A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding

Authors: MACCAFERRI, MARCO - University Of Bologna; RICCI, ANDREW - University Of Bologna; SALVI, SILVIO - University Of Bologna; MILNER, SARA - University Of Bologna; NOLI, ENRICO - University Of Bologna; MARTELLI, PIER - University Of Bologna; CASADIO, RITA - University Of Bologna; AKHUNOV, EDUARD - Kansas State University; AMMAR, KARIM - International Maize & Wheat Improvement Center (CIMMYT); BLANCO, ANTONIO - Universita Di Bari; DESIDERIO, FRANCESCA - Agricultural Research Council (CRA); DISTELFELD, ASSAF - Tel Aviv University; DUBCOVSKY, JORGE - University Of California; FAHIMA, TZION - University Of Haifa; Faris, Justin; KOROL, ABRAHAM - University Of Haifa; MASSI, ANDREA - Societa Produttori Sementi (PSB); MASTRANGELO, ANNA - Agricultural Research Council (CRA); MORGANTE, MICHELE - Istituto Di Genomica Applicata (IGA); POZNIAK, CURTIS - University Of Saskatchewan; Xu, Steven; TUBEROSA, ROBERTO - University Of Bologna

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2014
Publication Date: 11/26/2014
Publication URL: http://handle.nal.usda.gov/10113/60958
Citation: 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.D., Korol, A., Massi, A., Mastrangelo, A.M., Morgante, M., Pozniak, C., N'Diaye, A., Xu, S., 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. 13:648-663.

Interpretive Summary: Consensus linkage maps, which show the position and orders of known genes and genetic markers along each chromosome, are developed using multiple populations each comprised of individuals derived from a hybrid between two parental cultivars or lines. Consensus linkage maps are important tools for analyzing the genomes of crop plants. Although a high-density consensus map was recently developed for bread wheat, one has not been constructed for durum wheat. In this study, we assembled a consensus map of durum wheat using the marker data from 13 independent populations. The consensus map harbored 30,144 molecular markers and spanned 2,600 map units. The consensus map is different from the typical linkage maps developed from a single population in its high-density marker coverage with no large gaps between adjacent markers. Comparisons with the bread wheat consensus map revealed the value of this map for mapping markers and genes in both durum and bread wheat. In this study, we also used this consensus map to infer target genes, evaluate the relationship between the two sub-genomes of tetraploid wheat, and trace ancient events of chromosome interchanges. Because most molecular markers used in this study were previously mapped in bread wheat, this consensus map will greatly facilitate the integration and exploitation of genes for wheat breeding purposes.

Technical Abstract: Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 datasets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their wild ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harbored 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 2,631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, showed no linkage gaps. Marker density per genetic distance unit peaked at centromeric regions, likely reflecting both identity-by-descent relationships among parents and recombination rates. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping markers and genes of the A and B genomes in 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 non-nominal 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.