Identification of autophagy-related genes ATG4 and ATG8 from wheat (Triticum aestivum L.) and profiling of their expression patterns responding to biotic and abiotic stresses

The ubiquitin proteasome 26S system (UPS), involving monomeric and multimeric E3 ligases is one of the most important signaling pathways in many organisms, including plants. The SCF (SKP1/Cullin/F-box) multimeric complex is particularly involved in response to development and stress signaling. The SKP1 protein (S-phase kinase-associated protein 1) is the core subunit of this complex. In this work, we firstly identified 92 and 87 non-redundant Triticum aestivum SKP1-like (TaSKP) genes that were retrieved from the latest release of the wheat genome database (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0) and the genome annotation of the TGAC v1 respectively. We then investigated the structure, phylogeny, duplication events and expression patterns of the SKP1-like gene family in various tissues and environmental conditions using a wheat expression platform containing public data. TaSKP1-like genes were expressed differentially in response to stress conditions, displaying large genomic variations or short insertions/deletions which suggests functional specialization within TaSKP1-like genes. Finally, interactions between selected wheat FBX (F-box) proteins and putative ancestral TaSKP1-like proteins were tested using the yeast two-hybrid (Y2H) system to examine the molecular interactions. These observations suggested that six Ta-SKP1 genes are likely to be ancestral genes, having similar functions as ASK1 and ASK2 in Arabidopsis, OSK1 and OSK20 in rice and PpSKP1 and PpSKP2 in Physcomitrella patens.

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Genome-wide identification and expression analysis of NADPH oxidase genes in response to ABA and abiotic stresses, and in fibre formation in Gossypium

PeerJ ◽

10.7717/peerj.8404 ◽

2020 ◽

Vol 8 ◽

pp. e8404 ◽

Cited By ~ 4

Author(s):

Gaofeng Zhang ◽

Caimeng Yue ◽

Tingting Lu ◽

Lirong Sun ◽

Fushun Hao

Keyword(s):

Abiotic Stresses ◽

Growth And Development ◽

Expression Patterns ◽

Purifying Selection ◽

Fiber Formation ◽

Biotic And Abiotic Stresses ◽

Fibre Formation ◽

Genome Wide ◽

Regulation Mechanisms ◽

Respiratory Burst Oxidase

Plasma membrane NADPH oxidases, also named respiratory burst oxidase homologues (Rbohs), play pivotal roles in many aspects of growth and development, as well as in responses to hormone signalings and various biotic and abiotic stresses. Although Rbohs family members have been identified in several plants, little is known about Rbohs in Gossypium. In this report, we characterized 13, 13, 26 and 19 Rbohs in G. arboretum, G. raimondii, G. hirsutum and G. barbadense, respectively. These Rbohs were conservative in physical properties, structures of genes and motifs. The expansion and evolution of the Rbohs dominantly depended on segmental duplication, and were under the purifying selection. Transcription analyses showed that GhRbohs were expressed in various tissues, and most GhRbohs were highly expressed in flowers. Moreover, different GhRbohs had very diverse expression patterns in response to ABA, high salinity, osmotic stress and heat stress. Some GhRbohs were preferentially and specifically expressed during ovule growth and fiber formation. These results suggest that GhRbohs may serve highly differential roles in mediating ABA signaling, in acclimation to environmental stimuli, and in fiber growth and development. Our findings are valuable for further elucidating the functions and regulation mechanisms of the Rbohs in adaptation to diverse stresses, and in growth and development in Gossypium.

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

10.21203/rs.3.rs-17430/v2 ◽

2020 ◽

Author(s):

Chong Yang ◽

Juanjuan Li ◽

Faisal Islam ◽

Luyang Hu ◽

Jiansu Wang ◽

...

Keyword(s):

Helianthus Annuus ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Crop Improvement ◽

Plant Tolerance ◽

Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes. Therefore, these functional genes related to increasing the plant tolerance or improving the crop quality, could be applied for the crop improvement..

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Phenotype characterisation and analysis of expression patterns of genes related mainly to carbohydrate metabolism and sporopollenin in male-sterile anthers induced by high temperature in wheat (Triticum aestivum)

Crop and Pasture Science ◽

10.1071/cp18034 ◽

2018 ◽

Vol 69 (5) ◽

pp. 469 ◽

Cited By ~ 4

Author(s):

Hongzhan Liu ◽

Junsheng Wang ◽

Chaoqiong Li ◽

Lin Qiao ◽

Xueqin Wang ◽

...

