Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

Key message

High-throughput genotyping of Swiss bread wheat and spelt accessions revealed differences in their gene pools and identified bread wheat landraces that were not used in breeding.

Abstract

Genebanks play a pivotal role in preserving the genetic diversity present among old landraces and wild progenitors of modern crops and they represent sources of agriculturally important genes that were lost during domestication and in modern breeding. However, undesirable genes that negatively affect crop performance are often co-introduced when landraces and wild crop progenitors are crossed with elite cultivars, which often limit the use of genebank material in modern breeding programs. A detailed genetic characterization is an important prerequisite to solve this problem and to make genebank material more accessible to breeding. Here, we genotyped 502 bread wheat and 293 spelt accessions held in the Swiss National Genebank using a 15K wheat SNP array. The material included both spring and winter wheats and consisted of old landraces and modern cultivars. Genome- and sub-genome-wide analyses revealed that spelt and bread wheat form two distinct gene pools. In addition, we identified bread wheat landraces that were genetically distinct from modern cultivars. Such accessions were possibly missed in the early Swiss wheat breeding program and are promising targets for the identification of novel genes. The genetic information obtained in this study is appropriate to perform genome-wide association studies, which will facilitate the identification and transfer of agriculturally important genes from the genebank into modern cultivars through marker-assisted selection.

     

Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example

Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.     

Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat

Key message

A high level of genetic diversity was found in the A. E. Watkins bread wheat landrace collection. Genotypic information was used to determine the population structure and to develop germplasm resources.

Abstract

In the 1930s A. E. Watkins acquired landrace cultivars of bread wheat (Triticum aestivum L.) from official channels of the board of Trade in London, many of which originated from local markets in 32 countries. The geographic distribution of the 826 landrace cultivars of the current collection, here called the Watkins collection, covers many Asian and European countries and some from Africa. The cultivars were genotyped with 41 microsatellite markers in order to investigate the genetic diversity and population structure of the collection. A high level of genetic diversity was found, higher than in a collection of modern European winter bread wheat varieties from 1945 to 2000. Furthermore, although weak, the population structure of the Watkins collection reveals nine ancestral geographical groupings. An exchange of genetic material between ancestral groups before commercial wheat-breeding started would be a possible explanation for this. The increased knowledge regarding the diversity of the Watkins collection was used to develop resources for wheat research and breeding, one of them a core set, which captures the majority of the genetic diversity detected. The understanding of genetic diversity and population structure together with the availability of breeding resources should help to accelerate the detection of new alleles in the Watkins collection.     

Trends in Genetic Diversity Change of Spring Bread Wheat Cultivars Released in Russia in 1929–2003

Using genealogy analysis, we studied genetic diversity of 340 cultivars of spring bread wheat that were released on the territory of Russia in 1929–2003. Trends in the temporal change of genetic diversity were inferred from analysis of a set of n × m matrices, where n is the number of the released cultivars and m is the number of original ancestors. The pool of original ancestors of the spring bread wheat cultivars for the total period of study included 255 landraces, of which 88 were from the former USSR and modern Russia. The original ancestors showed great differences in their presence in the cultivar sets examined and, consequently, in their importance for the gene pool of Russian spring wheats. The distributions of contributions of dominant original ancestors to cultivar diversity were significantly different in different regions, indicating that the ancestors were specific for the cultivation conditions. During the last 75 years, the genetic diversity of the spring bread wheat cultivars has been increasing owing to the wide use of foreign material in Russian breeding programs. However, our analysis showed that about 60 landraces, including the Russian ones, were lost during the studied time period. The lost part makes up 35% of the gene pool of the Russian original ancestors. It is reasonable to assume that the lost landraces carried a gene complex f or adaptation to specific Russian environments. Specificity of the contributions of the original ancestors in the sets of cultivars produced in different breeding centers was established. A comparative analysis of genetic similarity of cultivars was carried out using coefficients of parentage. Significant differences in this parameter between breeding institutes and regions of cultivation were revealed.     

