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. 2014 May 8:15:54.
doi: 10.1186/1471-2156-15-54.

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

Hugo R Oliveira  1 , Jenny Hagenblad, Matti W Leino, Fiona J Leigh, Diane L Lister, Leonor Penã-Chocarro, Martin K Jones
Affiliations

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

Hugo R Oliveira et al. BMC Genet. .

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.

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Figures

Figure 1
Figure 1
Linkage disequilibrium (r2) between linked markers, located 20 cM or less apart, plotted against the genetic distance with a non-linear regression line fitted to the values. a) All tetraploid wheats; b) durum landraces only.
Figure 2
Figure 2
Results of Principal Component Analysis (PCA) of tetraploid wheat accessions based on 369 SNP markers. Each dot represents the location of a wheat accession along the first two principal components. Black = wild emmer; purple = landrace emmer; red = durum; orange = rivet.
Figure 3
Figure 3
Structure plot of a) tetraploid wheats in the K = 2 model and b) durums only in the K = 4 model. Each accession is depicted by a vertical line segmented into K coloured sections. The length of each section is proportional to the estimated membership coefficient (Q) of the accession to each one of the K number of clusters. Accessions are assembled by a) taxon and b) country of origin.
Figure 4
Figure 4
Results of Principal Component Analysis of durum wheat landrace accessions coloured and labelled by country of origin. PCA was based on the allele frequencies of 369 SNP markers.
Figure 5
Figure 5
Results of Principal Component Analysis of all wheats (excluding Yumai 34, Anahuac 75 and Ukrainka 3). Black = wild emmer; purple = landrace emmer; red = durum; orange = rivet; blue = landrace bread wheat; green = commercial bread wheat a) First and second PCs, b) third and fourth PCs.
Figure 6
Figure 6
Results of Structure analysis of the complete set of wheat accessions based on 369 SNPs for a) K = 2 model, b) K = 5 model.
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