Your browser doesn't support javascript.
loading
cDNA-AFLP-based genetical genomics in cotton fibers.
Claverie, Michel; Souquet, Marlène; Jean, Janine; Forestier-Chiron, Nelly; Lepitre, Vincent; Pré, Martial; Jacobs, John; Llewellyn, Danny; Lacape, Jean-Marc.
Afiliação
  • Claverie M; UMR AGAP, CIRAD, Avenue Agropolis, 34398, Montpellier, France.
Theor Appl Genet ; 124(4): 665-83, 2012 Mar.
Article em En | MEDLINE | ID: mdl-22080217
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 × 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.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Marcadores Genéticos / DNA Complementar / Gossypium / Perfilação da Expressão Gênica / Genômica / Análise do Polimorfismo de Comprimento de Fragmentos Amplificados Tipo de estudo: Prognostic_studies Idioma: En Revista: Theor Appl Genet Ano de publicação: 2012 Tipo de documento: Article País de afiliação: França País de publicação: Alemanha

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Marcadores Genéticos / DNA Complementar / Gossypium / Perfilação da Expressão Gênica / Genômica / Análise do Polimorfismo de Comprimento de Fragmentos Amplificados Tipo de estudo: Prognostic_studies Idioma: En Revista: Theor Appl Genet Ano de publicação: 2012 Tipo de documento: Article País de afiliação: França País de publicação: Alemanha