Association mapping of yellow pigment in an elite collection of durum wheat cultivars and breeding lines

Genome. 2008 Dec;51(12):1016-25. doi: 10.1139/G08-083.


Association mapping (AM) is an alternative or complementary strategy to QTL mapping for describing associations between genotype and phenotype based on linkage disequilibrium (LD). Yellow pigment (YP), an important end-use quality trait in durum wheat (Triticum turgidum L. var. durum), was evaluated to determine the ability of AM to identify previously published QTL and to identify genomic regions for further genetic dissection. The YP concentration was determined for 93 durum wheat accessions sampled from a variety of geographic origins. Analysis of population structure using distance- and model-based estimates indicated the presence of five subpopulations. Using subpopulation assignments as covariates, significant (P < 0.05) marker-trait associations for YP were detected on all chromosomes of the durum genome. Using AM, genomic regions housing known YP QTL were confirmed, most notably the group 7 chromosomes. In addition, several markers on the group 1, 2, and 3 chromosomes were identified where QTL have yet to be reported. A phytoene synthase gene, Psy1-B1, a potential candidate gene for YP, was significantly associated with YP and was in strong LD with microsatellite markers on the distal end of 7BL. Our results demonstrated that AM complemented traditional QTL mapping techniques and identified novel QTL that should be the target of further genetic dissection.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Breeding* / methods
  • Chromosome Mapping
  • Chromosomes, Plant
  • Genetic Variation / physiology
  • Linkage Disequilibrium
  • Osmolar Concentration
  • Phylogeny
  • Pigments, Biological / analysis
  • Pigments, Biological / genetics*
  • Quantitative Trait Loci
  • Selection, Genetic
  • Triticum / genetics*


  • Pigments, Biological