Adaptive introgression conferred salt tolerance to
allotetraploids
The phylogenetic pattern revealed in this study aligns with our previous
population genetic study based on RADseq, revealing that USnat is more
distant from the rest of the lineages, with AU and CN formed one clade,
and EU and Med in another clade (C. Wang, Liu, Yin, Eller, Brix, Wang,
Salojärvi, et al., 2021). Thirteen individuals representing all lineages
from the RADseq study were reanalyzed here using RNAseq data (including
AU1, AU2, AU3, Med1, Med2, Med3, Med5, EU2, EU3, EU4, CN1, CN2),
confirming the AU lineage is octoploid, and the other lineages are
tetraploids. Contrasting phylogenetic patterns between nuclear and
chloroplast genes were observed between the AU and CN lineages,
suggesting extensive ancient hybridization has happened between the two
lineages, therefore the individuals with discordant phylogenetic trees
can be visualized as ancient hybrids. This is plausible because AU
lineages are primarily distributed in regions further south than
southern China, extending to Australia, while CN lineages are found
along the Yellow River and further north (C. Wang, Liu, Yin, Eller,
Brix, Wang, Salojärvi, et al., 2021). As a result, much of eastern and
central China lies within a secondary contact zone. In the octoploid AU
lineage, both freshwater and salt-tolerant populations clustered
together with little genetic differentiation, which is indication that
they have strong tolerance to the saline levels in the ambient
environment. In contrast, the brackish water and freshwater populations
of CN lineage were distinctly separated, with freshwater population
embedded with the pure tetraploids and brackish water individuals placed
between tetraploids and octoploids. The CN brackish water population
retains chloroplast DNA from the AU lineage, suggesting this lineage
resulted from hybridization between AU and CN, and chloroplast capture
happened. This suggests that adaptive loci associated with salt
tolerance may have been conferred from the octoploid AU lineage to
tetraploid CN lineage through introgression, leaving the hybrid brackish
water population more resistant to high salinity.
This finding aligns with conclusions drawn from a previous gene
expression study on untreated common reed samples, wherein individuals
from lineages with higher ploidy levels were more likely to express
genes enriched in stress tolerance (C. Wang, Wang, et al., 2021). The
enhanced tolerance to abiotic stress in polyploids is a phenomenon
observed in many plant species. Plants with higher ploidy levels often
exhibit optimized morphological and anatomical structures in their
leaves, reducing water loss and maintaining cellular homeostasis during
salt or drought stress, as evidenced in common reed, Arabidopsis and
birches (Sheng et al., 2024; Van de Peer, Ashman, Soltis, & Soltis,
2021). In rice, diploids tend to synthesize higher levels of glucose,
fructose, and chlorophyll compared with autotetraploid under Cd stress
(Ghouri et al., 2023).
A genome scan between the AU and CN population, as well as between the
CN brackish and freshwater population, revealed many outliers with highF ST values. Since these differentiated loci could
be indicative of either speciation islands or adaptive loci, we focused
on regions only where F ST values overlapped
between lineages and ecotypes to identify loci that likely represent
adaptive traits. Nine of these genes are enriched in the biological
process of responding to salicylic acid, which is known to enhance plant
tolerance to various abiotic stresses, including salinity, temperature
extremes and heavy metals(Guozhang, Guchou, & Zhengxun, 2004). Among
these, the gene LOC133925052 codes for a S40-7-like protein playing a
role in response to environmental cues and leaf senescence in rice; the
gene LOC133925058 is known to positively mediates salt stress tolerance
by binding to an E-box like motif to regulate gene expression; the
protein OEL21155 is a receptor-like kinases (RLKs) in plant defense; the
protein XP_062206816.1 can positively regulate seed longevity in
Arabidopsis (Supplementary Table S4 ). These are all relevant to
the actual situation of the ecotypes involved in the study and the CVa
of these genes in response to Cd are higher than neutral genes,
indicating they are indeed responsive to abiotic stress and that our
screening method is effective.