Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize

Liu, Songtao; Zenda, Tinashe; Dong, Anyi; Yang, Yatong; Wang, Nan; Duan, Huijun

doi:10.3389/fgene.2021.645443

Cited by 32 publications

(24 citation statements)

References 71 publications

(85 reference statements)

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“…As an effective data mining method, WGCNA can screen genes related to specific traits and conduct modular classification on large samples to obtain co-expression modules with high biological significance ( Zhao et al, 2010 ). Weighted gene co-expression network analysis has been used widely for plants in recent years ( Zhao et al, 2020 ; Liu et al, 2021 ; Panahi and Hejazi, 2021 ). Therefore, we constructed a hybrid sweetgum gene co-expression network using a WGCNA approach and identified co-expression modules using transcriptome data.…”

Section: Discussionmentioning

confidence: 99%

Global Transcriptome and Coexpression Network Analyses Reveal New Insights Into Somatic Embryogenesis in Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)

Zhao

Yan

et al. 2021

Front. Plant Sci.

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Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Despite recent scientific headway in deciphering the difficulties of somatic embryogenesis, the overall picture of key genes, pathways, and co-expression networks regulating SE is still fragmented. Therefore, deciphering the molecular basis of somatic embryogenesis of hybrid sweetgum remains pertinent. In the present study, we analyzed the transcriptome profiles and gene expression regulation changes via RNA sequencing from three distinct developmental stages of hybrid sweetgum: non-embryogenic callus (NEC), embryogenic callus (EC), and redifferentiation. Comparative transcriptome analysis showed that 19,957 genes were differentially expressed in ten pairwise comparisons of SE. Among these, plant hormone signaling-related genes, especially the auxin and cytokinin signaling components, were significantly enriched in NEC and EC early. The K-means method was used to identify multiple transcription factors, including HB-WOX, B3-ARF, AP2/ERF, and GRFs (growth regulating factors). These transcription factors showed distinct stage- or tissue-specific expression patterns mirroring each of the 12 superclusters to which they belonged. For example, the WOX transcription factor family was expressed only at NEC and EC stages, ARF transcription factor was expressed in EC early, and GRFs was expressed in late SE. It was noteworthy that the AP2/ERF transcription factor family was expressed during the whole SE process, but almost not in roots, stems and leaves. A weighted gene co-expression network analysis (WGCNA) was used in conjunction with the gene expression profiles to recognize the genes and modules that may associate with specific tissues and stages. We constructed co-expression networks and revealed 22 gene modules. Four of these modules with properties relating to embryonic potential, early somatic embryogenesis, and somatic embryo development, as well as some hub genes, were identified for further functional studied. Through a combination analysis of WGCNA and K-means, SE-related genes including AUX22, ABI3, ARF3, ARF5, AIL1, AIL5, AGL15, WOX11, WOX9, IAA29, BBM1, MYB36, LEA6, SMR4 and others were obtained, indicating that these genes play an important role in the processes underlying the progression from EC to somatic embryos (SEs) morphogenesis. The transcriptome information provided here will form the foundation for future research on genetic transformation and epigenetic control of plant embryogenesis at a molecular level. In follow-up studies, these data could be used to construct a regulatory network for SE; Key genes obtained from coexpression network analysis at each critical stage of somatic embryo can be considered as potential candidate genes to verify these networks.

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Section: Discussionmentioning

confidence: 99%

Global Transcriptome and Coexpression Network Analyses Reveal New Insights Into Somatic Embryogenesis in Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)

Zhao

Yan

et al. 2021

Front. Plant Sci.

