Abstract
Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2–4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST-outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.
Highlights
Wild emmer wheat, Triticum dicoccoides, the progenitor of modern tetraploid and hexaploid cultivated wheats, is distributed over the Fertile Crescent and can be found in ecologically highly diverse environments (Peng et al, 2011; Chen et al, 2013; Ren et al, 2013b; Nevo, 2014)
This can be expected due to the more conserved nature of the coding sequences sampled by EST-related single nucleotide polymorphisms (SNPs) markers relative to non-coding sequences sampled by SSRs and randomly amplified polymorphic DNAs (RAPD)
The different contribution of A and B genome to genetic variation agrees well with previous studies by using SSR markers (Röder et al, 1998), RFLP markers (Liu and Tsunewaki, 1991), and AFLP markers (Peng et al, 2000) within common hexaploid wheat as well as in wild emmer wheat (Peng et al, 2011; Ren et al, 2013a). These results suggested a sufficient level of variation when using SNP markers to carry out analyses of genetic variations and association mapping in wild emmer wheat
Summary
Triticum dicoccoides, the progenitor of modern tetraploid and hexaploid cultivated wheats, is distributed over the Fertile Crescent and can be found in ecologically highly diverse environments (Peng et al, 2011; Chen et al, 2013; Ren et al, 2013b; Nevo, 2014). It consists of genomes AABB, resulting most probably from spontaneous hybridization of wild. The contrasted light environments can create different selective pressures; habitat-based selection may have promoted divergence between populations with respect to genetic variability
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