scholarly journals Identification of Defense-Related Rice Genes by Suppression Subtractive Hybridization and Differential Screening

2001 ◽  
Vol 14 (5) ◽  
pp. 685-692 ◽  
Author(s):  
Lizhong Xiong ◽  
Min-Woo Lee ◽  
Min Qi ◽  
Yinong Yang
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Zinc Finger Protein ◽  
De Novo ◽  
Subtractive Hybridization ◽  
Defense Responses ◽  
Rice Cultivar ◽  
Differential Screening ◽  
Mitogen Activated Protein Kinase ◽  
Japonica Rice ◽  
Bacterial Colony

Identification of host genes involved in defense responses is one of most critical steps leading to the elucidation of disease resistance mechanisms in plants. In this study, two different cloning strategies were employed to identify defense-related genes from a tropical japonica rice cultivar (Oryza sativa cv. Drew). With the use of bacterial colony arrays, differential screening of a blast fungus (Pyricularia grisea)-induced rice cDNA library led to the isolation of 22 distinct rice genes that are expressed differentially in response to blast infection. Sequence analysis indicates that most of them are full-length cDNAs encoding pathogenesis-related proteins or other relatively abundant proteins. In combination with treatments of cycloheximide plus jasmonic acid (JA) or benzothiadiazole (BTH) in rice seedlings, the polymerase chain reaction-based suppression subtractive hybridization also was conducted to search for immediate early (IE) defense-related genes whose transcription is independent of de novo protein synthesis. The initial screening of only 768 subtracted clones resulted in the identification of 34 distinct IE genes that are induced by JA, BTH, and/or blast infection. Database searches revealed that these IE genes encode putative mitogen-activated protein kinase, diacylglycerol kinase, zinc finger protein, RelA-SpoT protein, ankyrin-containing protein, ABC transporter, β-ketoacyl-CoA synthase, and other potential defense-signaling components. Further characterization of these novel IE genes will likely facilitate the elucidation of defense signal transduction in rice plants.

scholarly journals Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7268
Author(s):  
Kwanjai Pipatchartlearnwong ◽  
Piyada Juntawong ◽  
Passorn Wonnapinij ◽  
Somsak Apisitwanich ◽  
Supachai Vuttipongchaikij
Keyword(s):  
Dna Fingerprinting ◽  
Suppression Subtractive Hybridization ◽  
Transcriptome Sequencing ◽  
Large Scale ◽  
De Novo ◽  
Subtractive Hybridization ◽  
Pcr Analysis ◽  
Dna Fingerprints ◽  
Juvenile Period ◽  
Male And Female

BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries andde novotranscriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Althoughde novotranscriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

scholarly journals Identification of New Potential Regulators of the Medicago truncatula—Sinorhizobium meliloti Symbiosis Using a Large-Scale Suppression Subtractive Hybridization Approach

2007 ◽  
Vol 20 (3) ◽  
pp. 321-332 ◽  
Author(s):  
Laurence Godiard ◽  
Andreas Niebel ◽  
Fabienne Micheli ◽  
Jérôme Gouzy ◽  
Thomas Ott ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Suppression Subtractive Hybridization ◽  
Medicago Truncatula ◽  
Large Scale ◽  
Sinorhizobium Meliloti ◽  
Zinc Finger Protein ◽  
Gene Clusters ◽  
Subtractive Hybridization ◽  
Symbiotic Interaction ◽  
Genes Encoding