Microsatellite analysis of Aegilops tauschii germplasm

The highly polymorphic diploid grass Aegilops tauschii isthe D-genome donor to hexaploid wheat and represents a potential source for bread wheat improvement. In the present study microsatellite markers were used for germplasm analysis and estimation of the genetic relationship between 113 accessions of Ae. tauschii from the gene bank collection at IPK, Gatersleben. Eighteen microsatellite markers, developed from Triticum aestivum and Ae. tauschii sequences, were selected for the analysis. All microsatellite markers showed a high level of polymorphism. The number of alleles per microsatellite marker varied from 11 to 25 and a total of 338 alleles were detected. The number of alleles per locus in cultivated bread wheat germplasm had previously been found to be significantly lower. The highest levels of genetic diversity for microsatellite markers were found in accessions from the Caucasian countries (Georgia, Armenia and the Daghestan region of Russia) and the lowest in accessions from the Central Asian countries (Uzbekistan and Turkmenistan). Genetic dissimilarity values between accessions were used to produce a dendrogram of the relationships among the accessions. The result showed that all of the accessions could be distinguished and clustered into two large groups in accordance with their subspecies taxonomic classification. The pattern of clustering of the Ae. tauschii accessions is according to their geographic distribution. The data suggest that a relatively small number of microsatellites can be used to estimate genetic diversity in the germplasm of Ae. tauschii and confirm the good suitability of microsatellite markers for the analysis of germplasm collections. Received: 8 September 1999 / Accepted: 7 October 1999     

Analysis of Genetic Diversity of Spring Durum Wheat (<Emphasis Type="Italic">Triticum durum</Emphasis> Desf.) Cultivars Released in Russia in 1929–2004

Based on genealogical analysis, the genetic diversity of 78 spring durum wheat cultivars released in Russia in 1929–2004 have been examined. The temporal trends of change in diversity were studied using series of n × m matrices (where n is the number of the cultivars and m is the number of original ancestors) and calculating coefficients of parentage in sets of cultivars released in particular years. The pool of original ancestors of spring durum wheat cultivars includes 90 landraces and old varieties, more than a half (57%) of which originate from European countries, including Russia and Ukraine (45%). The original ancestors strongly differ in the frequency of presence in the cultivar pedigrees. Landraces Beloturka, Sivouska, Kubanka (T. durum Desf.), Transbaikalian emmer, Yaroslav emmer (T. dicoccum Schuebl.), Poltavka (T. aestivum L.), and the original ancestors of cultivars Kharkov 46, Narodnaya, and Melanopus 1932 enter in the pedigrees of more than half of cultivars created within the framework of various breeding programs. At that, their distribution by cultivars from different breeding centers strongly varies. Analysis of temporal dynamics of genetic diversity, based on genetic profiles and coefficients of parentage, has shown that the genetic diversity of Russian durum wheats increased during the period examined. Nevertheless, genetic erosion of the local material—a loss of approximately 20% of the pool of Russian original ancestors—has been found. The contribution of the original ancestors to the pedigrees of different cultivars, constructed in different breeding centers and recommended for cultivation in different regions, has been estimated. The variation of the released cultivars was highest in the Lower Volga region and lowest in the Ural region. In all, the lower threshold of genetic diversity in all regions does not reach the critical level, corresponding to the similarity of half-sibs. The set of modern cultivars included in the Russian Official List 2004 has a cluster structure.     

Detection of genetic diversity in closely related bread wheat using microsatellite markers

Wheat microsatellites (WMS) were used to estimate the extent of genetic diversity among 40 wheat cultivars and lines, including mainly European elite material. The 23 WMS used were located on 15 different chromosomes, and revealed a total of 142 alleles. The number of alleles ranged from 3 to 16, with an average of 6.2 alleles per WMS. The average dinucleotide repeat number ranged from 13 to 41. The correlation coefficient between the number of alleles and the average number of repeats was only slight (r _s = 0.55). Based on percentage difference a dendrogram is presented, calculated by the WMS-derived data. All but two of the wheat cultivars and lines could be distinguished. Some of the resulting groups are strongly related to the pedigrees of the appropriate cultivars. Values for co-ancestry (f) of 179 pairs of cultivars related by their pedigrees (f0.1) averaged 0.29. Genetic similarity (GS) based on WMS of the same pairs averaged 0.44. The rank correlation for these pairs was slight, with r _s = 0.55, but highly significant (P<0.001). The results suggest that a relatively small number of microsatellites can be used for the estimation of genetic diversity and cultivar identification in elite material of hexaploid bread wheat.     

