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

BMC Genetics

Martin K Jones⁵  Leonor Penã-Chocarro¹  Diane L Lister⁵  Fiona J Leigh²  Matti W Leino⁴  Jenny Hagenblad³  Hugo R Oliveira⁴ 

[1] Escuela Española de Historia y Arqueología en Roma-CSIC, Via di Torre Argentina 18, Roma 00186, Italy;The John Bingham Laboratory – National Institute for Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB3 0LE, UK;IFM Biology, Linköping University, Linköping SE-581 83, Sweden;Nordiska Museet, Swedish Museum of Cultural History, Julita SE-643 98, Sweden;McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK

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

Others  :  866257
DOI  :  10.1186/1471-2156-15-54

 received in 2014-01-20, accepted in 2014-04-22,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Oliveira et al.; licensee BioMed Central Ltd.

【 图 表 】

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