Distinct patterns of natural selection in Na(+)/H(+) antiporter genes in Populus euphratica and Populus pruinosa

Salt tolerance genes constitute an important class of loci in plant genomes. Little is known about the extent to which natural selection in saline environments has acted upon these loci, and what types of nucleotide diversity such selection has given rise to. Here, we surveyed genetic diversity in three types of Na(+)/H(+) antiporter gene (SOS, NhaD, and NHX, belonging to the cation/proton antiporter 1 family), which have well‐characterized essential roles in plant salt tolerance. Ten Na(+)/H(+) antiporter genes and 16 neutral loci randomly selected as controls were sequenced from 17 accessions of two closely related members of the genus Populus, Populus euphratica and Populus pruinosa, section Turanga, which are native to northwest China. The results show that salt tolerance genes are common targets of natural selection in P. euphratica and P. pruinosa. Moreover, the patterns of nucleotide variation across the three types of Na(+)/H(+) antiporter gene are distinctly different in these two closely related Populus species, and gene flow from P. pruinosa to P. euphratica is highly restricted. Our results suggest that natural selection played an important role in shaping the current distinct patterns of Na(+)/H(+) antiporter genes, resulting in adaptive evolution in P. euphratica and P. pruinosa.