Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels

Abstract

Background Rye (Secale cereale L.) is a cereal crop highly tolerant to environmental stresses, including abiotic and biotic stresses (e.g., fungal diseases). Among these fungal diseases, leaf rust (LR) is a major threat to rye production. Despite extensive research, the genetic basis of the rye immune response to LR remains unclear. Results An RNA-seq analysis was conducted to examine the immune response of three unrelated rye inbred lines (D33, D39, and L318) infected with compatible and incompatible Puccinia recondita f. sp. secalis (Prs) isolates. In total, 877 unique differentially expressed genes (DEGs) were identified at 20 and 36 h post-treatment (hpt). Most of the DEGs were up-regulated. Two lines (D39 and L318) had more up-regulated genes than down-regulated genes, whereas the opposite trend was observed for line D33. The functional classification of the DEGs helped identify the largest gene groups regulated by LR. Notably, these groups included several DEGs encoding cytochrome P450, receptor-like kinases, methylesterases, pathogenesis-related protein-1, xyloglucan endotransglucosylases/hydrolases, and peroxidases. The metabolomic response was highly conserved among the genotypes, with line D33 displaying the most genotype-specific changes in secondary metabolites. The effect of pathogen compatibility on metabolomic changes was less than the effects of the time-points and genotypes. Accordingly, the secondary metabolome of rye is altered by the recognition of the pathogen rather than by a successful infection. The results of the enrichment analysis of the DEGs and differentially accumulated metabolites (DAMs) reflected the involvement of phenylpropanoid and diterpenoid biosynthesis as well as thiamine metabolism in the rye immune response. Conclusion Our work provides novel insights into the genetic and metabolic responses of rye to LR. Numerous immune response-related DEGs and DAMs were identified, thereby clarifying the mechanisms underlying the rye response to compatible and incompatible Prs isolates during the early stages of LR development. The integration of transcriptomic and metabolomic analyses elucidated the contributions of phenylpropanoid biosynthesis and flavonoid pathways to the rye immune response to Prs. This combined analysis of omics data provides valuable insights relevant for future research conducted to enhance rye resistance to LR.

Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping

“…Notably, two markers forming a second QTL, SECCE1Rv1G0027270.1 and SECCE1Rv1G0028640.1 , were located in genes coding for folylpolyglutamate synthase and a kinase family protein, respectively; the former marker was located in an intron and the latter marker in an exon. Many of these 21 genes, such as those coding for a NBS-LRR disease resistance protein-like protein, leucine-rich repeat receptor-like protein kinase family protein, pathogenesis-related thaumatin family protein, phenylalanine ammonia-lyase, endoglucanase, MYB-related transcription factor, kinase (serine/threonine) family protein, and GDSL esterase/lipase ([ 34 – 41 ], respectively), have been proven to play a role in the immune response to rust fungi. One such gene, SECCE1Rv1G0013110.1 , encoding an endoglucanase (to which marker 3596652|F|0–30:A > G-30:A > G has been mapped), has previously been observed to be differentially expressed (highly up-regulated; log 2 estimated fold change = 4.7) in the rye inbred line L318 infected with compatible Prs strains [ 41 ].…”

“…Many of these 21 genes, such as those coding for a NBS-LRR disease resistance protein-like protein, leucine-rich repeat receptor-like protein kinase family protein, pathogenesis-related thaumatin family protein, phenylalanine ammonia-lyase, endoglucanase, MYB-related transcription factor, kinase (serine/threonine) family protein, and GDSL esterase/lipase ([ 34 – 41 ], respectively), have been proven to play a role in the immune response to rust fungi. One such gene, SECCE1Rv1G0013110.1 , encoding an endoglucanase (to which marker 3596652|F|0–30:A > G-30:A > G has been mapped), has previously been observed to be differentially expressed (highly up-regulated; log 2 estimated fold change = 4.7) in the rye inbred line L318 infected with compatible Prs strains [ 41 ]. Given the high scores for the marker ( p -value) and the gene (log 2 estimated fold change), we suggest that SECCE1Rv1G0013110 is a valuable candidate gene conferring resistance to LR and the marker 3596652|F|0–30:A > G-30:A > G is a valuable tool for marker-assisted selection.…”

“…Apart from this gene, none of the other aforementioned genes were identified as differentially expressed genes in our parallel transcriptome analyses. Nonetheless, many other genes encoding all of the above-mentioned antifungal proteins have been detected [ 41 ]. Other genes in this pool, for example, genes encoding an invertase/pectin methylesterase inhibitor family protein, GDSL esterase/lipase, and CHUP1 protein ([ 42 – 44 ], respectively), are associated with fungal pathogens but their role in the response to LR remains unclear.…”