Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways

Effects of drought stress on the secondary metabolism of Scutellaria baicalensis Georgi and the function of SbWRKY34 in drought resistance

The pharmacological properties of the dried root of Scutellaria baicalensis Georgi, a Chinese medicinal herb, include antioxidant, antibacterial, and antiviral effects. In S. baicalensis quality assessment, concentrations of baicalin, wogonoside, baicalein, and wogonin in the root are crucial. Drought stress commonly affects the biomass and build-up of active compounds in medicinal sections of medicinal plants and thus their quality. The molecular mechanisms underlying the response of S. baicalensis to drought stress remain unexplored. To delve into the impacts of drought stress on the growth and metabolic processes of S. baicalensis, as well as to unravel the underlying molecular mechanisms. We found prolonged and intensified drought treatment causes an initial surge in its fresh weight, plant height, and stem diameter followed by a gradual slowdown, while malondialdehyde (MDA) content rises; while the fresh weight, length, superoxide dismutase (SOD), and catalase (CAT) activities peak before declining, and the root's diameter continuously narrows. In this study, flavonoid index ingredient levels in S. baicalensis initially decreased, then rose as the drought duration extended, followed by a notable post-rehydration increase in baicalin, wogonoside, and baicalein content and decrease in levels of wogonin and oroxylin A. Transcriptome sequencing and KEGG analysis revealed a significant enrichment of DEGs involved in phenylpropanoid biosynthesis and plant hormone signal transduction pathways. The expression levels of SbPAL, SbCCL, Sb4CL, SbCHI, SbFNSII, SbF6H, and SbUGT genes in the flavonoid biosynthetic pathway and PYR/PYL, PP2C, ABF, and SnRK2 genes in the abscisic acid signal transduction pathway were significantly changed. Drought responsive SbWRKY34 was selected for the subsequent investigation. SbWRKY34 showed the highest level in stems, and the encoding protein was localized in the nucleus. Overexpression of SbWRKY34 in Arabidopsis thaliana (OE-SbWRKY34 lines) resulted in increased sensitivity to drought stress, with considerably reduced MDA content and elevated SOD and CAT activities. Concurrently, the expression levels of AtCAT3, AtDREB, AtRD22, AtRD29A, and AtRD29B were significantly reduced in these lines, suggesting that SbWRKY34 functions to negatively regulate drought resistance in A. thaliana.

Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard

Leaf mustard (Brassica juncea L. Czern & Coss), an important vegetable crop, experiences pronounced adversity due to seasonal drought stress, particularly at the seed germination stage. Although there is partial comprehension of drought-responsive genes, the role of long non-coding RNAs (lncRNAs) in adjusting mustard's drought stress response is largely unexplored. In this study, we showed that the drought-tolerant cultivar 'Weiliang' manifested a markedly lower base water potential (-1.073 MPa vs -0.437 MPa) and higher germination percentage (41.2% vs 0%) than the drought-susceptible cultivar 'Shuidong' under drought conditions. High throughput RNA sequencing techniques revealed a significant repertoire of lncRNAs from both cultivars during germination under drought stress, resulting in the identification of 2,087 differentially expressed lncRNAs (DELs) and their correspondingly linked 12,433 target genes. It was noted that 84 genes targeted by DEL exhibited enrichment in the photosynthesis pathway. Gene network construction showed that MSTRG.150397, a regulatory lncRNA, was inferred to potentially modulate key photosynthetic genes (Psb27, PetC, PetH, and PsbW), whilst MSTRG.107159 was indicated as an inhibitory regulator of six drought-responsive PIP genes. Further, weighted gene co-expression network analysis (WGCNA) corroborated the involvement of light intensity and stress response genes targeted by the identified DELs. The precision and regulatory impact of lncRNA were verified through qPCR. This study extends our knowledge of the regulatory mechanisms governing drought stress responses in mustard, which will help strategies to augment drought tolerance in this crop.

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

Suaeda glauca Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA3 effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA3 on S. glauca black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA3 treatment were analyzed and compared, and the TTF, H2O2, O2 -, starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA3 treatment significantly increased seed vigor, H2O2, and O2 - contents but decreased starch and soluble sugar contents of S. glauca black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (SgGA3ox1, SgKAO and SgGA2ox8) and ABA signal transduction (SgPP2Cs) could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA3 treatment conditions, especially many SgPER genes encoding peroxidase. In addition, exogenous GA3 treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA3-induced dormancy release, such as SgBAM, SgHXK2, and SgAGLU, etc. In a word, exogenous GA3 effectively increased the germination rate and seed vigor of S. glauca black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA3 on the dormancy release of S. glauca black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.