A population of wheat multiple synthetic derivatives: an effective platform to explore,harness and utilize genetic diversity of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> for wheat improvement

Key message

The multiple synthetic derivatives platform described in this study will provide an opportunity for effective utilization of Aegilops tauschii traits and genes for wheat breeding.

Abstract

Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61. We named this population multiple synthetic derivatives (MSD). To validate the suitability of this population for wheat breeding and genetic studies, we randomly selected 400 MSD lines and genotyped them by using Diversity Array Technology sequencing markers. We scored black glume as a qualitative trait and heading time in two environments in Sudan as a quantitative trait. Our results showed high genetic diversity and less recombination which is expected from the nature of the population. Genome-wide association (GWA) analysis showed one QTL at the short arm of chromosome 1D different from those alleles reported previously indicating that black glume in the MSD population is controlled by new allele at the same locus. For heading time, from the two environments, GWA analysis revealed three QTLs on the short arms of chromosomes 2A, 2B and 2D and two on the long arms of chromosomes 5A and 5D. Using the MSD population, which represents the diversity of 43 Ae. tauschii accessions representing most of its natural habitat, QTLs or genes and desired phenotypes (such as drought, heat and salinity tolerance) could be identified and selected for utilization in wheat breeding.

     

Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004

Analysis of genetic diversity changes in existing gene pools of cultivated crops is important for understanding the impact of plant breeding on crop genetic diversity and developing effective indicators for genetic diversity of cultivated plants. The objective of this study was to assess genetic diversity changes in 75 Canadian hard red wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 31 simple sequence repeats (SSRs) markers. A total of 267 SSR alleles were detected, and their allelic frequencies ranged from 0.01 to 0.97, with an average of 0.14. Significant allelic reduction was observed at only four SSR loci for the cultivars released from 1970 onwards. However, 51 alleles (about 19%) present in pre-1910 cultivars were undetected in cultivars released after 1990 and were spread over 27 SSR loci. The proportion of SSR variation accounted for by six breeding periods was 12.5%, by four ancestral families, 16.5%, and by eight breeding programs, 8.4%. The average genetic diversity measured by three different band-sharing methods did not change significantly among cultivars released from different breeding periods, breeding programs, and ancestral families. However, genetic shift was obvious in the cultivars released over the six breeding periods, reflecting well the various breeding efforts over years. These results clearly show the allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released over time. Consequently, more effort needs to be made to broaden the wheat breeding base and conserve wheat germplasm.     

Can spelt wheat be used as heterotic group for hybrid wheat breeding?

Key message

Spelt wheat is a distinct genetic group to elite bread wheat, but heterosis for yield and protein quality is too low for spelt to be recommended as heterotic group for hybrid breeding in wheat.

Abstract

The feasibility to switch from line to hybrid breeding is currently a hot topic in the wheat community. One limitation seems to be the lack of divergent heterotic groups within wheat adapted to a certain region. Spelt wheat is a hexaploid wheat that can easily be crossed with bread wheat and that forms a divergent genetic group when compared to elite bread wheat. The aim of this study was to investigate the potential of Central European spelt as a heterotic group for Central European bread wheat. We performed two large experimental field studies comprising in total 43 spelt lines, 14 wheat lines, and 273 wheat–spelt hybrids, and determined yield, heading time, plant height, resistance against yellow rust, leaf rust, and powdery mildew, as well as protein content and sedimentation volume. Heterosis of yield was found to be lower than that of hybrids made between elite wheat lines. Moreover, heterosis of the quality trait sedimentation volume was negative. Consequently, spelt wheat does not appear suited to be used as heterotic group in hybrid wheat breeding. Nevertheless, high combining abilities of a few spelt lines with elite bread wheat lines make them interesting resources for pre-breeding in bread wheat. Thereby, the low correlation between line per se performance and combining ability of these spelt lines shows the potential to unravel the breeding value of genetic resources by crossing them to an elite tester.

