Solar radiation-associated adaptive SNP genetic differentiation in wild emmer wheat, Triticum dicoccoides
Citation
Ren, J., Chen, L., Jin, X., Zhang, M., You, F.M., Wang, J., Frenkel, V., Yin, X., Nevo, E., Sun, D., Luo, M.C., Peng, J. (2017). Solar radiation-associated adaptive SNP genetic differentiation in wild emmer wheat, Triticum dicoccoides. Frontiers in Plant Science, [online] 8 http://dx.doi.org/10.3389/fpls.2017.00258
Plain language summary
Understanding adaptive differentiation is important in evolutionary biology. The adaptation to the local environment in natural populations is considered as a major driving force of phenotypic change and speciation. SNP marker is now the most frequently used type of molecular marker for genetic variation in many species because of their high abundance across the genome and the availability of cost-effective high-throughput genotyping assays.
In the present study, EST-related SNP markers were used to investigate adaptive genetic divergence in wild emmer wheat between shady and sunny micro-niches, separated apart by a short distance of 2-4 meters. The effect of solar radiation resulted from two stresses, sun and shade, could cause significant genetic differentiation of wild emmer wheat. A total of 21 outlier loci under positive selection were identified by using four FST-outlier testing algorithms. These outlier SNP markers and the residing genomic regions followed the known patterns of selection. Loci subjected to positive selection may be functionally important, and hence may be involved in adaptation evolution. In a word, the present works highlight both evolutionary theory and application importance of radiation-associated genetic divergence in wheat improvement.
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.