scholarly journals Global Identification of C2 Domain Contain Proteins And Characterization Of Genetic Variations For Involved Abiotic Stress Tolerance In Rice (Oryza sativa L.)

2021 ◽  
Author(s):  
Hongjia Zhang ◽  
Yuting Zeng ◽  
Jeonghwan Seo ◽  
Yu-Jin Kim ◽  
Sun Tae Kim ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Oryza Sativa L ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Rice Genome ◽  
C2 Domain ◽  
Mirna Regulation ◽  
Duplication Events ◽  
Global Identification ◽  
Redundancy Function

Abstract BackgroundC2DPs (C2 domain contain proteins) have been identified in different genomes that contain single or multiple C2 domains in their C or N-terminal, it possesses higher functional activity in the cell membrane between the cytoplasm and nucleus. Despite the identification of MCTPs and NTMC2s in rice, Arabidopsis, and cotton in a previous study, however, the C2DP gene family in rice has not been comprehensively studied, and the role of the C2DP gene in rice in response to abiotic stress is unclear.ResultsIn this study, we identified 82 C2DPs in the rice genome and divided them into seven groups through phylogenetic analysis. Synteny analysis revealed that duplication events were either exhibited within the genome of rice or between the genome of rice and other species. Through the analysis of cis-acting elements in promoters, expression profiles, and qRT-PCR results, the functions of OsC2DPs were found to be widely expressed in diverse tissues and were extensively involved in phytohormones and abiotic stress in rice. Prediction of the miRNA targets of OsC2DPs revealed that some of the homolog genes were regulated by consistent miRNAs and may carry out redundancy function. Notably, OsC2DP50/51/52 as a co-tandem duplication exhibited similar expression variations and involved the coincident miRNA-regulation pathway. Moreover, the results of SNP genotyping and haplotype analysis revealed that OsC2DP17, OsC2DP29, and OsC2DP49 possessed diverse haplotypes for impacted cold tolerance owing to genomic variations.ConclusionsThese findings provide a comprehensive sight for characterized OsC2DPs in rice and their roles for abiotic stress. Further, the genetic variation supports the theoretical reference for molecular breeding in rice.

scholarly journals Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.)

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0172515 ◽  
Author(s):  
Jauhar Ali ◽  
Jian-Long Xu ◽  
Yong-Ming Gao ◽  
Xiu-Fang Ma ◽  
Li-Jun Meng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Oryza Sativa L ◽  
Abiotic Stress Tolerance

scholarly journals Comprehensive analysis of the NAC gene family in Elaeis guineensis

Plant Omics ◽  
2018 ◽  
pp. 120-127 ◽  
Author(s):  
Yong Xiao ◽  
Haikuo Fan ◽  
Jianwei Ma ◽  
Xintao Lei ◽  
Yong Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Elaeis Guineensis ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Gene Expression Profiles ◽  
Comprehensive Analysis ◽  
Duplication Events ◽  
Drought And Salt Stresses ◽  
Nac Gene Family

The NAC gene family encode transcriptional regulator that contain a conserved NAM domain near the N-terminus and participate in the regulation of plant development and response to different abiotic stresses. In this study, 129 EgNAC genes were identified from the genome sequence of Elaeis guineensis and 97 EgNAC located on the chromsomes with an average of 4.56 EgNAC genes per chromosome. About 60% of EgNACs contained three exons and the gene sizes varied from 541 bp to 37,294 bp. Genomic duplication analysis showed that 10 EgNAC genes were involved in segmental duplication events and two genes were from tandem duplication. The gene expression profiles of EgNACs based on transcriptome database for different oil palm tissues showed that 30 EgNACs with low or no expression and 24 EgNACs were specifically expressed in one tissue. The trancriptome comparison between the control and cold stress samples demonstrated that thirty-seven EgNACs were down-regulated and 82 EgNACs were up-regulated under cold stress. Further RT-qPCR showed that the expression for 24 out of 32 validated EgNACs were induced under both cold, drought and salt stresses. Our comprehensive analysis of EgNAC genes has provided clues for candidate genes involved in abiotic stress tolerance.

scholarly journals Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11052
Author(s):  
Sushma Naithani ◽  
Daemon Dikeman ◽  
Priyanka Garg ◽  
Noor Al-Bader ◽  
Pankaj Jaiswal
Keyword(s):  
Gene Ontology ◽  
Abiotic Stress ◽  
Differential Expression ◽  
Functional Annotation ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Family Members ◽  
Gene Families ◽  
Structural Features ◽  
Response Expression

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.

scholarly journals Genome-wide and expression analysis of B-box gene family in pepper

