Integrated Analysis of Physiological, mRNA Sequencing, and miRNA Sequencing Data Reveals a Specific Mechanism for the Response to Continuous Cropping Obstacles in Pogostemon cablin Roots

Abstract

Pogostemon cablin (patchouli) is a commercially important medicinal and industrial crop grown worldwide for its medicinal and aromatic properties. Patchoulol and pogostone, derived from the essential oil of patchouli, are considered valuable components in the cosmetic and pharmaceutical industries. Due to its high application value in the clinic and industry, the demand for patchouli is constantly growing. Unfortunately, patchouli cultivation has suffered due to severe continuous cropping obstacles, resulting in a significant decline in yield and quality. Moreover, the physiological and transcriptional changes in patchouli in response to continuous cropping obstacles remain unclear. This has greatly restricted the development of the patchouli industry. To explore the mechanism underlying the rapid response of patchouli roots to continuous cropping stress, integrated analysis of the transcriptome and miRNA profiles of patchouli roots under continuous and noncontinuous cropping conditions in different growth periods was conducted using RNA sequencing (RNA-seq) and miRNA-seq and complemented with physiological data. The physiological and biochemical results showed that continuous cropping significantly inhibited root growth, decreased root activity, and increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the levels of osmoregulators (malondialdehyde, soluble protein, soluble sugar, and proline). Subsequently, we found 4,238, 3,494, and 7,290 upregulated and 4,176, 3,202, and 8,599 downregulated differentially expressed genes (DEGs) in the three growth periods of continuously cropped patchouli, many of which were associated with primary carbon and nitrogen metabolism, defense responses, secondary metabolite biosynthesis, and transcription factors. Based on miRNA-seq, 927 known miRNAs and 130 novel miRNAs were identified, among which 67 differentially expressed miRNAs (DEMIs) belonging to 24 miRNA families were induced or repressed by continuous cropping. By combining transcriptome and miRNA profiling, we obtained 47 miRNA-target gene pairs, consisting of 18 DEMIs and 43 DEGs, that likely play important roles in the continuous cropping response of patchouli. The information provided in this study will contribute to clarifying the intricate mechanism underlying the patchouli response to continuous cropping obstacles. In addition, the candidate miRNAs and genes can provide a new strategy for breeding continuous cropping-tolerant patchouli.

Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber species Phoebe bournei

“…Drought stress causes lipid peroxidation and cell membrane damage due to ROS accumulation. Plants prevent cellular damage from ROS accumulation by increasing the activities of SOD and POD ( Yan W. P. et al., 2022 ). However, severe drought can lead to a decrease in the efficiency of the antioxidant defense system in plants, decreasing the activities of antioxidant enzymes such as SOD and POD ( Chen et al., 2017 ).…”

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

“…miRNAs expression is affected by different stresses in plants which would regulate mRNA levels to respond to environmental alteration and affect plant development and growth [44,[51][52][53]. To clarify the targeted regulatory relationship between miRNAs and mRNAs, single miRNA to mRNA analysis or miRNA-mRNA integrated analysis are widely conducted [54,55]. In this study, we examined the miRNA expression alteration and its impact on target gene expression in the RL plants compared to the WT doner plants of rice cv.…”

Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus

“…Studies addressing the effects of continuous cropping have found that it has strong negative impacts on both plant and soil systems. These impacts include morphological, anatomical, physiological, and biochemical alterations in plants [11], altered soil microbial community structure [12], and accumulated allelopathic autotoxicity in the soil [13].…”