title: A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.
abstract: Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Maccaferri
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Ricci
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Silvio
authors.initials: S
authors.lastname: Salvi
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Sara Giulia
authors.initials: SG
authors.lastname: Milner
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Noli
authors.affiliation: Biocomputing Group, University of Bologna, Bologna, Italy.
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Martelli
authors.affiliation: Biocomputing Group, University of Bologna, Bologna, Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
authors.forename: Eduard
authors.initials: E
authors.lastname: Akhunov
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.|Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Scalabrin
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.|Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy.
authors.forename: Vera
authors.initials: V
authors.lastname: Vendramin
authors.affiliation: CIMMYT Carretera Mexico, Texcoco, Mexico.
authors.forename: Karim
authors.initials: K
authors.lastname: Ammar
authors.affiliation: Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Blanco
authors.affiliation: Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Desiderio
authors.affiliation: Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Assaf
authors.initials: A
authors.lastname: Distelfeld
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, USA.|Howard Hughes Medical Institute, Chevy Chase, MD, USA.
authors.forename: Jorge
authors.initials: J
authors.lastname: Dubcovsky
authors.affiliation: Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel.
authors.forename: Tzion
authors.initials: T
authors.lastname: Fahima
authors.affiliation: USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Faris
authors.affiliation: Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel.
authors.forename: Abraham
authors.initials: A
authors.lastname: Korol
authors.affiliation: Società Produttori Sementi Bologna (PSB), Argelato, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Massi
authors.affiliation: Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Mastrangelo
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.|Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.affiliation: Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
authors.forename: Curtis
authors.initials: C
authors.lastname: Pozniak
authors.affiliation: Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
authors.forename: Amidou
authors.initials: A
authors.lastname: N'Diaye
authors.affiliation: USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Xu
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Tuberosa
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D008040:Genetic Linkage; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics; D057891:Tetraploidy; D014908:Triticum / Q000235:genetics*
keywords: anchor markers; chromosome translocation events; consensus map; durum wheat; genomics-assisted breeding; homeologous loci; single nucleotide polymorphism