Selection in candidate genes associated with drought and freezing response in live oaks (Quercus series Virentes) across a latitudinal gradient

Background/Question/Methods

Live oaks (Quercus series Virentes) form a small monophyletic lineage that spans the tropical-temperate divide from North Carolina to Costa Rica. A previous study found genetically-based physiological variation in freezing stress and growth rate within and among live oak species spanning this latitudinal gradient (Koehler et al, 2011). Here, we examined genetic variation in eight well-annotated candidate genes associated with responses to freezing and drought stress within and among all seven live oak species. We sequenced candidate genes annotated in the peach and Arabidopsis genomes related to freezing tolerance (ICE1; HOS1), drought tolerance and dormancy (SDIR; DAM), vacuolar functions (TIP), the ethylene response pathway (ERS1) and two housekeeping genes (Chromatin Remodeling Protein 11, CHR11 and Glyceraldehyde Phosphate Dehydrogenase Subunit B, GAPD-B). Gene sequences were aligned and trimmed with ClustalW2 and Jalview, respectively. The sequences were tested for evidence of selection using BayeScan v2.1, a Bayesian model using single nucleotide polymorphisms (SNPs) to identify loci under selection through differences in allele frequencies. Variation in the SNPs was also tested for associations with freezing tolerance, growth rate, latitude, and climatic variables using stepwise linear regression.

Results/Conclusions

The BayeScan analysis for all seven species found a decisive signal of diversifying selection in the exon sequences of SDIR (salt and drought-induced ring-finger), DAM (dormancy associated MADS-box), HOS1 (highly expressed under osmotic stress), ICE1 (Inducer of CBF expression) and ERS1 (Ethylene Response Receptor).  For Q. virginiana, the species with the greatest number of individuals sequenced, BayeScan found a substantial signal of diversifying selection in the exon regions for SDIR and a strong signal of diversifying selection for HOS1 and ERS.  The study indicates that selection is occurring both within and between the live oak species.