The genus Triticum L. is one of the most important genera in the tribe Triticeae and has been the focus of many biosystematic studies. Four basic genomes, A, B, D and G are involved in the genomic constitution of all Triticum species [1,2]. The ancestral diploid species of A, B and D genome have diverged from a common ancestor about three million years ago [3]. From these ancestral diploids, two species hybridized somewhere along the Fertile Crescent to form the first tetraploid Triticum species [4]. The processes of polyploidization and genomic differentiation finally resulted in the present day genus Triticum with a ploidy series of di-, tetra- and hexaploid species, all based on x = 7 [5]. The A and D genomes which are less differentiated from those of the parental diploids, are considered as pivotal genomes [6,7]. Many reports indicated that the A genome has suffered different changes in T. urarto Thum. ex Gandil. (A^uA^u) and T. boeoticum Boiss. (A^bA^b) [2,8].

Since wheat cultivation commenced, the breeding and selection of particular genotypes have resulted in enormous loss of alleles and limited the genetic diversity of modern wheat cultivars [9,10]. Therefore, the remaining variability in the cultivated wheat gene pool is insufficient to address current and future breeding efforts [11]. For that reason, there is an essential and urgent need to explore the genetic potential among natural populations of wheat species and their closely related taxa. Germplasm accessions distinct from modern wheat cultivars are predicted to contain potentially useful alleles to broaden the genetic base of wheat [12].

Since the bread wheat (T. aestivum) most probably originated from the south eastern or south western Caspian Sea in Iran [13–15], the wild species and populations growing in Iran, as one of the putative centers of origin of cultivated wheat, can be valuable from this point of view. This opinion is strengthened by the fact that the chromosomes of A genome carry important genes such as adult plant resistance genes [16], milling yield genes [17], flour color genes[18], white salted noodle quality genes [19], supernumerary spikelet (SS) genes [20], sprouting resistance genes [21], chlorophyll synthesis genes [22], total florets per spike genes [23], cold tolerance genes [24], size of stomata genes [25], forest resistance genes [26,27] and yield traits such as tiller number, heading date and plant height genes [28]. Many workers have studied the Triticum species from different points of view: morphology [29,30], isozymes [14,31,32] restriction fragment length polymorphismes (RFLPs) [33–35], and microsatellites [36–39]. A high level of polymorphism in RFLPs and microsatellites among Triticum species accessions has been detected [37,40–43].

Microsatellites or simple sequence repeats (SSRs) have become the markers of choice among a variety of different molecular markers in order to evaluate genetic diversity and phylogenetic relationships [44,45]. It has been demonstrated that microsatellites are highly informative markers in many plant species [40,41,46–61] and it is believed that microsatellites show a much higher level of polymorphism in hexaploid wheat than any other marker systems.

More than a thousand wheat mapped microsatellite markers are available that are useful tools for genetic analyses. Genomic SSRs have been used in wheat for a variety of purposes including genomic mapping [33,40,62,63], gene tagging [39,64–66] and genetic diversity [41,67,68] analyses.

This study was aimed to use SSR markers to estimate the level of A genome polymorphism and to identify the relationships among the species carrying A genome of the genus Triticum native to Iran.

All 31 A genome specific SSR primers yielded 410 bands (alleles) from genomic DNA of all 55 accessions of eight A genome containing Triticum species from which 316 (0.77) were polymorphic (Table 1).

The number of alleles per microsatellite ranged from 5 (Xgwm512 and Xgwm179) to 22 (Xgwm666) with an average of 12.8 alleles per locus (Table 1). Major allele frequency ranged from 0.13 to 0.46 averaging 0.29 (Table 1). The mean value for polymorphism information content (PIC) for all microsatellites was 0.77. The microsatellite Xgwm427 with 20 alleles had the highest (0.92) and the microsatellite Xgwm136 with 6 alleles had the lowest (0.63) PIC value (Table 1).

A total of 47 accessions particularly collected for this study and eight accessions provided by the Institute of Plant Biology, University of Zurich (Table 4) were examined.

The materials were taxonomically identified based on Rahiminejad and Kharazyan [72]. DNA was isolated from fresh leaves of twenty individuals of each accession using CTAB DNA extraction method [76]. In order to assess genetic relationships and diversity of the species carrying A genome in the genus Triticum, 31 A genome specific SSR primers [36] were used. Markers name and other details regarding the SSR markers are presented in Table 1.

Polymerase chain reactions (PCRs) were performed based on Jakson and Matthews (2000) [77]. Briefly, the PCR was carried out in 10 μL containing 2.5 μL of the 13 ng/μL genomic DNA sample, 1 μL of 10 × reaction buffer, 0.3 μL of 30 mM MgCl₂, 1 U Taq polymerase, 0.5 μL of 2.5 mM dNTPs and 0.3 pmol each of IRD 800 dye and IRD 700 dye labeled arbitrary primers. The amplification program consisted of the following cycles: 95 °C for 4 min, 95 °C for 30 sec, 50 °C to 60 °C (depending on the primer set) for 30 sec, 72 °C for 1.5 min and a final extension at 72 °C for 10 min. After 4 min at 95 °C, 35 cycles were performed for 30 sec at 95 °C, 30 sec at annealing temperature (50–60 °C, see Table 1), 1.5 min at 72 °C, followed by a final extension step of 10 min at 72 °C. Upon completing the PCR cycles, 0.8 μL of PCR products of each sample was loaded onto a 6% polyacrylamide sequencing gel in a Li-COR Global DNA Sequencer, and electrophoresed at 2000 V for 1.5 h.

Based on the results of this study, and those previously reported [82,83], it can be concluded that a hypothetical process of hybridization, polyploidization and genomic differentiation can result in the A genome of bread wheat as below: T .   monococcum   →   T .   durum : T .   turgidum   →   T .   aestivumHuang et al. (2002) [29], and Wicker et al. (2003) [84] suggested that the genome of T. urartu (A^u) diverged about 0.5–3 Mya from the genome of T. monococcum (A^m). Therefore, it can be proposed that T. monococcum is the parental A genome species in the genus Triticum and the A genome of di-, tetra- and hexaploid species carrying A genome are directly or indirectly originated from this species. The populations of T. monococcum grow in restricted areas and the data (not shown) indicated low seed germination ability (about 10%) of this species. Therefore, this can be interpreted that T. monococcum is facing the risk of extinction in this area and we suggest that carrying out a wider sampling with more depth across its geographic range of distribution would be vital for gene pool conservation proposes.

As Figure 1 shows the materials provided by the Institute of Plant Biology, University of Zurich are clearly separated from the Iranian accessions. These originated from Turkey, Syria, Lebanon, Greece and Iran. In dendrogram, these accessions were mainly divided according to their country of origin. The T. dicoccoides accessions originating from Iran and Turkey were grouped together; however, because of less materials being studied no interpretation can be made about their genetic relationship. Since there were no materials belonging to T. dicoccum and T. dicoccoides among the 47 accessions specifically collected from Iran for this study, no comparison was made with their Iranian genepool (Table 4).

AMOVA analyses showed that the main portion of diversity is attributed to the variation among the accessions within species, suggesting high genetic diversity within the Triticum species in Iran. We would expect that a great sampling of each species in Iran and analysis of genetic diversity would be worthwhile to reveal the genetic structure of their gene pools and to discover new useful alleles for breeding proposes.