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Transcript-derived Fragments (transcript-derived + fragment)
Selected AbstractsA potato tuber-expressed mRNA with homology to steroid dehydrogenases affects gibberellin levels and plant developmentTHE PLANT JOURNAL, Issue 6 2001Christian W.B. Bachem Summary Using cDNA-AFLP RNA fingerprinting throughout potato tuber development, we have isolated a transcript-derived fragment (TDF511) with strong homology to plant steroid dehydrogenases. During in vitro tuberization, the abundance profile of the TDF shows close correlation to the process of tuber formation. However, when tuberization is inhibited by the addition of gibberellins (GAs) to the growth medium, the appearance of TDF511 in the fingerprint is delayed, then steadily increases in intensity during later stages of development. TDF511 was used to isolate the corresponding cDNA (CB12). The DNA and deduced amino-acid sequences of the cDNA show high homology to a fruit-ripening gene from tomato, a series of steroid dehydrogenases, and the maize Ts2 gene. A section of the cDNA was cloned in antisense orientation behind a 35S CaMV promoter and transformed into potato. Transgenic plants expressing the antisense gene showed significantly earlier emergence, an increase in height, and longer tuber shape. In vitro tuberization experiments reveal extended stolon lengths in comparison to the controls. The analysis of endogenous GA levels showed that the transgenic antisense plants have elevated levels of biologically active GAs and their respective precursors. We propose that this gene plays a role in the metabolism of plant-growth substances important for tuber life cycle and plant development. [source] cDNA-AFLP reveals genes differentially expressed during the hypersensitive response of cassavaMOLECULAR PLANT PATHOLOGY, Issue 2 2005BENJAMIN P. KEMP SUMMARY The tropical staple cassava is subject to several major diseases, such as cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis. Disease-resistant genotypes afford the only practical solution, yet despite the global importance of this crop, little is known about its defence mechanisms. cDNA-AFLP was used to isolate cassava genes differentially expressed during the hypersensitive reaction (HR) of leaves in response to an incompatible Pseudomonas syringae pathovar. Seventy-eight transcript-derived fragments (TDFs) showing differential expression (c. 75% up-regulated, 25% down-regulated) were identified. Many encoded putative homologues of known defence-related genes involved in signalling (e.g. calcium transport and binding, ACC oxidases and a WRKY transcription factor), cell wall strengthening (e.g. cinnamoyl coenzyme A reductase and peroxidase), programmed cell death (e.g. proteases, 26S proteosome), antimicrobial activity (e.g. proteases and ,-1,3-glucanases) and the production of antimicrobial compounds (e.g. DAHP synthase and cytochrome P450s). Full-length cDNAs including a probable matrix metalloprotease and a WRKY transcription factor were isolated from six TDFs. RT-PCR or Northern blot analysis showed HR-induced TDFs were maximally expressed at 24 h, although some were produced by 6 h; some were induced, albeit more slowly, in response to wounding. This work begins to reveal potential defence-related genes of this understudied, major crop. [source] Use of cDNA-AFLP for transcript profiling in narrow genetic pools; for example, cucumber (Cucumis sativus L.)PLANT BREEDING, Issue 5 2006K. M. Bae Abstract A cDNA-AFLP transcript profiling was employed to examine three representative tissues (seedling, ovary and leaf) of nine Korean cucumber (Cucumis sativus L.) F1 hybrids. Differential accumulation of transcript-derived fragments (TDFs) was detected in 92 profiles. Genetic distance-based cluster analysis partitioned these hybrids into four main groupings, consistent with their phenotypic relationships. Although several polymorphic profiles were confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) analysis, many were not reproducible, indicating that a large portion of the observed polymorphisms were based on sequence variation of transcripts rather than expression of variation. Thus, it is proposed that cDNA-AFLP profiling be based on a dual descriptor system (sequence and expression). Data indicate that such a system would provide an efficient genetic marker system for identifying polymorphisms in narrow genetic pools. [source] Transcriptome response of the Pacific oyster (Crassostrea gigas) to infection with Vibrio tubiashii using cDNA AFLP differential displayANIMAL GENETICS, Issue 5 2009N. Taris Summary We used qualitative complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) differential display analysis and real-time, quantitative PCR (RT-qPCR) to identify genes in the Pacific oyster Crassostrea gigas, whose transcription either changes in response to exposure to a pathogenic bacterium (Vibrio tubiashii) or varies between families known to differ in sensitivity to heat stress, before and at 12 and 36 h after bacterial exposure at a temperature of 25 °C. These conditions simulate those associated with summer mortality syndrome, a poorly understood cause of massive mortalities in cultured Pacific oysters in North America, Asia and Europe. Using 32 AFLP primer pairs, we identified 92 transcript-derived fragments that are qualitatively differentially expressed. We then cloned and sequenced 14 of these fragments, designed fragment-specific primers and quantified their transcription patterns using RT-qPCR. Most of the differences in transcription patterns between stress-tolerant and stress-sensitive families were evident before bacterial exposure, and genes that responded to bacterial exposure did so in parallel between stress-sensitive and stress-tolerant families. blast searches of sequence databases revealed that these fragments represent genes involved in immune response as well as genes related to metabolic processes. Our data support the hypothesis that family level differences in resistance to stress in Pacific oysters are largely attributable to constitutive differences in gene transcription or ,general vigour' that are detectable before and maintained after infection, rather than being due to induced responses at the transcriptome level. [source] Expression of Ht2 -related genes in response to the HT-Toxin of Exserohilum turcicum in MaizeANNALS OF APPLIED BIOLOGY, Issue 1 2010H. Wang Complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis was conducted to analyze differential expression of Ht2 -related genes between maize (Zea mays) near-isogenic lines (NILs), Huangzaosi (HZS) and HuangzaosiHt2 (HZSHt2), following treatment with a crude extract of the HT-toxin. Twenty-one transcript-derived fragments (TDFs), designated H1 to H21, were specifically expressed or upregulated in HZSHt2 following exposure to the HT-toxin. Among them, 4, 7, 4, 2, 2 and 2 TDFs were detected at 3, 6, 12, 24, 48 and 72 h after treatment, respectively. BLAST analysis showed that H1, H11, H13 and H15 are related to regulation of the defence response to environmental stresses. H3, H6 and H10 are associated with energy metabolism. H5, H17 and H18 are involved in photosynthesis. H9 is similar to ubiquitin-like domain containing CTD phosphatase. H8, H9, H16 and H20 are probably transcription factors. The genes associated with basal energy metabolism and signal of stress tolerance were mainly expressed at 3 h after treatment. Transcription factor and most genes for stress tolerance were expressed at 6 h after treatment. RT-PCR analysis demonstrated that H8 was upregulated in HZSHt2 only at 6 h after exposure to the HT-toxin and H13 was upregulated at 6 and 12 h. The full length cDNAs of H8 (GenBank accession number FJ600319) and H13 (FJ600320) were cloned. The deduced protein encoded by H8 cDNA showed 77% homology to the Plus-3 domain containing protein, which is found in yeast gene Rtf1. H13 cDNA encodes a QM-like protein, which is an important protein in plant tolerance to environmental stress. The mechanism regulating the resistance of Ht2 to the HT-toxin might involve a translation elongation factor or an upregulated QM-like protein. [source] | ||||||||||