Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology, as well as in studies of ecological and population genetics (Nevo list of wild cereals at http://evolution.haifa.ac.il) [1, 2]. The analyses of genetic diversity and structure are helpful for management, research and utilization of plant germplasm. It is also critical for studies of crop evolution and genetic improvement to identify and correctly interpret the associations between functional variation and molecular genetic diversity [2, 3]. Wild emmer wheat, Triticum dicoccoides, has been found in a wide range of environments, and shows high genetic and phenotypic diversity . The analysis of the genetic structure and population divergence of such high diversity is important for breeding purposes, especially to identify genes or genomic regions involved in environmental adaptation. Furthermore, wheat serves as a good model of polyploidy, one of the most common forms of plant evolution [4, 5]. Hence, it is cardinal to study adaptive genetic diversity in wild emmer, the progenitor of modern tetraploid and hexaploid cultivated wheats [1, 2, 6, 7].
Wild emmer wheat, T. dicoccoides (2n = 4x = 28, genome AABB), is a tetraploid predominantly self-pollinated plant. It originated from a spontaneous hybridization of wild diploid einkorn wheat, T. urartu (2n = 2x = 14, genome AA), with a close relative of the goat grass Aegilops speltoides (2n = 2x = 14, genome SS, where S is closely related to B) [8, 9]. Wild emmer wheat presumably originated in and adaptively diversified from north-eastern Israel and the Golan into the Near East Fertile Crescent, across a variety of ecological conditions . The wide range of ecological conditions, such as temperature [1, 11], soil [1, 12], water availability [1, 10], light intensity [1, 11], humidity [1, 13–16], etc., may exert diverse selection pressures, thus determine the evolutionary course while shaping its genetic structure. Wild emmer wheat has adapted to a broad range of environments and is rich in genetic resources that include drought and salt tolerances [10, 17], herbicide tolerances [1, 18], Zn and Fe contents [19, 20], biotic (viral, bacterial, and fungal) tolerances [1, 21], high-quantity and high-quality storage proteins , and many others. They represent one of the best hopes for crop improvement. Hence, genetic studies of wild emmer wheat are of paramount importance for wheat improvement.
In previous studies, genetic diversity of wild emmer wheat populations has been evaluated using various methods such as morphological traits [1, 17], allozyme analysis [1, 3, 13], and many molecular markers (SSRs, RAPDs, and SRAPs) [14, 15, 22]. Association between markers and ecogeographical factors were also discussed [13–15, 22]. However, genetic structure and population divergence revealed by EST-related SNP markers have not been reported in wild emmer wheat populations. EST-related markers discovered directly from the EST sequences or from genomic sequences amplified using PCR primers designed from ESTs, are useful resources for assaying functional genetic variation . Variation in functional regions, expressed or regulatory sequence, might reflect the past influences of natural selection. Besides, because this type of SNPs can be linked to functional genes, it is important to determine which markers have been likely associated with selection, especially to identify genes or genomic regions involved in environmental adaptation. Hence, SNP markers seem the best to meet needs of marker-assisted management of genetic resources, and of diversity studies and marker-assisted selection in breeding programs. At present, the majority of studies using these EST-related SNP markers have focused on model organisms [24, 25] with fewer applications to non-model taxa . Only a limited number of SNPs have been reported in wheat [27–30]. Large-scale SNP discovery in wheat is limited by both the polyploidy nature of the organism and the high sequence similarity found among the three homoeologous wheat genomes [29, 31].
In the present study, a large number of EST-related SNP markers were used to investigate genetic diversity and genetic structure of a natural collection of 200 accessions belonging to 25 wild emmer wheat populations. This germplasm was collected by E. Nevo from various locations in Israel and Turkey, which covers a wide range of ecological conditions such as soil, temperature, and water availability. Noteworthy, a F
-outlier method was used to identify loci that may be under positive selection and therefore might be linked to genome regions conferring the phenotypic variation present in analyzed germplasm for breeding programs.