Novel cotton homeobox gene and its expression profiling in root development and in response to stresses and phytohormones

Ni, Yongxiang; Wang, Xiulan; Li, Deng-Di; Yu, Wu; Xu, Wen‐Liang; Li, Xuebao

doi:10.1111/j.1745-7270.2008.00371.x

Cited by 34 publications

(28 citation statements)

References 25 publications

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“…In our study, GhbHLH1 was significantly up-regulated (see Additional file 2E), indicating its additional involvement in cotton salt-stress response. Seven TF genes (three GhNAC , two GhHB and two GhMYB genes) were identified at 4- and 24-h salt-stress time points, suggesting that their protein products may play an important role in salt-stress response in addition to the involvement in ABA signaling uncovered in previous research [22, 68, 69]. Transcripts encoding C2H2-type zinc finger proteins (ZAT10) that have been implicated in salt stress tolerance were up-regulated under 4- and 24-h salt stress.…”

Section: Discussionmentioning

confidence: 84%

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

et al. 2014

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BackgroundCotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology.ResultsWe investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs.ConclusionsOur comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-760) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 84%

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

et al. 2014

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“…The Homeobox-zip (HB family) TF members were suggested as excellent candidates to generate stress responses in transgenic plants and cotton root development regulation under salt stress involved GmHB1 gene expression [98], [99].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Salt Tolerant Common Bean (Phaseolus vulgaris L.) under Saline Conditions

et al. 2014

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Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.

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“…HD-Zip encoding genes have been isolated from various plants, such as Arabidopsis [22], rice [13], tomato [23], cotton [24], maize [25] and Physcomitrella patens [26]. HD-Zip proteins have been demonstrated to participate in transcriptional regulation of a series of biological processes related to plant growth and development.…”

Section: Introductionmentioning

confidence: 99%

Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize

et al. 2011

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BackgroundMembers of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.).Methods and FindingsIn this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55) were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR). All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution.ConclusionsOur results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.

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Novel cotton homeobox gene and its expression profiling in root development and in response to stresses and phytohormones

Cited by 34 publications

References 25 publications

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

Transcriptome Analysis of Salt Tolerant Common Bean (Phaseolus vulgaris L.) under Saline Conditions

Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize

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