Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton

Lacape Jean-Marc, Claverie Michel, Vidal Ramon Oliveira, Carazzolle Marcelo Falsarella, Guimarães Pereira Gonçalo Amarante, Ruiz Manuel, Pré Martial, Llewellyn Danny, Al-Ghazi Yves, Jacobs John, Dereeper Alexis, Huguet Stéphanie, Giband Marc, Lanaud Claire. 2012. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PloS One, 7 (11):e48855, 16 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
[img] Published version - Anglais
Use under authorization by the author or CIRAD.

Télécharger (1MB)


Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Gossypium hirsutum, Gossypium barbadense, Hybridation interspécifique, Expression des gènes, Fibre végétale, Développement biologique, Séquence nucléotidique, Gène, ADN, Transcription

Mots-clés complémentaires : QTL, Séquencage, Fibre de coton

Classification Agris : F30 - Plant genetics and breeding
F62 - Plant physiology - Growth and development

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Lacape Jean-Marc, CIRAD-BIOS-UMR AGAP (FRA)
  • Claverie Michel
  • Vidal Ramon Oliveira, UNICAMP (BRA)
  • Carazzolle Marcelo Falsarella, UNICAMP (BRA)
  • Guimarães Pereira Gonçalo Amarante, UNICAMP (BRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
  • Pré Martial
  • Llewellyn Danny, CSIRO (AUS)
  • Al-Ghazi Yves, CSIRO (AUS)
  • Jacobs John, Bayer (BEL)
  • Dereeper Alexis, IRD (FRA)
  • Huguet Stéphanie, INRA (FRA)
  • Giband Marc, CIRAD-BIOS-UMR AGAP (BRA)
  • Lanaud Claire, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6411-7310

Autres liens de la publication

Source : Cirad - Agritrop (

View Item (staff only) View Item (staff only)

[ Page générée et mise en cache le 2020-10-07 ]