Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016, Xining, Qinghai Province, China.
Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, 434000, Jingzhou, Hubei, China.
BMC Genomics. 2021 Dec 2;22(1):868. doi: 10.1186/s12864-021-08183-z.
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.
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.
This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.
作为一种流行且有价值的技术，嫁接被广泛用于保护蔬菜生产免受土传病害和线虫的侵害。越来越多的证据表明，长非编码基因间 RNA（lincRNA）受到严格调控，在植物发育和应激反应中发挥着重要作用。然而，辣椒 lincRNA 的全基因组鉴定和功能解析，特别是它们在提高嫁接辣椒对辣椒疫霉抗性中的作用，在很大程度上仍是未知的。
本研究利用嫁接和对照辣椒在接种或不接种辣椒疫霉时的 RNA-seq 数据来鉴定 lincRNA。总共鉴定出 2388 个可靠的 lincRNA。它们的长度相对较长，并且比编码蛋白的基因包含的外显子更少。与编码基因类似，lincRNA 在常染色质区域的密度更高；并且转录更长的染色体转录更多的 lincRNA。表达模式分析表明，lincRNA 的表达通常低于 mRNA。总共鉴定出 607 个差异表达的 lincRNA（DE-lincRANs），其中 172 个在对辣椒疫霉有抗性的嫁接辣椒样本 GR 和易感样本 LDS 之间。DE-lincRNA 的邻近基因和被 DE-lincRNA 竞争性结合的 miRNA 被鉴定出来。随后，通过 qRT-PCR 进一步验证了 DE-lincRNA 的表达水平，并验证了 DE-lincRNA 与其邻近 mRNAs 之间的调控模式。功能注释表明，DE-lincRNA 通过调控与疾病防御相关基因的表达，通过顺式调控和/或 lincRNA-miRNA-mRNA 相互作用网络，增加嫁接辣椒对辣椒疫霉的抗性。
本研究鉴定了辣椒 lincRNA，并提出了它们在提高嫁接辣椒对辣椒疫霉抗性水平中的潜在作用。
