title: Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development.
abstract: QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA.
authors.forename: Junkang
authors.initials: J
authors.lastname: Rong
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
authors.forename: Vijay N
authors.initials: VN
authors.lastname: Waghmare
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Pierce
authors.forename: Peng W
authors.initials: PW
authors.lastname: Chee
authors.forename: Xavier
authors.initials: X
authors.lastname: Draye
authors.forename: Yehoshua
authors.initials: Y
authors.lastname: Saranga
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Wright
authors.forename: Thea A
authors.initials: TA
authors.lastname: Wilkins
authors.forename: O Lloyd
authors.initials: OL
authors.lastname: May
authors.forename: C Wayne
authors.initials: CW
authors.lastname: Smith
authors.forename: John R
authors.initials: JR
authors.lastname: Gannaway
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D002874:Chromosome Mapping; D032561:Cotton Fiber; D003433:Crosses, Genetic; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D018745:Genome, Plant; D003368:Gossypium / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D005810:Multigene Family; D009154:Mutation; D010641:Phenotype; D011123:Polyploidy; D040641:Quantitative Trait Loci
chemical_list: D018744:DNA, Plant