Re-watering solution facilitates seed germination and seedling growth of Carex schmidtii: Implication for species re-introduction in degraded semi-arid wetlands

Water deficiency threatens the health and function of wetlands in semi-arid areas. Optimum re-watering is an effective method for close-to-natural restoration to mitigate wetland degradation. Although the ecological importance of optimal re-watering as a nature-based solution for promoting wetland plant growth has been widely recognized, the response mechanisms of seed germination and seedling growth to re-watering are still poorly understood despite their decisive impact on plant life history. To fill this gap, this study compared the characteristics of seed germination and seedling growth in Carex schmidtii under initial water content with three levels (30%, 50%, and 70%) and five re-watering treatments (maintained at constant water content and re-watering to 100% on 7th, 14th, 21st, and 28th day). Moreover, the degree of reserve mobilization during four germination stages (seed suckering, sprouting, 20% germination, and seedling growth) was investigated. The results showed that water deficiency and re-watering treatments significantly affected C. schmidtii seed germination, seedling growth, and reserve mobilization. Compared with the other treatments, 50% moisture content and re-watering to 100% on the 14th day (50%-RT3) treatment significantly improved germination traits (germination rate, daily germination rate, germination index, and vigor index) and seedling growth characteristics (shoot length, root length, shoot biomass, root biomass, and total biomass). Furthermore, the degree of mobilization of starch, soluble protein, fat, and soluble sugar accumulation in C. schmidtii seeds under 50%-RT3 was higher than that in the other treatments. The structural equation model showed that the characteristics of seed germination and seedling growth of C. schmidtii were directly related to water deficiency and re-watering treatments, whereas reserve mobilization indirectly affected seed germination and seedling growth. These findings demonstrated that water deficiency and re-watering treatments have a crucial regulatory effect on seed germination and seedling growth of wetland plant species through a dual mechanism. This study provides information for the formulation of an optimum re-watering strategy for wetland vegetation restoration in semi-arid areas of the world.

Key anti-freeze genes and pathways of Lanzhou lily (Lilium davidii, var. unicolor) during the seedling stage

Temperature is one of the most important environmental factors for plant growth, as low-temperature freezing damage seriously affects the yield and distribution of plants. The Lanzhou lily (Lilium davidii, var. unicolor) is a famous ornamental plant with high ornamental value. Using an Illumina HiSeq transcriptome sequencing platform, sequencing was conducted on Lanzhou lilies exposed to two different temperature conditions: a normal temperature treatment at 20°C (A) and a cold treatment at -4°C (C). After being treated for 24 hours, a total of 5848 differentially expressed genes (DEGs) were identified, including 3478 significantly up regulated genes and 2370 significantly down regulated genes, accounting for 10.27% of the total number of DEGs. Quantitative real-time PCR (QRT-PCR) analysis showed that the expression trends of 10 randomly selected DEGs coincided with the results of high-throughput sequencing. In addition, genes responding to low-temperature stress were analyzed using the interaction regulatory network method. The anti-freeze pathway of Lanzhou lily was found to involve the photosynthetic and metabolic pathways, and the key freezing resistance genes were the OLEO3 gene, 9 CBF family genes, and C2H2 transcription factor c117817_g1 (ZFP). This lays the foundation for revealing the underlying mechanism of the molecular anti-freeze mechanism in Lanzhou lily.

Integrative analysis of the transcriptome and metabolome reveals Bacillus atrophaeus WZYH01-mediated salt stress mechanism in maize (Zea mays L.)

