Open Access Highly Accessed Research article

Wheat in the Mediterranean revisited – tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers

Hugo R Oliveira123*, Jenny Hagenblad1, Matti W Leino13, Fiona J Leigh4, Diane L Lister5, Leonor Penã-Chocarro6 and Martin K Jones5

Author Affiliations

1 IFM Biology, Linköping University, Linköping SE-581 83, Sweden

2 CIBIO-Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão. R. Padre Armando Quintas, Vairão 4485-661, Portugal

3 Nordiska Museet, Swedish Museum of Cultural History, Julita SE-643 98, Sweden

4 The John Bingham Laboratory – National Institute for Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB3 0LE, UK

5 McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK

6 Escuela Española de Historia y Arqueología en Roma-CSIC, Via di Torre Argentina 18, Roma 00186, Italy

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BMC Genetics 2014, 15:54  doi:10.1186/1471-2156-15-54

Published: 8 May 2014

Additional files

Additional file 1:

SNPs used (primers, mapping and Blast information retrieved from [[27]]). Markers that were removed before the final analysis are highlighted in red.

Format: XLSX Size: 176KB Download file

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Additional file 2:

Accessions used in this study. Tetraploid landrace accessions were originally screened for this work. The remaining accessions were screened by the Crop Improvement Research Club, as described in [27] and in [24] and genotypes for these accessions is publically available at these references.

Format: XLSX Size: 177KB Download file

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Additional file 3:

List of SNPs mapping to the D genome that successfully amplified in some or all of the tetraploid test panel accessions described in this work.

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Additional file 4:

Distribution of linkage disequilibrium values calculated between pairs of loci located on different chromosomes. a) All values of r2, b) Values of r2 from 0.2 and higher.

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Additional file 5:

Linkage disequilibrium (r2) between linked markers plotted against genetic distance with a non-linear regression line fitted to the values. a) All tetraploid wheats; b) all durum landraces.

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Additional file 6:

Results of Structure analysis of wheat accessions based on 369 SNPs using the “admixture” option (top panel) and the “ no admixture” option (bottom panel) for a) K = 2 model with the durum accessions; b) K = 4 model with durum accessions; c) K = 2 model with the complete set of accessions; d) K = 5 model with the complete set of accessions.

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Additional file 7:

Results of Structure analysis of the K =3 model for the tetraploid wheat set.

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Additional file 8:

Results of Structure analysis of the set of durum accessions for the K = 2 model based on a) 369 SNPs and b) 29 SSRs respectively.

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Additional file 9:

Results of Principal Component Analysis of the complete set of wheat accessions. The distinctiveness of Yumai 34, Anahuac 75 and Ukrainka is evident (top left corner). Black = wild emmer; purple = landrace emmer; red = durum; orange = rivet; blue = landrace bread wheat; green = commercial bread wheat.

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Additional file 10:

Results of Structure analysis of the complete set of wheat accessions for the a) K = 8 model and b) K = 9 model.

Format: PDF Size: 7MB Download file

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