Transcriptome analysis of sesame (Sesamum indicum L.) reveal the LncRNAs and mRNAs regulatory network responding to low nitrogen stress

Abstract

Background Nitrogen is one of the important factors restricting the development of sesame planting and industry in China. Cultivating sesame varieties tolerant to low nitrogen is an effective way to solve the problem of crop nitrogen deficiency. Up to date, the mechanism of low nitrogen tolerance in sesame has not been elucidated at the transcriptional level. Result In this study, two sesame varieties Zhengzhi HL05 (ZZ, nitrogen efficient) and Burmese prolific (MD, nitrogen inefficient) in low nitrogen were used for RNA-sequencing. A total of 3964 DEGs and 221 DELs were identified in two sesame varieties at 3d and 9d after low nitrogen stress. Among them, 1227 genes related to low nitrogen tolerance are mainly located in amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and participate in the process of transporter activity and antioxidant activity. In addition, a total of 209 pairs of lncRNA-mRNA were detected, including 21 pairs of trans and 188 cis. WGCNA analysis divided the obtained genes into 29 modules; phenotypic association analysis identified 3 low-nitrogen response modules; through lncRNA-mRNA co-expression network, a number of hub genes and cis / trans regulatory factors were identified in response to response low-nitrogen stress including GS1-2, PAL, CHS, CAB21 and transcription factors MYB54, MYB88 and NAC75 and so on. As a trans regulator, lncRNA MSTRG.13854.1 affects the expression of some genes related to low nitrogen response by regulating the expression of MYB54, thus responding to low nitrogen stress. Conclusion Combining WGCNA and co-expression analysis, consistently low nitrogen responsive candidate genes and lncRNAs were identified. In the co-expression networks responding to low nitrogen stress, some TFs were targeted by the lncRNAs, which further regulated the low nitrogen tolerance-related functional transcripts. Our research is the first to provide a more comprehensive understanding of DEGs involved in low nitrogen stress of sesame at transcriptome level. These results may reveal insights into the molecular mechanisms of low nitrogen tolerance in sesame and provide diverse genetic resources involved in low nitrogen tolerance research.