Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics

Abstract

Basil downy mildew (BDM), caused by the oomycete pathogen Peronospora belbahrii, is the most significant disease threatening sweet basil production across the world. A downy mildew resistant sweet basil cultivar Mrihani (MRI) was identified in a germplasm screen, and fertile progeny were produced through a breeding program with BDM-susceptible commercial sweet basil cultivar Newton (SB22). However, the specific genes and molecular mechanisms which confer the resistance in MRI and selected progeny remain unknown. This study was designed to identify candidate resistance genes and the potential mechanisms that enable BDM resistance through a comparative transcriptomic approach. RNA samples from BDM-infected MRI and SB22 plants were harvested at 4 time points during the first 3 days of infection to capture genes, pathways, and biological processes involved in disease resistance. This global transcription expression profile confirmed the continuous growth of the pathogen only in the susceptible cultivar SB22, consistent with the infection phenotype. Three categories of genes uniquely induced in the MRI cultivar upon pathogen challenge were identified: the plant pathogen recognition nucleotide-binding leucine rich repeat proteins (NLRs), the multi-functional receptor-like kinases, and secondary metabolic enzymes. Validation of the top resistance candidate NLR gene confirmed its unique presence in the MRI cultivar as well as two out of four resistant MRIxSB22 F2 progeny. Additionally, unique upregulation of the salicylic acid synthesis pathway genes in MRI suggests the importance of this hormone signaling pathway in BDM resistance. This study demonstrates the feasibility of using comparative transcriptomics to identify resistance genes in non-model crops for rapid improvement in marker-assisted breeding approaches.

Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles

“…A repeat library specific to sweet basil was generated using RepeatMasker [62] and MITE-Hunter [63]. The 'RUSB22' trinity assembly from Allen et al [64] and the proteome from Arabidopsis thaliana and Thymus vulgaris [65] along with the repeat library served as the input fasta files for the maker opts control file. Initial MAKER annotations were generated based on the aligned transcript and protein sequence alignment.…”