     

Genetic diversity in European wheat and spelt breeding material based on RFLP data

Fifty-two winter wheat (Triticum aestivum L.), nine spring wheat, and 20 spelt (Triticum spelta L.) lines representing part of the European breeding germplasm, were assayed for RFLPs (restriction fragment length polymorphisms) with 56 wheat DNA clones and two barley cDNA clones. Objectives of this study were to (1) determine the level of variation for RFLPs in the wheat and spelt breeding lines, (2) characterize the genetic diversity within the European winter wheat germplasm, and (3) evaluate the usefulness of RFLP markers for pedigree analysis and the grouping of wheat and spelt lines of various origins. Seventy-three of the 166 RFLP loci detected with 58 probes and one restriction enzyme were polymorphic for the 81 lines. The percentage of polymorphic loci was greatest for the B genome (58%) and smallest for the D genome (21%). Among the 81 lines, 271 different RFLP bands were detected. RFLP band frequencies of the winter wheat lines differed considerably (0.5) from those of the spring wheat lines at five loci, and from those of the spelt lines at 17 loci. Eight cultivars that had a major impact as progenitors on the development of improved winter wheat cultivars accounted for 93% of the observed RFLP bands in winter wheat. Genetic distance (GD) estimates between two lines ranged between 0.01 and 0.21. Mean GD estimates within winter wheat (0.083), within spring wheat (0.108) and within spelt (0.096) were smaller than between spring and winter wheat (0.114), and greatest between winter wheat and spelt (0.132) and spring wheat and spelt (0.148). Principal coordinate analysis performed on GD estimates revealed a clear separation of wheat and spelt germplasm. Novel spelt lines with various proportions of wheat germplasm were positioned between wheat and traditional spelt lines. The spring wheat lines formed a distinct group at the periphery of the distribution of the winter wheat lines. Subgroupings of the winter wheat lines according to the cluster analysis were in good agreement with their origin, and lines with common ancestors were grouped together.     

Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat

Aegilops tauschii, the diploid progenitor of the wheat D genome, is a readily accessible germplasm pool for wheat breeding as genes can be transferred to elite wheat cultivars through direct hybridization followed by backcrossing. Gene transfer and genetic mapping can be integrated by developing mapping populations during backcrossing. Using direct crossing, two genes for resistance to the African stem rust fungus race TTKSK (Ug99), were transferred from the Ae. tauschii accessions TA10187 and TA10171 to an elite hard winter wheat line, KS05HW14. BC₂ mapping populations were created concurrently with developing advanced backcross lines carrying rust resistance. Bulked segregant analysis on the BC₂ populations identified marker loci on 6DS and 7DS linked to stem rust resistance genes transferred from TA10187 and TA10171, respectively. Linkage maps were developed for both genes and closely linked markers reported in this study will be useful for selection and pyramiding with other Ug99-effective stem rust resistance genes. The Ae. tauschii-derived resistance genes were temporarily designated SrTA10187 and SrTA10171 and will serve as valuable resources for stem rust resistance breeding.     

Domestication evolution,genetics and genomics in wheat

Domestication of plants and animals is the major factor underlying human civilization and is a gigantic evolutionary experiment of adaptation and speciation, generating incipient species. Wheat is one of the most important grain crops in the world, and consists mainly of two types: the hexaploid bread wheat (Triticum aestivum) accounting for about 95% of world wheat production, and the tetraploid durum wheat (T. durum) accounting for the other 5%. In this review, we summarize and discuss research on wheat domestication, mainly focusing on recent findings in genetics and genomics studies. T. aestivum originated from a cross between domesticated emmer wheat T. dicoccum and the goat grass Aegilops tauschii, most probably in the south and west of the Caspian Sea about 9,000 years ago. Wild emmer wheat has the same genome formula as durum wheat and has contributed two genomes to bread wheat, and is central to wheat domestication. Domestication has genetically not only transformed the brittle rachis, tenacious glume and non-free threshability, but also modified yield and yield components in wheat. Wheat domestication involves a limited number of chromosome regions, or domestication syndrome factors, though many relevant quantitative trait loci have been detected. On completion of the genome sequencing of diploid wild wheat (T. urartu or Ae. tauschii), domestication syndrome factors and other relevant genes could be isolated, and effects of wheat domestication could be determined. The achievements of domestication genetics and robust research programs in Triticeae genomics are of greatly help in conservation and exploitation of wheat germplasm and genetic improvement of wheat cultivars.     

