Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici

Abstract

Background As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. Results In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. Conclusions This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

“…Then, miRNA and CsDUF966 CDS sequences were submitted to the online tool psRNATarget with default parameters ( , accessed on 18 June 2022) [ 45 , 46 ]. The targeting relationships of miRNA to CsDUF966 were further visualized by R package ‘ggalluvial’ [ 47 ].…”

Roles of long non-coding RNAs in plant immunity

“…The differentially expressed pepper lncRNAs in response to P . capsici were found to increase pepper resistance to soil-borne diseases by interacting with their coordinated miRNA-mRNA and regulating the expression of disease-defense–related genes [ 213 ] ( Fig 3D and Table 1 ). Genes encoding zinc finger proteins, pentatricopeptide repeat-containing proteins, and LRR receptor-like serine/threonine-protein kinases are potentially regulated by lncRNAs to regulate plant immune responses to P .…”

“…Genes encoding zinc finger proteins, pentatricopeptide repeat-containing proteins, and LRR receptor-like serine/threonine-protein kinases are potentially regulated by lncRNAs to regulate plant immune responses to P . capsici [ 213 ]. On the other hand, the expression levels of lncRNAs in oomycetes were also altered during their infection of plant.…”

WRKY41/WRKY46-miR396b-5p-TPR module mediates abscisic acid-induced cold tolerance of grafted cucumber seedlings

“…Grafting alters the expression of miRNA and its target genes, indicating that miRNA plays an important role in regulating the physiological process of grafted seedlings at a post-transcriptional level ( Khaldun et al, 2016 ; Li et al, 2016 ; Kehr and Kragler, 2018 ). In recent years, a large number of grafting-related miRNAs have been obtained by sRNA-Seq technology ( Pagliarani et al, 2017 ; Yin et al, 2021 ; Hu et al, 2022 ). In our previous study on cucumber/pumpkin grafting compatibility, we isolated and identified 60 differentially expressed miRNAs in scions of grafted seedlings through high-throughput sequencing, but no specific miRNA was found ( Ren et al, 2018 ), suggesting that the rootstock regulated a series of physiological characteristics mainly by inducing differential expression of miRNA inherent in the scion.…”