compared to the virus-resistant cultivar Delta Opal, however, significantly higher expression of DCL1 was observed in the susceptible cultivar at 5 and 15 dpi compared to the resistant cultivar [35]. On the other hand, DCL1 showed no differential expression in leaves, flowers or cones of hop cultivar Celeia infected with hop latent viroid or citrus bark cracking viroid [28].…”