Correlations between the expression of drought tolerance candidate genes and photosynthetic performance in Coffea canephora

Identifying correlated transcriptional profiles among candidate genes (CGs) for drought tolerance can reveal functionally related genes or those controlled by shared transcriptional mechanisms. Moreover, correlations between gene transcription levels and physiological parameters help elucidate drought tolerance mechanisms, guiding future gene-specific functional studies. This study explored correlations between transcription levels of drought tolerance CGs and photosynthetic rates in Coffea canephora. Two conilon coffee genotypes, 120 (drought-tolerant) and 109 (drought-susceptible), were exposed to four sequential water deficit stages in a greenhouse: irrigated (Initial), moderate deficit (Ψpd = -1.5 MPa), severe deficit (Ψpd = -3.0 MPa), and recovery (5 days of rehydration). Each treatment had three biological replicates. At each stage, we measured Net Photosynthetic Rate (A), Stomatal Conductance (gs), Electron Transport Rate (ETR), and Carbon Use Efficiency (A/gs). Leaf samples were collected for mRNA isolation and RT-qPCR analysis of nine drought tolerance CGs in C. canephora, using CcUBQ10 as an endogenous control. Spearman correlation matrices with Benjamini-Hochberg p-value adjustment (α = 5%) were generated using the R package corrplot to identify correlations between gene transcription levels and photosynthetic parameters. Results showed a significant positive correlation between transcription factors CcWRKY2 and CcRAP2.4 (r = 0.660, p = 0.046), and a strong positive correlation between CcRAP2.4 and CcPIP2;3 (r = 0.679, p = 0.002), supporting previous findings that PIP2;3 is regulated by RAP2.4 in other species. All aquaporins except CcPIP2;3 displayed coordinated transcription, with significant correlations between CcTIP1;2 and CcTIP2;1 (r = 0.766, p < 0.001) and between CcTIP2;1 and CcPIP2;4 (r = 0.746, p = 0.005). Significant correlations also appeared between photosynthetic parameters and gene transcription: A with CcRAP2.4 (r = 0.520, p = 0.049), ETR with CcEDR2 (r = 0.540, p = 0.042) and CcPIP2;4 (r = 0.570, p = 0.042), and A/gs with aquaporins CcTIP1;2 (r = 0.540, p = 0.042), CcTIP2;1 (r = 0.550, p = 0.042), CcPIP2;4 (r = 0.640, p = 0.027), and CcCCoAOMT1 (r = 0.540, p = 0.042). However, gs did not significantly correlate with any tested gene. These findings underscore a coordinated transcriptional regulation of aquaporin genes and their potential role in sustaining A/gs under drought stress. Although CcPIP2;3 is linked to CO2 diffusion, it did not show a significant correlation with A (r = 0.50, p = 0.059), while CcRAP2.4 did, indicating its role in maintaining photosynthetic rates through alternative mechanisms. The significant correlation between CcEDR2 and ETR aligns with its proposed role in protecting the photosynthetic apparatus and dissipating excess energy. The results suggest a crucial role for aquaporins, particularly CcTIP1;2, CcTIP2;1, and CcPIP2;4, in maintaining carbon use efficiency (A/gs) under drought conditions. Genes involved in the regulation of these aquaporins hold promise for facilitating their co-expression under stress, while CcRAP2.4 emerges as a potential target for enhancing photosynthetic rates. These genes represent valuable targets for advancing the understanding of drought tolerance mechanisms in C. canephora.