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jing Ma ◽  
Jia-xi Dai ◽  
Xiao-wei Liu ◽  
Duo Lin
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transient Expression Assay ◽  
Specific Expression ◽  
Tissue Specific ◽  
Duplication Events ◽  
Onion Inner Epidermis

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

scholarly journals The DUBs Family in Populus: Identification, Characterization, Evolution and Expression Patterns

2020 ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Genome Structure ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Motif Analysis ◽  
Duplication Events ◽  
The Stability

Abstract Background: The deubiquitinases (DUB) family are a class of enzymes that regulate the stability or reverse the ubiquitination modification of many proteins in the cell, participating in cell cycle regulation, cell division and differentiation, various physiological activities such as DNA damage repair, growth and development, and response to stress. However, little is known about these genes in the woody plants. Results: In the present study, 88 DUB genes were identified in woody model plant Populus trichocarpa, including 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM with similar domains. According to the phylogenetic analysis, the 44 PtrUBP genes were classified into 14 subfamily, three PtrUCHs were classified into two groups, 23 PtrOTUs had six groups, four PtrMJDs had two groups, and 14 PtrJAMMs had six groups. The structure and motif analysis indicated that the same subfamily had similar genome structure and motif distribution characteristics. Ks/Ka analysis showed that the segmental duplication events played a major role in the expansion of Populus DUB genes. Synteny analysis of Populus DUB genes and four other species provided deep perception into the evolutionary traits of DUB genes. Expression profiles derived from transcriptome data exhibited distinct expression patterns of DUB genes in various tissues. Based on the result of promoter cis-regulatory elements analysis, we selected 16 representative PtrUBP genes to test their response to different hormonal treatments. The results showed that most of PtrUBPs were upregulated in the ABA, SA, and MeJA treatments, implying that their potential roles in abiotic stress response in Populus. Conclusion: The results in this study broaden our understanding of the DUB gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the DUBs provide a solid foundation for exploring their specific functions in Populus as well as indicate potential role of PtrUBP gene in abiotic stress.

Rice (Oryza sativa L.) tau class glutathione S-transferase (OsGSTU30) overexpression in Arabidopsis thaliana modulates a regulatory network leading to heavy metal and drought stress tolerance

Metallomics ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 375-389 ◽  
Author(s):  
Dipali Srivastava ◽  
Giti Verma ◽  
Abhishek Singh Chauhan ◽  
Veena Pande ◽  
Debasis Chakrabarty
Keyword(s):  
Heavy Metal ◽  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
Catalytic Activity ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Regulatory Network ◽  
Oryza Sativa L ◽  
Abiotic Stress Tolerance ◽  
Glutathione S Transferase

OsGSTU30 increases the abiotic stress tolerance in plants either by its catalytic activity or by modulating the expression of stress responsive genes.

scholarly journals Nitrogen Use Efficiency in Rice under Abiotic Stress: Plant Breeding Approach

2020 ◽  
Author(s):  
Satyen Mondal ◽  
Jamil Hasan ◽  
Priya Lal Biswas ◽  
Emam Ahmed ◽  
Tuhin Halder ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Nitrogen Use Efficiency ◽  
Abiotic Stresses ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Abiotic Stress Tolerance ◽  
Rice Variety ◽  
Rice Varieties ◽  
Nitrogen Use ◽  
Use Efficiency

Nitrogenous fertilizer has remarkably improved rice (Oryza sativa L.) yield across the world since its discovery by Haber-Bosch process. Due to climate change, future rice production will likely experience a wide range of environmental plasticity. Nitrogen use efficiency (NUE) is an important trait to confer adaptability across various abiotic stresses such as flooding, drought and salinity. The problem with the increased N application often leads to a reduction in NUE. New solutions are needed to simultaneously increase yield and maximize the NUE of rice. Despite the differences among flooding, salinity and drought, these three abiotic stresses lead to similar responses in rice plants. To develop abiotic stress tolerant rice varieties, speed breeding seems a plausible novel approach. Approximately 22 single quantitative trait loci (QTLs) and 58 pairs of epistatic QTLs are known to be closely associated with NUE in rice. The QTLs/genes for submergence (SUB1A) tolerance, anaerobic germination (AG, TPP7) potential and deepwater flooding tolerance (SK1, SK2) are identified. Furthermore, phytochrome-interacting factor-like14 (OsPIL14), or loss of function of the slender rice1 (SLR1) genes enhance salinity tolerance in rice seedlings. This review updates our understanding of the molecular mechanisms of abiotic stress tolerance and discusses possible approaches for developing N-efficient rice variety.

Sign in / Sign up

Export Citation Format

Share Document