A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

Authors: MACCAFERRI, MARCO - Universita Di Bologna; CANE, MARIA - Universita Di Bologna; SANGUINETI, MARIA - Universita Di Bologna; SALVI, SILVIO - Universita Di Bologna; COLALONGO, MARIA - Universita Di Bologna; MASSI, ANDREA - Societa Produttori Sementi (PSB); CLARKE, FRAN - Agriculture And Agri-Food Canada; KNOX, RON - Agriculture And Agri-Food Canada; POZNIAK, CURTIS - University Of Saskatchewan; CLARKE, JOHN - University Of Saskatchewan; FAHIMA, TZION - University Of Haifa; DUBCOVSKY, JORGE - University Of California; Xu, Steven; AMMAR, KARIM - International Maize & Wheat Improvement Center (CIMMYT); KARSAI, ILDIKO - Hungarian Academy Of Sciences; VIDA, GYULA - Hungarian Academy Of Sciences; TUBEROSA, ROBERTO - Universita Di Bologna

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/23/2014
Publication Date: 10/7/2014
Publication URL: http://handle.nal.usda.gov/10113/60138
Citation: Maccaferri, M., Cane, M.A., Sanguineti, M.C., Salvi, S., Colalongo, M.C., Massi, A., Clarke, F., Knox, R., Pozniak, C.J., Clarke, J.M., Fahima, T., Dubcovsky, J., Xu, S., Ammar, K., Karsai, I., Vida, G., Tuberosa, R. 2014. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. BMC Genomics. 15:873.

Interpretive Summary: A genetic linkage map in a plant species, which shows the position and orders of known genes and genetic markers along each chromosome, is constructed from a single population of individuals derived from a hybrid between two parental cultivars or lines. However, a consensus map is created based on the ordering of genes and markers from many populations. In modern wheat crops, a consensus map of hexaploid bread wheat has been widely used as a reference for wheat genomics studies for more than a decade, but a dense and accurate consensus map specific for tetraploid durum wheat has not been available. Here, we report the construction of a consensus map of durum wheat using the molecular marker data from 14 mapping populations of durum wheat. In this study, we first established a consensus framework map of 598 anchor markers (common across populations) using high quality genotypic data from six core populations. We then inserted additional markers based on the markers common to the consensus framework map from eight additional populations. Integration of unique markers from the 14 maps allowed us to position a total of 2,575 molecular markers in a consensus map. The consensus map was used to carry out a whole-genome search for genetic difference and association to heading date in 183 durum cultivars and lines adapted to the Mediterranean area. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. The consensus map presented here was used as a reference for genetic diversity and mapping analyses in durum wheat, providing nearly complete genome coverage and even marker density. The consensus map will facilitate genetic mapping, marker implementation, functional genomics and marker-assisted improvement of durum wheat.

Technical Abstract: Genomics applications in durum (Triticum durum Desf.) 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. Here, we reported the construction of a consensus framework map of durum wheat using the genotypic data from 14 mapping populations of tetraploid wheat. In this study, high quality genotypic data from six core recombinant inbred populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology(R) (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' rank correlation r 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. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. 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. The consensus map also provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.