Genetic structure of Argentinean hexaploid wheat germplasm

The identification of genetically homogeneous groups of individuals is an ancient issue in population genetics and in the case of crops like wheat, it can be valuable information for breeding programs, genetic mapping and germplasm resources. In this work we determined the genetic structure of a set of 102 Argentinean bread wheat (Triticum aestivum L.) elite cultivars using 38 biochemical and molecular markers (functional, closely linked to genes and neutral ones) distributed throughout 18 wheat chromosomes. Genetic relationships among these lines were examined using model-based clustering methods. In the analysis three subpopulations were identified which correspond largely to the origin of the germplasm used by the main breeding programs in Argentina.     

Trends in genetic diversity change of spring bread wheat cultivars released in Russia in 1929-2003

Using genealogy analysis, we studied genetic diversity of 340 cultivars of spring bread wheat that were released on the territory of Russia in 1929-2003. Trends in the temporal change of genetic diversity were inferred from analysis of a set of n x m matrices, where n is the number of the released cultivars and m is the number of original ancestors. The pool of original ancestors of the spring bread wheat cultivars for the total period of study included 255 landraces, of which 88 were from the former USSR and modern Russia. The original ancestors showed great differences in their presence in the cultivar sets examined and, consequently, in their importance for the gene pool of Russian spring wheats. The distributions of contributions of dominant original ancestors to cultivar diversity were significantly different in different regions, indicating that the ancestors were specific for the cultivation conditions. During the last 75 years, the genetic diversity of the spring bread wheat cultivars has been increasing owing to the wide use of foreign material in Russian breeding programs. However, our analysis showed that about 60 landraces, including the Russian ones, were lost during the studied time period. The lost part makes up 35% of the gene pool of the Russian original ancestors. It is reasonable to assume that the lost landraces carried a gene complex f or adaptation to specific Russian environments. Specificity of the contributions of the original ancestors in the sets of cultivars produced in different breeding centers was established. A comparative analysis of genetic similarity of cultivars was carried out using coefficients of parentage. Significant differences in this parameter between breeding institutes and regions of cultivation were revealed.     

New data on the distribution of hybrid necrosis genes in winter bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) cultivars

Hybrid necrosis genotypes have been identified in 125 Russian cultivars of winter bread wheat. More than half of them (56%) carry the Ne2 gene (genotype ne1ne1Ne2Ne2); others are free of necrosis genes (genotype ne1ne1ne2ne2). The possible causes of the increase in the Ne2 allele frequency and the loss of the Ne1Ne1ne2ne2 genotype in modern Russian cultivars of winter wheat are discussed. The principal component method has been used to compare the structures of the genetic diversity of cultivars differing in the hybrid necrosis genotype. It has been found that the Ne2 allele in winter wheat cultivars from northern Russia has originated from the cultivar Mironovskaya 808, whereas the cultivar Bezostaya 1 is not a source of this gene. In cultivars from southern Russia, the presence of the Ne2 allele is also mainly accounted for by the use of Mironovskaya 808 wheat in their breeding. The recessive genotype is explained by the presence of descendants of the cultivar Odesskaya 16 in the pedigrees of southern Russian winter wheats. The genetic relationship of cultivars with identical and different necrosis genotypes has been analyzed in nine regions of the Russian Federation.     