We set up a large-scale suppression subtractive hybridization (SSH) approach to identify Medicago truncatula genes differentially expressed at different stages of the symbiotic interaction with Sinorhizobium meliloti, with a particular interest for regulatory genes. We constructed 7 SSH libraries covering successive stages from Nod factor signal transduction to S. meliloti infection, nodule organogenesis, and functioning. Over 26,000 clones were differentially screened by two rounds of macroarray hybridizations. In all, 3,340 clones, corresponding to genes whose expression was potentially affected, were selected, sequenced, and ordered into 2,107 tentative gene clusters, including 767 MtS clusters corresponding to new M. truncatula genes. In total, 52 genes encoding potential regulatory proteins, including transcription factors (TFs) and other elements of signal transduction cascades, were identified. The expression pattern of some of them was analyzed by quantitative reverse-transcription polymerase chain reaction in wild-type and in Nod¯ M. truncatula mutants blocked before or after S. meliloti infection. Three genes, coding for TFs of the bHLH and WRKY families and a C2H2 zinc-finger protein, respectively, were found to be upregulated, following S. meliloti inoculation, in the infection-defective mutant lin, whereas the bHLH gene also was expressed in the root-hair-curling mutant hcl. The potential role of these genes in early symbiotic steps is discussed.

Identification of stage-specifically expressed genes of Trichinella spiralis by suppression subtractive hybridization

Parasitology ◽  
2007 ◽  
Vol 134 (10) ◽  
pp. 1443-1455 ◽  
Author(s):  
M. Y. LIU ◽  
X. L. WANG ◽  
B. Q. FU ◽  
C. Y. LI ◽  
X. P. WU ◽  
...  
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Serine Proteases ◽  
Zinc Finger Protein ◽  
Trichinella Spiralis ◽  
Gene Families ◽  
Subtractive Hybridization ◽  
Cdna Clones ◽  
Dnase Ii ◽  
Finger Protein ◽  
Old Adult

SUMMARYNewborn larvae (NBL) and adult (Ad) stage-specifically expressed genes or members of gene families of Trichinella spiralis were identified by suppression subtractive hybridization (SSH)†. Six cDNA clones were identified as NBL stage-specific, including 1 member of the T. spiralis gene family encoding glutamic acid-rich proteins, 2 clones encoding novel serine proteases, 2 closely related clones encoding proteins that are members of a deoxyribonuclease II (DNase II)-like family and 1 clone with no similarity to known genes. Four stage-specific clones encoding homologues of retinoid X receptor, caveolin, C2H2 type zinc finger protein and a putative protein with no homology to known sequences were obtained from 3-day-old adult worms. One gene specifically up-regulated in the 5-day-old adult worms encoding a putative cuticle collagen was also identified.

scholarly journals Suppression Subtractive Hybridization and Differential Screening Reveals Endodormancy-associated Expression of an SVP/AGL24-type MADS-box Gene in Lateral Vegetative Buds of Japanese Apricot

2008 ◽  
Vol 133 (5) ◽  
pp. 708-716 ◽  
Author(s):  
Hisayo Yamane ◽  
Yukinobu Kashiwa ◽  
Tomomi Ooka ◽  
Ryutaro Tao ◽  
Keizo Yonemori
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Subtractive Hybridization ◽  
Differential Screening ◽  
Gene Pools ◽  
Mads Box ◽  
Japanese Apricot ◽  
Cell Wall Modification ◽  
Gibberellin Metabolism ◽  
Lateral Buds ◽  
Mirror Orientation Selection

To understand the molecular basis of the endodormancy of buds of perennial plants, we searched for the genes that are expressed preferentially in endodormant lateral buds of the deciduous fruit tree japanese apricot (Prunus mume Sieb. et Zucc.) using suppression subtractive hybridization with mirror orientation selection (SSH/MOS). We generated two SSH/MOS libraries containing gene pools that are expressed preferentially in endodormant buds in comparison with paradormant or ecodormant buds to search for the genes that are upregulated by endodormancy induction or down-regulated by endodormancy release, respectively. Differential screening and sequencing indicated that genes involved in gibberellin metabolism, stress resistance, cell wall modification, and signal transduction, such as transcription factors, are upregulated in endodormant buds. After a further expression survey and full-length cDNA cloning, we found that a gene similar to the SVP/AGL24-type MADS-box transcription factor showed endodormancy-associated expression. Seasonal expression analysis suggested that the SVP/AGL24 homolog in japanese apricot might be involved in endodormancy regulation of its lateral buds.

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