title: Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population.
abstract: BACKGROUND
  Cotton fibers (produced by Gossypium species) are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb) and G. hirsutum (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh x Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years.
  
  
  RESULTS
  The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3.
  
  
  CONCLUSIONS
  Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.
authors.affiliation: UMR-DAP, CIRAD, Montpellier, France. marc.lacape@cirad.fr
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Lacape
authors.forename: Danny
authors.initials: D
authors.lastname: Llewellyn
authors.forename: John
authors.initials: J
authors.lastname: Jacobs
authors.forename: Tony
authors.initials: T
authors.lastname: Arioli
authors.forename: David
authors.initials: D
authors.lastname: Becker
authors.forename: Steve
authors.initials: S
authors.lastname: Calhoun
authors.forename: Yves
authors.initials: Y
authors.lastname: Al-Ghazi
authors.forename: Shiming
authors.initials: S
authors.lastname: Liu
authors.forename: Oumarou
authors.initials: O
authors.lastname: Palaï
authors.forename: Sophie
authors.initials: S
authors.lastname: Georges
authors.forename: Marc
authors.initials: M
authors.lastname: Giband
authors.forename: Henrique
authors.initials: H
authors.lastname: de Assunção
authors.forename: Paulo Augusto Vianna
authors.initials: PA
authors.lastname: Barroso
authors.forename: Michel
authors.initials: M
authors.lastname: Claverie
authors.forename: Gérard
authors.initials: G
authors.lastname: Gawryziak
authors.forename: Janine
authors.initials: J
authors.lastname: Jean
authors.forename: Michèle
authors.initials: M
authors.lastname: Vialle
authors.forename: Christopher
authors.initials: C
authors.lastname: Viot
mesh_terms: D000704:Analysis of Variance; D001947:Breeding; D002874:Chromosome Mapping; D016000:Cluster Analysis; D032561:Cotton Fiber / Q000592:standards*; D004777:Environment; D014644:Genetic Variation; D003368:Gossypium / Q000235:genetics*; D010641:Phenotype; D040641:Quantitative Trait Loci