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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 Jun; 13(5):648-63.PB

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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Publisher Full Text (DOI)

Authors+Show Affiliations

Maccaferri M
Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
Ricci A
Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
Salvi S
Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
Milner SG
Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
Noli E
Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
Martelli PL
Biocomputing Group, University of Bologna, Bologna, Italy.
Casadio R
Biocomputing Group, University of Bologna, Bologna, Italy.
Akhunov E
Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
Scalabrin S
Istituto di Genomica Applicata, Udine, Italy. Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy.
Vendramin V
Istituto di Genomica Applicata, Udine, Italy. Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy.
Ammar K
CIMMYT Carretera Mexico, Texcoco, Mexico.
Blanco A
Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy.
Desiderio F
Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy.
Distelfeld A
Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel.
Dubcovsky J
Department of Plant Sciences, University of California, Davis, CA, USA. Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Fahima T
Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel.
Faris J
USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA.
Korol A
Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel.
Massi A
Società Produttori Sementi Bologna (PSB), Argelato, Italy.
Mastrangelo AM
Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy.
Morgante M
Istituto di Genomica Applicata, Udine, Italy. Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy.
Pozniak C
Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
N'Diaye A
Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
Xu S
USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA.
Tuberosa R
Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.

MeSH

BreedingChromosome MappingChromosomes, PlantGenetic LinkageGenome, PlantGenomicsPolymorphism, Single NucleotideQuantitative Trait LociTetraploidyTriticum

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25424506

Citation

Maccaferri, Marco, et al. "A High-density, SNP-based Consensus Map of Tetraploid Wheat as a Bridge to Integrate Durum and Bread Wheat Genomics and Breeding." Plant Biotechnology Journal, vol. 13, no. 5, 2015, pp. 648-63.
Maccaferri M, Ricci A, Salvi S, et al. 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(5):648-63.
Maccaferri, M., Ricci, A., Salvi, S., Milner, S. G., Noli, E., Martelli, P. L., 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., ... Tuberosa, R. (2015). A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnology Journal, 13(5), 648-63. https://doi.org/10.1111/pbi.12288
Maccaferri M, et al. 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(5):648-63. PubMed PMID: 25424506.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. AU - Maccaferri,Marco, AU - Ricci,Andrea, AU - Salvi,Silvio, AU - Milner,Sara Giulia, AU - Noli,Enrico, AU - Martelli,Pier Luigi, AU - Casadio,Rita, AU - Akhunov,Eduard, AU - Scalabrin,Simone, AU - Vendramin,Vera, AU - Ammar,Karim, AU - Blanco,Antonio, AU - Desiderio,Francesca, AU - Distelfeld,Assaf, AU - Dubcovsky,Jorge, AU - Fahima,Tzion, AU - Faris,Justin, AU - Korol,Abraham, AU - Massi,Andrea, AU - Mastrangelo,Anna Maria, AU - Morgante,Michele, AU - Pozniak,Curtis, AU - N'Diaye,Amidou, AU - Xu,Steven, AU - Tuberosa,Roberto, Y1 - 2014/11/26/ PY - 2014/08/05/received PY - 2014/09/26/revised PY - 2014/10/03/accepted PY - 2014/11/27/entrez PY - 2014/11/27/pubmed PY - 2016/2/20/medline KW - anchor markers KW - chromosome translocation events KW - consensus map KW - durum wheat KW - genomics-assisted breeding KW - homeologous loci KW - single nucleotide polymorphism SP - 648 EP - 63 JF - Plant biotechnology journal JO - Plant Biotechnol J VL - 13 IS - 5 N2 - 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. SN - 1467-7652 UR - https://www.unboundmedicine.com/medline/citation/25424506/A_high_density_SNP_based_consensus_map_of_tetraploid_wheat_as_a_bridge_to_integrate_durum_and_bread_wheat_genomics_and_breeding_ DB - PRIME DP - Unbound Medicine ER -