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Abiotic stresses, including cold and drought, negatively affect maize (Zea mays L.) seed field emergence and later yield and quality. In order to reveal the molecular mechanism of maize seed resistance to abiotic stress at seed germination, the global transcriptome of high- vigour variety Zhongdi175 exposed to cold- and drought- stress was analyzed by RNA-seq. In the comparison between the control and different stressed sample, 12,299 differentially expressed genes (DEGs) were detected, of which 9605 and 7837 DEGs were identified under cold- and drought- stress, respectively. Functional annotation analysis suggested that stress response mediated by the pathways involving ribosome, phenylpropanoid biosynthesis and biosynthesis of secondary metabolites, among others. Of the obtained DEGs (12,299), 5,143 genes are common to cold- and drought- stress, at least 2248 TFs in 56 TF families were identified that are involved in cold and/or drought treatments during seed germination, including bHLH, NAC, MYB and WRKY families, which suggested that common mechanisms may be originated during maize seed germination in response to different abiotic stresses. This study will provide a better understanding of the molecular mechanism of response to abiotic stress during maize seed germination, and could be useful for cultivar improvement and breeding of high vigour maize cultivars.
Pubmed ID: 34588562
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Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.
View all literature mentionsSoftware environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsComputable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsA portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsBioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
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