Dataset Information

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum).

ABSTRACT: BACKGROUND:The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered. RESULTS:In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a 'blue' module highly associated with cellulose synthesis and a 'turquoise' module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes. CONCLUSIONS:This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.

SUBMITTER: Zhang W

PROVIDER: S-EPMC7678330 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum).

Zhang Wenqing W Zhang Shengkui S Lu Xianqin X Li Can C Liu Xingwang X Dong Geyu G Xia Tao T

BMC plant biology 20201119 1

<h4>Background</h4>The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered.<h4>Results</h4>In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from dif ...[more]

PMID: 33213376

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Project description:BackgroundAlong with global warming, resulting in crop production, exacerbating the global food crisis. Therefore, it is urgent to study the mechanism of plant heat resistance. However, crop resistance genes were lost due to long-term artificial domestication. By analyzing the potential heat tolerance genes and molecular mechanisms in other wild materials, more genetic resources can be provided for improving the heat tolerance of crops. Elephant grass (Pennisetum purpureum Schum.) has strong adaptability to heat stress and contains abundant heat-resistant gene resources.ResultsThrough sequence structure analysis, a total of 36 RWP-RK members were identified in elephant grass. Functional analysis revealed their close association with heat stress. Four randomly selected RKDs (RKD1.1, RKD4.3, RKD6.6, and RKD8.1) were analyzed for expression, and the results showed upregulation under high temperature conditions, suggesting their active role in response to heat stress. The members of RWP-RK gene family (36 genes) in elephant grass were 2.4 times higher than that of related tropical crops, rice (15 genes) and sorghum (15 genes). The 36 RWPs of elephant grass contain 15 NLPs and 21 RKDs, and 73% of RWPs are related to WGD. Among them, combined with the DAP-seq results, it was found that RWP-RK gene family expansion could improve the heat adaptability of elephant grass by enhancing nitrogen use efficiency and peroxidase gene expression.ConclusionsRWP-RK gene family expansion in elephant grass is closely related to thermal adaptation evolution and speciation. The RKD subgroup showed a higher responsiveness than the NLP subgroup when exposed to high temperature stress. The promoter region of the RKD subgroup contains a significant number of MeJA and ABA responsive elements, which may contribute to their positive response to heat stress. These results provided a scientific basis for analyzing the heat adaptation mechanism of elephant grass and improving the heat tolerance of other crops.

Project description:BackgroundElephant grass (Pennisetum purpureum Schumach) and Hybrid Pennisetum (Pennisetum americanum × P. purpureum Schumach) are tall, fast-growing perennial C4 bunchgrasses that have been in recent developed as the most appropriate biomass feedstock in many countries for exploring various biofuel products. However, the challenges of increasing plant biomass yield and enhancing their stress tolerance, especially on marginal lands, have been existed for a long while. In the past several years, bacterial endophytes used as bio-fertilizers for improving crop production have offered an opportunity to facilitate high biomass yield of energy crops in a more sustainable manner.ResultsA total of 16 endophytic bacteria strains were isolated and purified from the roots of elephant grass, which were classified into four bacterial genera: Sphingomonas, Pantoea, Bacillus, and Enterobacter. Four strains, pp01, pp02, pp04, and pp06, represented four different genera, were then selected and tested in vitro for their plant growth promoting properties, effects on plant growth and salt stress tolerance of Hybrid Pennisetum. The inoculation with these four bacterial mixture demonstrated a significant plant growth promotion for Hybrid Pennisetum from the normal to salt stress conditions at 0, 50, 100, and 200 mM NaCl, respectively. The highest promotion rate for biomass yield was 116.01 and 81.72 % for shoot fresh weight and dry weight, respectively. The bacterial strains tested were shown to solubilize insoluble phosphate, fix nitrogen, produce indole acetic acid and ammonia, but only strains from Sphingomonas, Bacillus, and Enterobacter can produce siderophore. In addition, the endophyte strains tested were all able to successfully colonize the roots of Hybrid Pennisetum, reaching upto 12.12 ± 0.98 CFU/g fresh roots at the 3rd day of inoculation.ConclusionThe four endophytic bacteria from elephant grass significantly promoted plant growth and biomass yield, alleviated the harmful effects of salt stress on Hybrid Pennisetum. These bacteria have indicated some unique properties that are very valuable for exploiting bio-inoculants aiding in the efforts to establish a sustainable and large-scale feedstock production system for Hybrid Pennisetum, particularly, on the saline marginal lands.

