Simple sequence repeat identification for RSS1 gene in multiple varieties of Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20014 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1884280.fastq.gz | Fastqsanger.gz | |||
| ERR1884281.fastq.gz | Fastqsanger.gz | |||
| ERR1884282.fastq.gz | Fastqsanger.gz | |||
| ERR1884283.fastq.gz | Fastqsanger.gz | |||
| ERR1884284.fastq.gz | Fastqsanger.gz |
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Project description:Studies have shown that Rice Salt Sensitive 1 (RSS1) is involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RSS1. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
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Project description:Simple sequence repeat identification for RBOHB gene in multiple varieties of Oryza sativa
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Project description:The worldwide demand for potato production requires the constant development of new potato varieties with improved yield, quality, disease resistance, and abiotic tolerance. However, cultivar registration is preceded by a long process to morphologically and physiologically characterize the plants. Notably, this process can be expedited by DNA marker analysis. Simple sequence repeats (SSRs), also known as microsatellites, are the most common reliable DNA markers used to discriminate between genotypes. In this study, 20 potato varieties, including five new genotypes developed in Alberta, Canada, were fingerprinted using 10 SSR markers selected for their high discriminatory power. Different SSRs were amplified from potato DNA using specific primers, and the DNA fragment sizes were analyzed by denaturing polyacrylamide gel electrophoresis. The number of alleles per locus ranged from two for the SSR marker STPoAc58 to six for STM0030 and STM0037 with an average of 4.4. In addition, a total of 77 unique patterns were observed for the 10 SSR markers. The polymorphic information content ranged from 0.477 to 0.802 with an average of 0.675 per locus. In this study, STM0037, STM1016, and STM1104 were found to be the best SSR markers to detect genetic differences between potato varieties. A minimum of two markers was required to distinguish between all 20 genotypes. Most importantly, this highly informative molecular tool confirmed that the developed potato varieties were genetically different from their respective maternal lines and potentially constituted new cultivars.
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Project description:MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets. Small RNA sequencing was done for 10 days old seedlings of Phaseolus vulgaris Cv. Anupam
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2015-04-28 | GSE68305 | GEO
Project description:Simple sequence repeat identification for RBOHB gene in multiple varieties of Oryza sativa
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Project description:Simple sequence repeat identification for RSS1 gene in multiple varieties of Oryza sativa
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Project description:Waterlogging leads to major crop losses globally, particularly for waterlogging sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related QTLs have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging, and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA-sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called ‘core hypoxia response genes’, thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study ‘predisposition’ to waterlogging tolerance or sensitivity in barley.
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Project description:Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag-simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits.
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