Identification of key modules and hub genes regulating drought stress response in rice drought sensitive line PY6 by weighted gene co-expression network analysis

Abstract Background: Drought stress is an adverse factor with deleterious effects on several facets of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. In order to genetically understand the potential molecular mechanism for drought response in rice, a drought sensitive Chromosome Segment Substitution Line (CSSL) PY6, which was constructed by the introgression of genomic segments of drought sensitive variety LAMBAYEQUE1 into drought-resistance variety PR403 via backcrossing, was used to map the QTL locus dss-1 for its sensitive phenotype, and to reveal the impact of dss-1 on the transcriptional profiling of PY6 via RNA-seq and WGCNA (weighted gene co-expression network analysis) analysis. Results: The genetic linkage analysis showed that dss-1 was located on the short arm of chromosome 1 of rice. In contrast to PR403, the over-accumulation of H 2 O 2 and MDA that might result in drought sensitive phenotype was observed in PY6 under drought stress. In the analysis of RNA-seq data, the identified differentially expressed genes (DEGs) mainly enriched in photosynthesis-related GO terms and exhibited a down-regulation pattern of their expressions in both PY6 and PR403 in response to drought stress, indicating that the photosynthesis was greatly inhibited in rice. Further WGCNA analysis constructed a co-expression network with 26 gene modules in which 4 and 3 modules that were highly correlated with H 2 O 2 and MDA, respectively. Likewise, the GO analysis of the differentially expressed hub genes (DEHGs) enriched in H 2 O 2 -correlated modules showed that the photosynthesis related GO terms were consistently over-represented. Furthermore, functional annotation of DEHGs in H 2 O 2 and MDA correlated modules revealed a cross talk between abiotic and biotic stresses. This was reflected by the differential expression alterations of hub genes which were annotated as encoding MYBs, laccases, WRKYs, and PRs family proteins, and ZFP36 were notably observed between PY6 and PR403 in response drought stress. Conclusions: Collectively, we speculated that drought-induced the inhibition of photosynthesis lead to the accumulation of H 2 O 2 and MDA that can trigger the reprogramming the profiling of transcriptome in rice. This included the differential regulation of hub genes that involve in ROS eliminated pathways to prevent the damage of rice plants from oxidative stress.

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Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

10.21203/rs.3.rs-56040/v4 ◽

2020 ◽

Author(s):

Baiyang Yu ◽

Jianbin Liu ◽

Di Wu ◽

Ying Liu ◽

Weijian Cen ◽

...

Keyword(s):

Network Analysis ◽

Drought Resistance ◽

Differentially Expressed ◽

Chromosome 1 ◽

Coexpression Network ◽

Gene Coexpression Network ◽

Hub Genes ◽

Gene Coexpression ◽

Go Terms ◽

Coexpression Network Analysis

Abstract Background: Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling.Results: The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403.Conclusions: We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

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Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

10.21203/rs.3.rs-56040/v3 ◽

2020 ◽

Author(s):

Baiyang Yu ◽

Jianbin Liu ◽

Di Wu ◽

Ying Liu ◽

Weijian Cen ◽

...

Keyword(s):

Network Analysis ◽

Drought Resistance ◽

Differentially Expressed ◽

Chromosome 1 ◽

Coexpression Network ◽

Gene Coexpression Network ◽

Hub Genes ◽

Gene Coexpression ◽

Go Terms ◽

Coexpression Network Analysis

Abstract Background: Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. Results: The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403.Conclusions: We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

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Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

10.21203/rs.3.rs-56040/v2 ◽

2020 ◽

Author(s):

Baiyang Yu ◽

Jianbin Liu ◽

Di Wu ◽

Ying Liu ◽

Weijian Cen ◽

...

Keyword(s):

Network Analysis ◽

Drought Resistance ◽

Differentially Expressed ◽

Chromosome 1 ◽

Coexpression Network ◽

Gene Coexpression Network ◽

Hub Genes ◽

Gene Coexpression ◽

Go Terms ◽

Coexpression Network Analysis

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Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

BMC Plant Biology ◽

10.1186/s12870-020-02705-9 ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Baiyang Yu ◽

Jianbin Liu ◽

Di Wu ◽

Ying Liu ◽

Weijian Cen ◽

...

