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

Hugo R Oliveira,Matti W Leino,Martin K Jones,Jenny Hagenblad,Leonor Penã-Chocarro,Fiona J Leigh,Diane L Lister

doi:10.1186/1471-2156-15-54

Abstract

BackgroundSingle 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.ResultsWe 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.ConclusionsSNP 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.

Highlights

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 rapid development of sequencing methods recently enabled the completion of the wheat genome sequence [5], which has led to the development of SNP panels [6,7]
These genome-wide SNP panels allow wheat breeding to be addressed at a whole new level, but analysis of the evolution of domesticated wheat species can be approached on a genomic scale

Summary

Introduction

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. The rapid development of sequencing methods recently enabled the completion of the wheat genome sequence [5], which has led to the development of SNP panels [6,7] These genome-wide SNP panels allow wheat breeding to be addressed at a whole new level, but analysis of the evolution of domesticated wheat species can be approached on a genomic scale. Bread wheat is believed to have arisen from a cross between a domesticated tetraploid wheat and the diploid wild grass Aegilops tauschii [8] it is not clear whether the tetraploid ancestor was the naked durum or the hulled emmer [11,13,14]

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