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Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
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.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
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