Correlation analysis showed strong positive relationships among pigment-related traits (Fig 4). Total chlorophyll was strongly correlated with chlorophyll a (r>0.90, p<0.001), chlorophyll b (r>0.95, p<0.001) and total carotenoids (r = 0.98, p<0.001). Chlorophyll a and chlorophyll b were also positively correlated.
Proline showed positive correlations with green weight (r = 0.40) and leaf area (r = 0.66, p<0.05). Correlations between proline and chlorophyll-related parameters were weak (r<0.20). Plant height showed low negative correlations with other traits (ranging from -0.05 to -0.30). Leaf area and chlorophyll (SPAD) values were positively correlated (p<0.01).
Principal component analysis (PCA)
PCA separated treatments along PC1–PC2 based on combined morphological and biochemical variation (Fig 5). Growth/biomass traits loaded mainly on one axis, whereas pigment/biochemical variables loaded on the other. Pigment vectors were long and similarly oriented, while proline pointed in a distinct direction. Controls clustered near pigment variables; Na
2SO
4 40 mM separated and aligned with biomass traits and proline. NaCl and Na
2SO
4 treatments diverged and Na
2SO
4 20 mM was close to NaCl 40 mM in associations with leaf area and growth traits.
Pigment traits
Pigment traits differed among treatments (Fig 6; Table 2-3): controls showed the highest values and reductions increased with salinity, particularly at 40 mM. The chlorophyll a/b ratio varied, with higher values under some salt treatments (notably Na
2SO
4 40 mM). Low-salt treatments occasionally matched or slightly exceeded control values, but both salts at 40 mM reduced pigments overall.
Hierarchical clustering
Clustering grouped treatments into high-salt (Na
2SO
4 40 mM, NaCl 40 mM) vs control/low-salt (control, Na
2 SO
4 20 mM, NaCl 20 mM) clusters (Fig 7). Na
2SO
4 40 mM showed lower dry weight, green weight and SPAD with higher proline; NaCl 40 mM showed the lowest pigment traits. Pigments clustered together, whereas proline formed a separate cluster. Genotypes separated (Fig 8): G3 had higher pigments, proline and green/dry weight, while plant height was not higher; G13 showed lower values.
Agronomic traits
Plant height was not affected by treatments (p = 0.886; 35.35-39.97 cm) (Table 1). SPAD was significantly influenced (p = 0.002), with the highest value at 40 mM Na
2 SO
4 (34.45) and the lowest at 20 mM NaCl (28.32). Green weight did not differ among treatments (p = 0.435; 0.38-0.47 g). Genotype effects were significant for plant height (p = 0.001) and green weight (p = 0.005) (Table 1).
Dry weight was not treatment-significant (p = 0.603; 0.06-0.12 g; highest at 40 mM Na
2SO
4) (Table 2). Leaf area was not affected by treatments (p = 0.131; 20.50-27.79 cm²), but genotype effects were significant (p = 0.002).
Pigment traits (Table 2-3) generally declined at higher salinity; chlorophyll a was relatively higher at 20 mM NaCl (Table 2), whereas chlorophyll b was lower at 20 mM Na
2SO
4 and 40 mM NaCl (Table 3). Total chlorophyll and carotenoids decreased at higher salt levels. Proline did not differ among treatments (Table 4), but genotype effects were significant for pigments and proline (Table 2-4).
Multivariate analyses indicate that salt stress modifies common bean performance through coordinated shifts in photosynthetic pigments and more variable responses in growth and osmotic traits. This pattern supports the view that salinity acts through partially independent physiological pathways, with photosynthesis, biomass accumulation and osmotic adjustment differing according to salt type, stress intensity and genotype
(Hasan et al., 2016; Zhu et al., 2020; Mir et al., 2024).