Maize is an important food crop that is affected by salt stress during growth, which can hinder plant growth and result in a significant decrease in yield. The application of plant growth-promoting rhizobacteria can improve this situation to a certain extent. However, the gene network of rhizosphere-promoting bacteria regulating the response of maize to salt stress remains elusive. Here, we used metabolomics and transcriptomics techniques to elucidate potential gene networks and salt-response pathways in maize. Phenotypic analysis showed that the Bacillus atrophaeus treatment improved the plant height, leaf area, biomass, ion, nutrient and stomatal indicators of maize. Metabolomic analysis identified that differentially expressed metabolites (DEMs) were primarily concentrated in the arginine, proline and phytohormone signaling metabolic pathways. 4-Hydroxyphenylacetylglutamic acid, L-histidinol, oxoglutaric acid, L-glutamic acid, L-arginine, and L-tyrosine were significantly increased in the Bacillus atrophaeus treatment. Weighted gene coexpression network analysis (WGCNA) identified several hub genes associated with salt response: Zm00001eb155540 and Zm00001eb088790 (ABC transporter family), Zm00001eb419060 (extra-large GTP-binding protein family), Zm00001eb317200 (calcium-transporting ATPase), Zm00001eb384800 (aquaporin NIP1-4) and Zm00001eb339170 (cytochrome P450). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that genes related to plant hormone signal transduction and the MAPK signaling pathway were involved in the response to the effect of Bacillus atrophaeus under salt stress. In the plant hormone signal transduction pathway, 3 differentially expressed genes (DEGs) encoding EIN3/EILs protein, 3 DEGs encoding GH3, 1 DEG encoding PYR/PYL and 6 DEGs encoding PP2C were all upregulated in Bacillus atrophaeus treatment. In the MAPK signaling pathway, 2 DEGs encoding CAT1 and 2 DEGs encoding WRKY22/WRKY29 were significantly upregulated, and the expression of DEGs encoding RbohD was downregulated by the application of Bacillus atrophaeus. In conclusion, the application of Bacillus atrophaeus under salt stress regulated key physiological and molecular processes in plants, which could stimulate the expression of genes related to ion transport and nutrients in maize, alleviate salt stress and promote maize growth to some extent, deepening our understanding of the application of Bacillus atrophaeus under salt stress to improve the salt-response gene network of maize growth.

Role of Microbes in Alleviating Crop Drought Stress: A Review

Drought stress is an annual global phenomenon that has devastating effects on crop production, so numerous studies have been conducted to improve crop drought resistance. Plant-associated microbiota play a crucial role in crop health and growth; however, we have a limited understanding of the key processes involved in microbiome-induced crop adaptation to drought stress. In this review, we summarize the adverse effects of drought stress on crop growth in terms of germination, photosynthesis, nutrient uptake, biomass, and yield, with a focus on the response of soil microbial communities to drought stress and plant-microbe interactions under drought stress. Moreover, we review the morpho-physiological, biochemical, and molecular mechanisms underlying the mitigation effect of microbes on crop drought stress. Finally, we highlight future research directions, including the characterization of specific rhizosphere microbiome species with corresponding root exudates and the efficiency of rhizobacteria inoculants under drought conditions. Such research will advance our understanding of the complex interactions between crops and microbes and improve crop resistance to drought stress through the application of beneficial drought-adaptive microbes.

Utilization of crop wild relatives for biotic and abiotic stress management in Indian mustard [Brassica juncea (L.) Czern. & Coss.]

Brassica juncea (L.) Czern. & Coss. (Indian mustard) is an economically important edible oil crop. Over the years, plant breeders have developed many elite varieties of B. juncea with better yield traits, but research work on the introgression of stress resilience traits has largely been lagging due to scarcity of resistant donors. Crop wild relatives (CWRs) are the weedy relatives of domesticated plant species which are left unutilized in their natural habitat due to the presence of certain undesirable alleles which hamper their yield potential, and thus, their further domestication. CWRs of B. juncea namely include Sinapis alba L. (White mustard), B. tournefortii Gouan. (African mustard), B. fruticulosa Cirillo (Twiggy turnip), Camelina sativa L. (Gold-of-pleasure), Diplotaxis tenuisiliqua Delile (Wall rocket), D. erucoides L. (White wall rocket), D. muralis L. (Annual wall rocket), Crambe abyssinica R.E.Fr. (Abyssinian mustard), Erucastrum gallicum Willd. (Common dogmustard), E. cardaminoides Webb ex Christ (Dogmustard), Capsella bursa-pastoris L. (Shepherds purse), Lepidium sativum L. (Garden Cress) etc. These CWRs have withstood several regimes of biotic and abiotic stresses over the past thousands of years which led them to accumulate many useful alleles contributing in resistance against various environmental stresses. Thus, CWRs could serve as resourceful gene pools for introgression of stress resilience traits into Indian mustard. This review summarizes research work on the introgression of resistance against Sclerotinia stem rot (caused by Sclerotinia sclerotiorum), Alternaria blight (caused by Alternaria brassicae), white rust (caused by Albugo candida), aphid attack, drought and high temperature from CWRs into B. juncea. However, various pre- and post-fertilization barriers due to different ploidy levels are major stumbling blocks in the success of such programmes, therefore, we also insightfully discuss how the advances made in -omics technology could be helpful in assisting various breeding programmes aiming at improvisation of stress resilience traits in B. juncea.