Document Detail


Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.
MedLine Citation:
PMID:  23166598     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Cotton (Gossypium) fiber is the most prevalent natural product used in the textile industry. The two major cultivated species, G. hirsutum (Gh) and G. barbadense (Gb), are allotetraploids with contrasting fiber quality properties. To better understand the molecular basis for their fiber differences, EST pyrosequencing was used to document the fiber transcriptomes at two key development stages, 10 days post anthesis (dpa), representing the peak of fiber elongation, and 22 dpa, representing the transition to secondary cell wall synthesis. The 617,000 high quality reads (89% of the total 692,000 reads) from 4 libraries were assembled into 46,072 unigenes, comprising 38,297 contigs and 7,775 singletons. Functional annotation of the unigenes together with comparative digital gene expression (DGE) revealed a diverse set of functions and processes that were partly linked to specific fiber stages. Globally, 2,770 contigs (7%) showed differential expression (>2-fold) between 10 and 22 dpa (irrespective of genotype), with 70% more highly expressed at 10 dpa, while 2,248 (6%) were differentially expressed between the genotypes (irrespective of stage). The most significant genes with differential DGE at 10 dpa included expansins and lipid transfer proteins (higher in Gb), while at 22 dpa tubulins, cellulose, and sucrose synthases showed higher expression in Gb. DGE was compared with expression data of 10 dpa-old fibers from Affymetrix microarrays. Among 543 contigs showing differential expression on both platforms, 74% were consistent in being either over-expressed in Gh (242 genes) or in Gb (161 genes). Furthermore, the unigene set served to identify 339 new SSRs and close to 21,000 inter-genotypic SNPs. Subsets of 88 SSRs and 48 SNPs were validated through mapping and added 65 new loci to a RIL genetic map. The new set of fiber ESTs and the gene-based markers complement existing available resources useful in basic and applied research for crop improvement in cotton.
Authors:
Jean-Marc Lacape; Michel Claverie; Ramon O Vidal; Marcelo F Carazzolle; Gonçalo A Guimarães Pereira; Manuel Ruiz; Martial Pré; Danny Llewellyn; Yves Al-Ghazi; John Jacobs; Alexis Dereeper; Stéphanie Huguet; Marc Giband; Claire Lanaud
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2012-11-15
Journal Detail:
Title:  PloS one     Volume:  7     ISSN:  1932-6203     ISO Abbreviation:  PLoS ONE     Publication Date:  2012  
Date Detail:
Created Date:  2012-11-20     Completed Date:  2013-05-06     Revised Date:  2013-07-11    
Medline Journal Info:
Nlm Unique ID:  101285081     Medline TA:  PLoS One     Country:  United States    
Other Details:
Languages:  eng     Pagination:  e48855     Citation Subset:  IM    
Affiliation:
CIRAD, UMR AGAP, Montpellier, France. marc.lacape@cirad.fr
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MeSH Terms
Descriptor/Qualifier:
Age Factors
Agriculture / methods*
Base Sequence
Breeding / methods
Contig Mapping
Cotton Fiber*
DNA, Complementary / genetics
Expressed Sequence Tags
Gene Expression Profiling
Gene Expression Regulation, Developmental / genetics*
Gossypium / genetics*
High-Throughput Nucleotide Sequencing / methods
Microarray Analysis
Molecular Sequence Annotation
Molecular Sequence Data
Polymorphism, Single Nucleotide / genetics
Species Specificity
Transcriptome*
Chemical
Reg. No./Substance:
0/DNA, Complementary
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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