A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function

Aegilops tauschii (Coss.) Schmal. (2n=2x=14, DD) (syn. A. squarrosa L.; Triticum tauschii) is well known as the D-genome donor of bread wheat (T. aestivum, 2n=6x=42, AABBDD). Because of conserved synteny, a high-density map of the A. tauschii genome will be useful for breeding and genetics within the tribe Triticeae which besides bread wheat also includes barley and rye. We have placed 249 new loci onto a high-density integrated cytological and genetic map of A. tauschii for a total of 732 loci making it one of the most extensive maps produced to date for the Triticeae species. Of the mapped loci, 160 are defense-related genes. The retrotransposon marker system recently developed for cultivated barley (Hordeum vulgare L.) was successfully applied to A. tauschii with the placement of 80 retrotransposon loci onto the map. A total of 50 microsatellite and ISSR loci were also added. Most of the retrotransposon loci, resistance (R), and defense-response (DR) genes are organized into clusters: retrotransposon clusters in the pericentromeric regions, R and DR gene clusters in distal/telomeric regions. Markers are non-randomly distributed with low density in the pericentromeric regions and marker clusters in the distal regions. A significant correlation between the physical density of markers (number of markers mapped to the chromosome segment/physical length of the same segment in m) and recombination rate (genetic length of a chromosome segment/physical length of the same segment in m) was demonstrated. Discrete regions of negative or positive interference (an excess or deficiency of crossovers in adjacent intervals relative to the expected rates on the assumption of no interference) was observed in most of the chromosomes. Surprisingly, pericentromeric regions showed negative interference. Islands with negative, positive and/or no interference were present in interstitial and distal regions. Most of the positive interference was restricted to the long arms. The model of chromosome structure and function in cereals with large genomes that emerges from these studies is discussed.     

A high-density genetic linkage map of Aegilops tauschii, the D-genome progenitor of bread wheat

 Aegilops tauschii is the diploid D-genome progenitor of bread wheat (Triticum aestivum L. em Thell, 2n=6x=42, AABBDD). A genetic linkage map of the Ae. tauschii genome was constructed, composed of 546 loci. One hundred and thirty two loci (24%) gave distorted segregation ratios. Sixty nine probes (13%) detected multiple copies in the genome. One hundred and twenty three of the 157 markers shared between the Ae. tauschii genetic and T. aestivum physical maps were colinear. The discrepancy in the order of five markers on the Ae. tauschii 3DS genetic map versus the T. aestivum 3D physical map indicated a possible inversion. Further work is needed to verify the discrepancies in the order of markers on the 4D, 5D and 7D Ae. tauschii genetic maps versus the physical and genetic maps of T. aestivum. Using common markers, 164 agronomically important genes were assigned to specific regions on Ae. tauschii linkage, and T. aestivum physical, maps. This information may be useful for map-based cloning and marker-assisted plant breeding. Received: 23 March 1998 / Accepted: 27 October 1998     

Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species,as genome progenitors of bread wheat,using SCoT markers

We assessed the molecular genetic diversity and relationships among some Aegilops and Triticum species using 15 start codon-targeted (SCoT) polymorphism markers. A total of 166 bands amplified, of which 164 (98.79%) were polymorphic. Analysis of molecular variance and inter-population differentiation (Gst) indicated high genetic variation within the studied populations. Our analyses revealed high genetic diversity in T. boeoticum, Ae. cylindrica, T. durum and Ae. umbellulata, low diversity in Ae. crassa, Ae. caudata and Ae. speltoides, and a close relationship among Ae. tauschii, T. aestivum, T. durum, T. urartu, and T. boeoticum. Cluster analysis indicated 180 individuals divided into 8 genome homogeneous clades and 11 sub-groups. T. aestivum and T. durum accessions were grouped together, and accessions with the C and U genomes were grouped into the same clade. Our results support the hypothesis that T. urartu and Ae. tauschii are two diploid ancestors of T. aestivum, and also that Ae. caudata and Ae. umbellulata are putative donors of C and U genomes for other Aegilops species that possess these genomes. Our results also revealed that the SCoT technique is informative and can be used to assess genetic relationships among wheat germplasm.