Genome scan reveals selective genes with high FST values between
populations
Consistent with expectations, principal component analysis (PCA) based
on the nuclear gene dataset revealed that the tetraploid USnat lineage
is genetically distinct from the other lineages and accounts for the
largest proportion of variations (Fig. 2a ). The octoploid AU
lineage is separated from the rest of the tetraploid lineages
(Supplementary Figure S1 ). We selected individuals representing
pure CN and AU lineages and estimated F ST between
these populations. Furthermore, we conducted F STestimation between the CN brackishwater and freshwater populations. To
identify regions potentially under selection, we applied a threshold
corresponding to the top 1% of F ST values across
the genome. The analysis identified a total of 811 regions with highF ST values between the AU and CN lineages,
predominantly located on chromosome 1 (79 windows) and chromosome 18 (74
windows) (Fig. 2b ). Among these, 111 windows overlapped with
high F ST regions identified between the CN
Brackish water and freshwater populations (Fig. 2d ). Most of
these windows were found on chromosome 18, 10 and 1, suggesting strong
adaptive introgression from the AU lineage into the CN lineage
(Fig. 2c ). Within these overlapping regions, we identified 46
genes and regard them as candidate selective genes. Of these, nine genes
were enriched in Gene Ontology (GO) terms related to responses to
salicylic acid (Supplementary Table S3 ). These genes were
proved to involve in response to environmental cues, gene expression
regulation, plant defense, and see longevity (Supplementary
Table S4 ). Interestingly, five of these nine genes are tandem
duplicates.