Molecular evolution of drought tolerance and wood strength related candidate genes in loblolly pine (Pinus taeda L.)

Loblolly pine (Pinus taeda L.) is an intensely studied species that has become a model system for conifers. It is one of the most important commercial crops in the southeastern United States and grows across a vast territory. Due to exposure to this current diverse environment and the fluctuating climatic conditions of the past, it has likely accumulated substantial variation in adaptive trait and wood strength related genes. We merged a set of newly collected and previously published genomic DNA sequence data and analyzed them for departures from neutrality in 32 drought tolerance and wood strength related candidate genes using neutrality tests, such as Tajima’s D, HKA, MK and nonsynonymous to synonymous substitutions ratio (Z-test). Three other major Southern pines closely related to P. taeda (Pinus echinata Mill., P. elliottii Engelm., and P. palustris Mill.) were used as outgroups in interspecific tests. In three loci (4-coumarate: CoA ligase, putative cell-wall protein and trans-cinnamate 4-hydroxylase 2) neutrality was rejected by both intra- and interspecific tests, consistent with purifying selection. Neutrality was also rejected in several other loci (alpha-tubulin, arabinogalactan 4, arabinogalactan 6, cinnamate 4-hydroxylase 1, cinnamoyl CoA reductase, cinnamyl alcohol dehydrogenase, caffeoyl CoA O-methyltransferase 1, early response to drought 3, glycine hydroxymethyltransferase, ABI1 protein phosphatase 2C-like, putative wall-associated protein kinase, and unknown gene ug_2-498); however, these results are difficult to interpret because only one of the tests proved significant. This study contributes to the ongoing discussion about natural selection in putative adaptive genes in loblolly pine. However, unambiguous interpretation of the results often remains problematic.