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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

Abstract

Background

Single Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat.

Results

We genotyped more than 100 tetraploid wheat landraces and wild emmer wheat accessions, some of which had previously been screened with SSR markers, for an existing SNP panel and obtained publically available genotypes for the same SNPs for hexaploid wheat varieties and landraces. Results showed that quantification of genetic diversity can be affected by ascertainment bias but that the effects of ascertainment bias can at least partly be alleviated by merging SNPs to haplotypes. Analyses of population structure and genetic differentiation show strong subdivision between the tetraploid wheat subspecies, except for durum and rivet that are not separable. A more detailed population structure of durum landraces could be obtained than with SSR markers. The results also suggest an emmer, rather than durum, ancestry of bread wheat and with gene flow from wild emmer.

Conclusions

SNP markers developed for elite cultivars show great potential for inferring population structure and can address evolutionary questions in landrace wheat. Issues of marker genome specificity and mapping need, however, to be addressed. Ascertainment bias does not seem to interfere with the ability of a SNP marker system developed for elite bread wheat accessions to detect population structure in other types of wheat.

Keywords:
Ascertainment bias; Domestication; Linkage disequilibrium; Population structure; Single Nucleotide Polymorphism; Triticum turgidum