The correlation matrix (Fig 4) showed strong clustering among pigment traits, with total chlorophyll strongly and positively associated with chlorophyll a, chlorophyll b and total carotenoids. This suggests that the pigment system functions as an integrated unit under salinity, consistent with the protective roles of chlorophylls and carotenoids in maintaining photosystem integrity
(Mir et al., 2024). Previous studies report greater sensitivity of chlorophyll a and overall chlorophyll decline under increasing salinity (
Aşcı et al., 2021;
Kibar et al., 2020) and the present results indicate that pigment reductions occur in a coordinated rather than isolated manner.
Proline related positively to green weight and leaf area but weakly to pigment traits, indicating its accumulation isn’t merely due to pigment decline and may be controlled by different pathways affected by genotype and stress duration.
(Mir et al., 2024). The linkage between leaf area and chlorophyll status, as well as the positive association between leaf area and SPAD values, supports coordinated variation in leaf development and chlorophyll density under stress
(Zhang et al., 2024). Compensatory physiological adjustments may partly explain why morphological correlations were weaker than pigment correlations (
Karakaş et al., 2019).
PCA (Fig 5) showed treatment responses driven by stress intensity and salt type. Separation along growth/biomass and pigment/biochemical axes indicates salinity disrupts photosynthesis and prompts adaptive changes.
(Hasan et al., 2016; Zhu et al., 2020). The control group’s proximity to pigment vectors reflects expected pigment decline under salinity
(Zhang et al., 2024; Aşcı et al., 2021). Divergence between NaCl and Na
2SO
4 indicates partially distinct metabolic reorganization pathways (
Levitt, 1985). The proximity of 20 mM Na
2SO
4 and 40 mM NaCl in certain morphological associations suggests that once stress thresholds are exceeded, different salts may impose comparable growth constraints while operating through different biochemical routes
(Mi et al., 2024).
Na
2SO
4 (40 mM) aligned with proline and biomass variables, indicating disrupted homeostasis and potential water and nutrient uptake limitations.
(Farzana et al., 2021). In contrast, stronger pigment depletion under NaCl is consistent with higher photo-oxidative pressure and direct effects on chlorophyll stability
(Zhang et al., 2024; Aşcı et al., 2021). The synchronized pigment vectors versus the proline direction support independent regulation of osmotic adjustment and pigment maintenance.
(Mir et al., 2024).
Controls showed the highest pigment values, while high salinity significantly reduced them, confirming chlorophylls and carotenoids are highly responsive to salt stress.
(Mir et al., 2024; Zong et al., 2021). More pronounced NaCl losses align with inhibited chlorophyll synthesis and faster pigment degradation.
(Zhang et al., 2024; Emirzeoğlu and Başak, 2020). Shifts in the chlorophyll a/b ratio suggest stress-driven restructuring of light-harvesting complexes (
Kaymak and Acar, 2020;
Tuna and Eroğlu, 2017;
Elsiddig et al., 2023). Slight low-salinity increases may indicate hormesis
(Mankar et al., 2021), while higher concentrations harm pigment biosynthesis and photosystem II stability.
(Fitzner et al., 2023; Zhang et al., 2024). Thus, pigment traits are particularly informative for early screening, although multiple pigment parameters should be integrated for robust evaluation
(Mi et al., 2024).
Hierarchical clustering (Fig 7) separated high- from low-salt treatments, highlighting concentration as the dominant driver (
Fidan and Ekincialp, 2017). Within the high-salt cluster, Na
2SO
4 (40 mM) showed lower biomass and SPAD but higher proline, while NaCl (40 mM) caused stronger pigment suppression, indicating different stress signatures of sulfate-and chloride-based salinity.
(Elsiddig et al., 2023; Farzana et al., 2021; Mir et al., 2024). Similar growth reductions under salinity have been widely reported (
Fidan and Ekincialp, 2020;
Kibar et al., 2020; Temizgül, 2025).
Although genotype-dependent responses to salinity are documented
(Aini et al., 2014), this study included only two genotypes; findings should be seen as genotype-specific, not generalizable. Differences in pigment and biomass traits indicate genetic background influences photosynthetic stability and biomass partitioning under salt stress. Because salt tolerance is polyfactorial, integrating morphological and biochemical traits is essential, but broader conclusions need validation with more genotypes sets
(Mi et al., 2024).