Project description:Elephant grass is widely used in feed production and ecological restoration because of its huge biomass and low occurrence of diseases and insect pets. However, drought seriously affects growth and development of this grass. Strigolactone (SL), a small molecular phytohormone, reportedly participates in improving resilience to cope with arid environment. But the mechanism of SL regulating elephant grass to response to drought stress remains unknown and needs further investigation. We conducted RNA-seq experiments and identified 84,296 genes including 765 and 2325 upregulated differential expression genes (DEGs) and 622 and 1826 downregulated DEGs, compared drought rehydration with spraying SL in roots and leaves, respectively. Combined with targeted phytohormones metabolite analysis, five hormones including 6-BA, ABA, MeSA, NAA, and JA had significant changes under re-watering and spraying SL stages. Moreover, a total of 17 co-expression modules were identified, of which eight modules had the most significant correlation with all physiological indicators with weighted gene co-expression network analysis. The venn analysis revealed the common genes between Kyoto Encyclopedia of Genes and Genomes enriched functional DEGs and the top 30 hub genes of higher weights in eight modules, respectively. Finally, 44 DEGs had been identified as key genes which played a major role in SL response to drought stress. After verification of its expression level by qPCR, six key genes in elephant grass including PpPEPCK, PpRuBPC, PpPGK, PpGAPDH, PpFBA, and PpSBPase genes regulated photosynthetic capacity under the SL treatment to respond to drought stress. Meanwhile, PpACAT, PpMFP2, PpAGT2, PpIVD, PpMCCA, and PpMCCB regulated root development and phytohormone crosstalk to respond to water deficit conditions. Our research led to a more comprehensive understanding about exogenous SL that plays a role in elephant grass response to drought stress and revealed insights into the SL regulating molecular mechanism in plants to adapt to the arid environment.

Project description:BACKGROUND:Elephant grass [Cenchrus purpureus (Schumach.) Morrone] is used for bioenergy and animal feed. In order to identify candidate genes that could be exploited for marker-assisted selection in elephant grass, this study aimed to investigate changes in predictive accuracy using genomic relationship information and simple sequence repeats for eight traits (height, green biomass, dry biomass, acid and neutral detergent fiber, lignin content, biomass digestibility, and dry matter concentration) linked to bioenergetics and animal feeding. RESULTS:We used single-step, genome-based best linear unbiased prediction and genome association methods to investigate changes in predictive accuracy and find candidate genes using genomic relationship information. Genetic variability (p < 0.05) was detected for most of the traits evaluated. In general, the overall means for the traits varied widely over the cuttings, which was corroborated by a significant genotype by cutting interaction. Knowing the genomic relationships increased the predictive accuracy of the biomass quality traits. We found that one marker (M28_161) was significantly associated with high values of biomass digestibility. The marker had moderate linkage disequilibrium with another marker (M35_202) that, in general, was detected in genotypes with low values of biomass digestibility. In silico analysis revealed that both markers have orthologous regions in other C4 grasses such as Setaria viridis, Panicum hallii, and Panicum virgatum, and these regions are located close to candidate genes involved in the biosynthesis of cell wall molecules (xyloglucan and lignin), which support their association with biomass digestibility. CONCLUSIONS:The markers and candidate genes identified here are useful for breeding programs aimed at changing biomass digestibility in elephant grass. These markers can be used in marker-assisted selection to grow elephant grass cultivars for different uses, e.g., bioenergy production, bio-based products, co-products, bioactive compounds, and animal feed.

Dataset Information

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum).

Publications

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum).

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