Leymus chinensis is an allotetraploid perennial grass that supports the dual functions, ecological and foraging, of the vast saline-alkaline eroded Songnen grassland of northern China. Two leaf-colored ecotypes, gray-green (GG) and yellow-green (YG), of L. chinensis frequently grow sympatrically yet differ in photosynthetic performance and stress responses. The molecular basis underlying the morphophysiological divergence between the two ecotypes, particularly the contribution of subgenome-level regulation, remains unclear. Here we combine common-garden phenotyping with homoeolog-resolved transcriptome analyses and RNA-seq-based variant profiling to dissect divergence between GG and YG. GG maintained higher photosynthetic capacity and chlorophyll content than YG and exhibited distinct chloroplast ultrastructure. Although extensive sequence differentiation separates the ecotypes, predicted high-impact coding changes were rare, implicating regulatory divergence as a primary contributor. Transcriptome analyses showed that GG-upregulated genes were enriched for light and heat responses, chlorophyll biosynthesis, and photoprotection, whereas YG-upregulated genes were enriched for osmotic regulation, carbohydrate metabolism, and cellular maintenance. Homoeolog-specific expression patterns indicated that ecotype differences were frequently driven by Xm homoeolog-specific shifts, including an Xm-localized tandem array of six ELIP-like genes. Ka-Ks analyses showed broadly comparable mean constraints across groups but revealed group-specific nonlinear Ka-Ks scaling, consistent with heterogeneous substitution dynamics among functionally distinct homoeolog sets. Together, these results are consistent with a conceptual bet-hedging model in which allopolyploid regulatory plasticity enables alternative stress-response strategies to coexist in sympatry under fluctuating saline-alkaline conditions. The identified regulatory modules and homoeolog signatures provide candidates for stress-gradient germplasm evaluation and marker prioritization aimed at improving performance stability and stress resilience in L. chinensis . • Gray-green (GG) and yellow-green (YG) ecotypes occur sympatrically in L. chinensis • GG exceeds YG in photosynthesis, chlorophyll and chloroplast structure • GG upregulates light/heat response and photoprotection, YG upregulates osmotic genes • GG-YG divergence is driven by Xm homeolog shifts, including a tandem ELIP-like array • Allopolyploid plasticity may drive regulatory bet-hedging in saline-alkaline habitats
Sun et al. (Sun,) studied this question.