Accéder directement au contenu Accéder directement à la navigation
Article dans une revue

cDNA-AFLP-based genetical genomics in cotton fibers

Abstract : Genetical genomics, or genetic analysis applied to gene expression data, has not been widely used in plants. We used quantitative cDNA-AFLP to monitor the variation in the expression level of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum 9 G. barbadense recombinant inbred lines (RILs). Two key fiber developmental stages, elongation (10 days post anthesis, dpa), and secondary cell wall thickening (22 dpa), were studied. Normalized intensity ratios of 3,263 and 1,201 transcript-derived fragments (TDFs) segregating over 88 RILs were analyzed for quantitative trait loci (QTL) mapping for the 10 and 22 dpa fibers, respectively. Two-thirds of all TDFs mapped between 1 and 6 eQTLs (LOD[3.5). Chromosome 21 had a higher density of eQTLs than other chromosomes in both data sets and, within chromosomes, hotspots of presumably trans-acting eQTLs were identified. The eQTL hotspots were compared to the location of phenotypic QTLs for fiber characteristics among the RILs, and several cases of co-localization were detected. Quantitative RT-PCR for 15 sequenced TDFs showed that 3 TDFs had at least one eQTL at a similar location to those identified by cDNA-AFLP, while 3 other TDFs mapped an eQTL at a similar location but with opposite additive effect. In conclusion, cDNA-AFLP proved to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling. Because TDFs are anonymous, further validation and interpretation (in silico analysis, qPCR gene profiling) of the eQTL and eQTL hotspots will be facilitated by the increasing availability of cDNA and genomic sequence resources in cotton. (Résumé d'auteur) AD -; ; CIRAD-PERSYST-UPR SCA (FRA); CIRAD-PERSYST-UMR Qualisud (FRA); CIRAD-BIOS-UMR PVBMT (REU); UM2 (FRA); Bayer (BEL); CSIRO (AUS); CIRAD-BIOS-UMR AGAP (FRA)
Mots-clés : fibre de coton GENOMIQUE
Type de document :
Article dans une revue
Liste complète des métadonnées
Déposant : Claire Tessier <>
Soumis le : vendredi 4 septembre 2015 - 16:50:57
Dernière modification le : mercredi 8 juillet 2020 - 17:24:04

Lien texte intégral



Michel Claverie, Marlène Souquet, Janine Jean, Nelly Forestier-Chiron, Vincent Lepitre, et al.. cDNA-AFLP-based genetical genomics in cotton fibers. TAG Theoretical and Applied Genetics, Springer Verlag, 2012, 124 (4), pp.665--683. ⟨10.1007/s00122-011-1738-x⟩. ⟨hal-01193231⟩



Consultations de la notice