Keyword(s):

Network Analysis ◽

Drought Resistance ◽

Differentially Expressed ◽

Chromosome 1 ◽

Coexpression Network ◽

Gene Coexpression Network ◽

Hub Genes ◽

Gene Coexpression ◽

Go Terms ◽

Coexpression Network Analysis

Abstract Background Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. Results The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403. Conclusions We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

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Weighted Gene Coexpression Network Analysis-Based Identification of Key Modules and Hub Genes that Regulate the Drought Stress Response in the Rice Drought-Sensitive Line PY6

10.21203/rs.3.rs-56040/v1 ◽

2020 ◽

Author(s):

Baiyang Yu ◽

Jianbin Liu ◽

Di Wu ◽

Ying Liu ◽

Weijian Cen ◽

...

Keyword(s):

Drought Stress ◽

Network Analysis ◽

Drought Resistance ◽

Differentially Expressed ◽

Coexpression Network ◽

Gene Coexpression Network ◽

Hub Genes ◽

Gene Coexpression ◽

Go Terms ◽

Coexpression Network Analysis

Abstract Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. The dss-1 locus was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), 4 and 3 modules were strongly correlated with H2O2 and MDA, respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the DEGs in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403.We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

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Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

BMC Plant Biology ◽

10.1186/s12870-020-02818-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Z. Y. Su ◽

J. J. Powell ◽

S. Gao ◽

M. Zhou ◽

C. Liu

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Crown Rot ◽

Differentially Expressed ◽

Transcriptional Responses ◽

Drought Treatment ◽

Crop Species ◽

Fusarium Crown Rot ◽

Important Relationship ◽

The Impact

Abstract Background Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops. Results In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection. Conclusions Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

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Drought tolerance molecular responses of two cultivated varieties Jerusalem artichoke (Helianthus tuberosus L.) as revealed by RNA-Seq

10.21203/rs.3.rs-124586/v1 ◽

2020 ◽

Author(s):

Shipeng Yang ◽

Lihui Wang ◽

Qiwen Zhong ◽

Guangnan Zhang ◽

Haiwang Zhang ◽

...

Keyword(s):

Drought Stress ◽

Drought Resistance ◽

Metabolic Pathways ◽

Jerusalem Artichoke ◽

Tibet Plateau ◽

Helianthus Tuberosus ◽

Rna Seq ◽

Concentration Gradients ◽

Light Reaction ◽

Metabolic Activities

Abstract Background Jerusalem artichoke (Helianthus tuberosus L.) is a highly stress-resistant crop, especially it grows normally in the desertified land of Qinghai-Tibet Plateau in the past two years, and has become a crop with agricultural, industrial and ecological functions. However, there are few studies on drought resistance of Jerusalem artichoke at present, and studies on the mechanisms of stress resistance of Jerusalem artichoke breeding and fructan are seriously lagging behind. In this study, we selected two differentially resistant cultivars for drought stress experiments with different concentration gradients, the aim was finding DEGs and metabolic pathways associated with drought stress. Results Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. It was suggested that flavonoids could help Jerusalem artichoke to resist drought stress and maintain normal metabolic activities. In addition, the gene analysis of the abscisic acid (ABA) key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1, but QY1 had more genes in response to drought stress as a whole. By combining RNA-Seq and WGCNA, a weighted gene co-expression network was constructed and divided into modules. By analyzing specifically the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase had the highest significance in these pathways. Conclusions These findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the excavation of related genes.

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Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽

10.3390/genes11010030 ◽

2019 ◽

Vol 11 (1) ◽

pp. 30

Author(s):

Yaodong Zhao ◽

Wenjing Ma ◽

Xiaohong Wei ◽

Yu Long ◽

Ying Zhao ◽

...

