A global study of miRNAome dynamics in response to Fusarium basal rot infection in onion (Allium cepa L.)

Abstract

Fusarium oxysporum f. sp. cepae (Foc), the cause of Fusarium basal rot (FBR) is one of the most virulent fungal phytopathogens that damages onion and related crops worldwide. miRNAs have a crucial role in the transcriptional and post-transcriptional regulation of genes throughout the development of defense responses. However, the miRNA repertoire of onion and its associated regulation of onion-Foc interaction is yet unclear. In the current work, we compared the miRNA profiles of resistant (Ac77) and susceptible (Arka Kirthiman-AK) onion cultivars and detected 37 differentially expressed miRNAs that could be categorized as prominent regulators of defense against Foc. Intriguingly, the expression of a novel microRNA-ace-miRn3a, was markedly increased in Ac77 but mostly suppressed in AK genotype after Foc infection. Subsequently, the upregulated expression of ace-miRn3a in Ac77 displayed improved resistance to Foc, as demonstrated by reduced growth of the fungus, negligible disease symptoms and induction of host defense genes. As expected, the expression of its two target genes encoding the TIR1 type F-box proteins was reduced in Ac77 as well as in the miRn3a over-expressed AK lines. Moreover, the transient co-expression of the novel onion miRNAs and their target genes in Nicotiana benthamiana confirmed the specific binding and cleavage of the two-onion specific TIR1 type F-box genes by ace-miRn3a. Overall, our research suggest that ace-miRn3a may offer a miRNA-mediated strategy for engineering Foc resistance in onions by suppressing TIR1 F-box proteins and reducing fungal colonization.