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“…Protein kinases (PKs) are messengers which phosphorylation cascades and play key parts in drought responses 24 . We can propose that a complex of signalling was prompted under drought conditions, which relayed messages through the plasma membrane to the cell, activating a signal transduction cascade.…”

Section: Daps With Higher Abundance In Tolerant Genotypementioning

confidence: 99%

“…Several protein kinases have been showed to be involved in the plant nitrogen regulatory network 24,25 . Many studies have suggested that manipulation of proteins for primary and secondary nitrogen assimilatory pathways is also an favourable strategy to improve nitrogen use e ciency 25,26 .…”

Section: Daps With Higher Abundance In Tolerant Genotypementioning

confidence: 99%

Comparative Proteome Analysis of the Penultimate Internodes of Barley Genotypes Differing in Stem Reserve Remobilization Under Drought Stress

Hajibarat

Saïdi

Shahbazi

et al. 2022

Preprint

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Barley yield relies more on stem reserves under stress conditions at the grain filling stage. At terminal drought stresses, the remobilization of reserved assimilates from stem to seed contributes a major role in yield. To understand the molecular mechanism of stem reserve utilization during drought stress, a comparative proteome and physiological analyses were performed on the penultimate internodes of three genotypes of barley Yousef (tolerant), Morocco (susceptible), and PBYT17 (semi-tolerant) under drought stress at 21 and 28 days after anthesis (DAA). Under water stress and well-watered conditions Yousef showed significantly higher RWC, grain yield, and stem reserve remobilization capacity than susceptible and semi-tolerant genotypes. The proteome analysis led to the identification of 1580 differentially abundant proteins (DAPs), of which 759 and 821 proteins were differentially expressed at 21 and 28 DAA, respectively. Tolerant genotype in response to drought stress increased the abundance of several plant cell wall polysaccharide degradation proteins and protein kinases associated with posttranslational-associated, which might accelerate remobilization process for seed biomass formation compared to susceptible one under drought stress. However, the susceptible genotype increased the abundance of proteins involved in RNA metabolism and transcriptional changes to save energy sources for the growth and survival during drought stress. These findings suggest that barley might response to water stress by efficiently remobilize assimilates from stem to grain through specific remobilization processes.

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“…In other words, knowledge about the gene co-expression network involved in rose drought and recovery is very limited. WGCNA has become an important tool to identify gene co-expression related to associating with function, which has been widely used in the research of horticultural plants (Lu et al, 2019;Liu et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis ‘Old Blush’ After Exposure to a Gradual Drought Stress Followed by Recovery

Jia

Feng

et al. 2021

Front. Genet.

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Rose is one of the most fundamental ornamental crops, but its yield and quality are highly limited by drought. The key transcription factors (TFs) and co-expression networks during rose’s response to drought stress and recovery after drought stress are still limited. In this study, the transcriptomes of leaves of 2-year-old cutting seedlings of Rosa chinensis ‘Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network, which was associated with the physiological traits of drought response to discovering the hub TFs involved in drought response. More than 45 million high-quality clean reads were generated from the sample and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones including ABA, auxin, brassinosteroid (BR), cytokinin, ethylene (ET), jasmonic acid (JA) and salicylic acid (SA), primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules showed a high degree of correlation with physiological traits. In addition, 42 TFs including members of NACs, WRKYs, MYBs, AP2/ERFs, ARFs, and bHLHs with high connectivity in navajowhite1 and blue modules were screened. This study provides the transcriptome sequencing report of R. chinensis ‘Old Blush’ during drought stress and rewatering process. The study also identifies the response of candidate TFs to drought stress, providing guidelines for improving the drought tolerance of the rose through molecular breeding in the future.

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Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize

Cited by 32 publications

References 71 publications

Global Transcriptome and Coexpression Network Analyses Reveal New Insights Into Somatic Embryogenesis in Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)

Global Transcriptome and Coexpression Network Analyses Reveal New Insights Into Somatic Embryogenesis in Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)

Comparative Proteome Analysis of the Penultimate Internodes of Barley Genotypes Differing in Stem Reserve Remobilization Under Drought Stress

Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis ‘Old Blush’ After Exposure to a Gradual Drought Stress Followed by Recovery

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