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Wheat in the Mediterranean revisited - tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. CIBIO-Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão. R. Padre Armando Quintas, Vairão 4485-661, Portugal .
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
National Institute Agriculture Bot NIAB, England .
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2014 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 15, no 54Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
BioMed Central , 2014. Vol. 15, no 54
Keyword [en]
Ascertainment bias; Domestication; Linkage disequilibrium; Population structure; Single Nucleotide Polymorphism; Triticum turgidum
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Engineering and Technology
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URN: urn:nbn:se:liu:diva-108171DOI: 10.1186/1471-2156-15-54ISI: 000336862000001OAI: oai:DiVA.org:liu-108171DiVA: diva2:729567
Available from: 2014-06-26 Created: 2014-06-26 Last updated: 2017-12-05

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Hagenblad, JennyLeino, Matti

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