Keyword(s):

Triticum Aestivum ◽

High Temperature ◽

Male Sterility ◽

Carbohydrate Metabolism ◽

Higher Plants ◽

Expression Patterns ◽

Triticum Aestivum L ◽

Male Sterile ◽

Tetrad Stage ◽

Expression Levels

Male reproductive development in higher plants is highly sensitive to various stressors, including high temperature (HT). In this study, physiological male-sterile plants of wheat (Triticum aestivum L.) were established using HT induction. The physiological changes and expression levels of genes mainly related to carbohydrate metabolism and sporopollenin in male-sterile processes were studied by using biological techniques, including iodine–potassium iodide staining, paraffin sectioning, scanning electron microscopy (SEM) and fluorescent quantitative analysis. Results of paraffin sectioning and SEM revealed that parts of HT male-sterile anthers, including the epidermis and tapetum, were remarkably different from those of normal anthers. The expression levels of TaSUT1, TaSUT2, IVR1 and IVR5 were significantly lower than of normal anthers at the early microspore and trinucleate stages. The RAFTIN1 and TaMS26 genes may contribute to biosynthesis and proper ‘fixation’ of sporopollenin in the development of pollen wall; however, their expression levels were significantly higher at the early tetrad stage and early microspore stage in HT sterile anthers. The recently cloned MS1 gene was expressed at the early tetrad and early microspore stages but not at the trinucleate stage. Moreover, this gene showed extremely significant, high expression in HT sterile anthers compared with normal anthers. These results demonstrate that HT induction of wheat male sterility is probably related to the expression of genes related to carbohydrate metabolism and sporopollenin metabolism. This provides a theoretical basis and technological approach for further studies on the mechanisms of HT induction of male sterility.

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Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

International Journal of Molecular Sciences ◽

10.3390/ijms23010469 ◽

2021 ◽

Vol 23 (1) ◽

pp. 469

Author(s):

Kai Tong ◽

Xinyang Wu ◽

Long He ◽

Shiyou Qiu ◽

Shuang Liu ◽

...

Keyword(s):

Triticum Aestivum ◽

Gene Family ◽

Expression Profiles ◽

Stomatal Closure ◽

Expression Patterns ◽

Family Members ◽

Triticum Aestivum L ◽

Free Calcium ◽

Cis Acting ◽

Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

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A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

10.7287/peerj.preprints.27374v1 ◽

2018 ◽

Author(s):

Yongkai Li ◽

Xiaojie Cheng ◽

Yaqin Fu ◽

Qinqin Wu ◽

Yuli Guo ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Early Stage ◽

Expression Profiles ◽

Expression Patterns ◽

Cellulose Synthase ◽

Biotic And Abiotic Stresses ◽

A Genome ◽

Evolutionary Features ◽

Different Tissues

Cell walls play an important role in the structure and morphology of plants as well as stress response, including various biotic and abiotic stresses. Although the comprehensive analysis of genes involved in cellulose synthase have been performed in model plants, such as Arabidopsis thaliana and rice, information regarding cellulose synthase-like (Csl) genes in maize is extremely limited. In this study, a total of 56 members of Csl gene family were identified in maize genome, which were classified into six subfamilies. Analysis of gene structure and conserved motif indicated functional similarities among the ZmCsl proteins within the same subfamily. Additionally, the 56 ZmCsl genes were dispersed on 10 chromosomes. The expression patterns of ZmCsl genes in different tissues using the transcriptome data revealed that most of ZmCsl genes had a relatively high expression in root and tassel tissues. Moreover, the expression profiles of ZmCsl genes under drought and re-watering indicated that the expression of ZmCsl genes were mainly responsive to early stage of drought stress. The protein-protein interaction network of ZmCsl genes proposed some potential interacted proteins. The data presented a comprehensive survey of Csl gene family in maize. The detailed description of maize Csl genes will be beneficial to understand their structural, functional, and evolutionary features. Importantly, we have described the differential expression profiles of these members across different tissues and under drought. This information will provide an important foundation for studying the roles of these ZmCsl genes in response to biotic and abiotic stresses.

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

10.21203/rs.3.rs-17430/v1 ◽

2020 ◽

Author(s):

Chong Yang ◽

Juanjuan Li ◽

Faisal Islam ◽

Luyang Hu ◽

Jiansu Wang ◽

...

Keyword(s):

Helianthus Annuus ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Crop Improvement ◽

Gene Families ◽

Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes and will be beneficial to crop improvement.

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