Saffron corms transcriptome analysis reveals genes associated with corm rot disease

Saffron (Crocus sativus L.) is by far the most expensive spice in the world. Low water requirements, straightforward agricultural practices, diverse applications in the food, pharmaceutical and textile industries, are major advantages for its widely cultivation worldwide. Saffron is genetically sterile and hence it is propagated through corms. As a perennial plant, its corms remain in the field for at least three consecutive cultivation seasons, increasing their susceptibility to soilborne pathogens. Among devastating soilborne plant pathogens, Fusarium oxysporum f. sp., the causal agent of corm rot, poses a significant threat to saffron cultivation globally. The development of effective management strategies against F. oxysporum is impeded by the absence of resistant genotypes and a limited understanding of its pathogenicity. To assess and find genes associated with the response to F. oxysporum infection, the corm transcriptome was analyzed following F. oxysporum inoculation by RNA-seq. More than 294,520 and 243,328 transcripts were documented. Out of 168,448 identified unigenes, 34,862, 15,234 and 27,213 unigenes were annotated in NCBI non-redundant (Nr) protein database, GO and UniProtKB/Swiss-Prot databases, respectively. Out of 38,643 annotated genes, 2169 genes exhibited differential expression in response to F. oxysporum. Among these, 1832 genes showed decreased expression, whereases 337 genes displayed increased expression. Quantitative RT-PCR analysis confirmed the expression patterns of 10 hub genes, including chitinase, a serine/threonine kinase and a WRKY transcription factor gene. In contrast, the relative expression of a pectin methylesterase, a Flavodoxin-like quinone oxidoreductase and HSP genes were found to be down-regulated. The findings of this study clearly demonstrate that F. oxysporum infection significantly perturbs the expression of corms R-genes, suggesting that such genes can be used to improve saffron plant resistance to fungal and oomycetes soilborne pathogens in future breeding programs.