Keyword(s):

Nitric Oxide ◽

Drought Stress ◽

Medicago Sativa ◽

High Throughput ◽

Drought Resistance ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

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Transcriptome Analyses Revealed the Ultraviolet B Irradiation and Phytohormone Gibberellins Coordinately Promoted the Accumulation of Artemisinin in Artemisia Annua L.

10.21203/rs.3.rs-31458/v1 ◽

2020 ◽

Author(s):

Tingyu Ma ◽

Han Gao ◽

Dong Zhang ◽

Yuhua Shi ◽

Tianyuan Zhang ◽

...

Keyword(s):

Network Analysis ◽

Artemisia Annua ◽

Enrichment Analysis ◽

Ultraviolet B ◽

Differentially Expressed ◽

Hub Genes ◽

Uv Treatment ◽

Artemisia Annua L ◽

Ultraviolet B Irradiation ◽

Artemisinin Biosynthesis

Abstract Background: Artemisinin-based combination therapy has become the preferred approach for treating malaria and has successfully reduced malaria-related mortality. Currently, the main source of artemisinin is Artemisia annua L., and thus, it is of strategic importance to enhance artemisinin contents in A. annua plants. Phytohormones and illumination are known to be important external environmental factor that can have notable effects on the production of secondary metabolite. The activities of different hormones can be influenced to varying degrees by light, and thus light and hormones may jointly regulate various processes in plants. Here, we performed transcriptome and metabolome analyses revealed that ultraviolet B irradiation and phytohormone gibberellins coordinately promoted the accumulation of artemisinin in Artemisia annua.Methods: Artemisinin analysis was performed by ultra-high performance liquid chromatography-tandem quadrupole mass spectrometry (UPLC-ESI-QqQ-MS/MS). RNA sequencing, GO and KEGG enrichment analysis were applied to analyzing the differentially expressed genes (DEGs) under ultraviolet B irradiation and gibberellins treatments. Weighted gene co-expression network (WGCNA) analyzed the genes in artemisinin‑related modules and identified candidate hub genes in these modules.Results: In this study, we found that cross-talk between UV-B and GA induced processes leading to modifications in artemisinin accumulation. A total of 14,762 genes differentially expressed (DEGs) among different treatments were identified by transcriptome analysis. UV-B and GA treatments enhanced the accumulation of artemisinin by up-regulating the expression of the key artemisinin biosynthesis genes ADS and CYP71AV1. According to the high degree value and high expression level, a total of 84 co-expressed transcription factors were identified. Among them, MYB and NAC TFs mainly involved in regulating the biosynthesis of artemisinin. Weighted gene co-expression network analysis revealed that GA+UV in blue modules was positively correlated with artemisinin synthesis, suggesting that the candidate hub genes in these modules should be up-regulated to enhance artemisinin synthesis in response to GA+UV treatment.Conclusion: Our study demonstrated the co-regulation of artemisinin biosynthetic pathway genes under ultraviolet B irradiation and phytohormone gibberellins treatment. The co-expression was analysis revealed that the selected MYB and NAC TFs might have regulated the artemisinin biosynthesis gene expression with ADS and CYP71AV1 genes. Weighted gene co-expression network analysis revealed that GA+UV treatment in blue modules was positively correlated with artemisinin synthesis. We established the network to distinguish candidate hub genes in blue modules might be up-regulated to enhance artemisinin synthesis in response to GA+UV treatment.

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Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

Frontiers in Plant Science ◽

10.3389/fpls.2021.675903 ◽

2021 ◽

Vol 12 ◽

Author(s):

Rui Shi ◽

Wei Jiao ◽

Lan Yun ◽

Zhiqiang Zhang ◽

Xiujuan Zhang ◽

...

Keyword(s):

Drought Stress ◽

Drought Resistance ◽

Small Rna ◽

Mirna Target ◽

Expression Patterns ◽

Functional Characterization ◽

Differentially Expressed ◽

Limiting Factor ◽

Degradome Sequencing ◽

Medicago Ruthenica

Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

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