Cargando…

Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton

BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information a...

Descripción completa

Detalles Bibliográficos
Autores principales: Lai, Deyong, Li, Huaizhu, Fan, Shuli, Song, Meizhen, Pang, Chaoyou, Wei, Hengling, Liu, Junjie, Wu, Dong, Gong, Wenfang, Yu, Shuxun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232235/
https://www.ncbi.nlm.nih.gov/pubmed/22163052
http://dx.doi.org/10.1371/journal.pone.0028676
_version_ 1782218340964499456
author Lai, Deyong
Li, Huaizhu
Fan, Shuli
Song, Meizhen
Pang, Chaoyou
Wei, Hengling
Liu, Junjie
Wu, Dong
Gong, Wenfang
Yu, Shuxun
author_facet Lai, Deyong
Li, Huaizhu
Fan, Shuli
Song, Meizhen
Pang, Chaoyou
Wei, Hengling
Liu, Junjie
Wu, Dong
Gong, Wenfang
Yu, Shuxun
author_sort Lai, Deyong
collection PubMed
description BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST–simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis.
format Online
Article
Text
id pubmed-3232235
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-32322352011-12-09 Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton Lai, Deyong Li, Huaizhu Fan, Shuli Song, Meizhen Pang, Chaoyou Wei, Hengling Liu, Junjie Wu, Dong Gong, Wenfang Yu, Shuxun PLoS One Research Article BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST–simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis. Public Library of Science 2011-12-06 /pmc/articles/PMC3232235/ /pubmed/22163052 http://dx.doi.org/10.1371/journal.pone.0028676 Text en Lai et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Lai, Deyong
Li, Huaizhu
Fan, Shuli
Song, Meizhen
Pang, Chaoyou
Wei, Hengling
Liu, Junjie
Wu, Dong
Gong, Wenfang
Yu, Shuxun
Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton
title Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton
title_full Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton
title_fullStr Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton
title_full_unstemmed Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton
title_short Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton
title_sort generation of ests for flowering gene discovery and ssr marker development in upland cotton
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232235/
https://www.ncbi.nlm.nih.gov/pubmed/22163052
http://dx.doi.org/10.1371/journal.pone.0028676
work_keys_str_mv AT laideyong generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT lihuaizhu generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT fanshuli generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT songmeizhen generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT pangchaoyou generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT weihengling generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT liujunjie generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT wudong generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT gongwenfang generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton
AT yushuxun generationofestsforfloweringgenediscoveryandssrmarkerdevelopmentinuplandcotton