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.