title: A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping.
abstract: BACKGROUND
  Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.
  
  
  RESULTS
  High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.
  
  
  CONCLUSIONS
  The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.
authors.affiliation: Department of Agricultural Sciences (DipSA), Viale Fanin 44, University of Bologna, 40127 Bologna, Italy. marco.maccaferri@unibo.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Maccaferri
authors.forename: Maria Angela
authors.initials: MA
authors.lastname: Cane'
authors.forename: Maria C
authors.initials: MC
authors.lastname: Sanguineti
authors.forename: Silvio
authors.initials: S
authors.lastname: Salvi
authors.forename: Maria C
authors.initials: MC
authors.lastname: Colalongo
authors.forename: Andrea
authors.initials: A
authors.lastname: Massi
authors.forename: Fran
authors.initials: F
authors.lastname: Clarke
authors.forename: Ron
authors.initials: R
authors.lastname: Knox
authors.forename: Curtis J
authors.initials: CJ
authors.lastname: Pozniak
authors.forename: John M
authors.initials: JM
authors.lastname: Clarke
authors.forename: Tzion
authors.initials: T
authors.lastname: Fahima
authors.forename: Jorge
authors.initials: J
authors.lastname: Dubcovsky
authors.forename: Steven
authors.initials: S
authors.lastname: Xu
authors.forename: Karim
authors.initials: K
authors.lastname: Ammar
authors.forename: Ildikó
authors.initials: I
authors.lastname: Karsai
authors.forename: Gyula
authors.initials: G
authors.lastname: Vida
authors.forename: Roberto
authors.initials: R
authors.lastname: Tuberosa
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics; D015810:Linkage Disequilibrium; D040641:Quantitative Trait Loci / Q000235:genetics; D014908:Triticum / Q000235:genetics*