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Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery

Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we r...

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Autores principales: Guo, Baozhu, Chen, Xiaoping, Hong, Yanbin, Liang, Xuanqiang, Dang, Phat, Brenneman, Tim, Holbrook, Corley, Culbreath, Albert
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703745/
https://www.ncbi.nlm.nih.gov/pubmed/19584933
http://dx.doi.org/10.1155/2009/715605
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author Guo, Baozhu
Chen, Xiaoping
Hong, Yanbin
Liang, Xuanqiang
Dang, Phat
Brenneman, Tim
Holbrook, Corley
Culbreath, Albert
author_facet Guo, Baozhu
Chen, Xiaoping
Hong, Yanbin
Liang, Xuanqiang
Dang, Phat
Brenneman, Tim
Holbrook, Corley
Culbreath, Albert
author_sort Guo, Baozhu
collection PubMed
description Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT-C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high-quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST-SSRs identified. A total of 290 new EST-based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense-related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS-LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to ES768453.
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spelling pubmed-27037452009-07-07 Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery Guo, Baozhu Chen, Xiaoping Hong, Yanbin Liang, Xuanqiang Dang, Phat Brenneman, Tim Holbrook, Corley Culbreath, Albert Int J Plant Genomics Research Article Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT-C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high-quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST-SSRs identified. A total of 290 new EST-based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense-related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS-LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to ES768453. Hindawi Publishing Corporation 2009 2009-06-24 /pmc/articles/PMC2703745/ /pubmed/19584933 http://dx.doi.org/10.1155/2009/715605 Text en Copyright © 2009 Baozhu Guo et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Guo, Baozhu
Chen, Xiaoping
Hong, Yanbin
Liang, Xuanqiang
Dang, Phat
Brenneman, Tim
Holbrook, Corley
Culbreath, Albert
Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery
title Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery
title_full Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery
title_fullStr Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery
title_full_unstemmed Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery
title_short Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery
title_sort analysis of gene expression profiles in leaf tissues of cultivated peanuts and development of est-ssr markers and gene discovery
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703745/
https://www.ncbi.nlm.nih.gov/pubmed/19584933
http://dx.doi.org/10.1155/2009/715605
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