Differential expression of proanthocyanidin-related candidate genes in contrasting seed coat colors of Chilean common bean landraces under deficit irrigation

Chilean common bean (Phaseolus vulgaris L.) landraces belong to the Andean gene pool, and they are an important genetic resource for seed coat color and antioxidant-related phenolic composition. This study shows that the Chilean landrace 'Peumo' accumulates between 4 and 30-fold higher levels of condensed tannins, including the flavan-3-ols catechin and epicatechin, in the seed coat than the light grey 'Tórtola' landrace during grain filling. The largest quantitative differences were observed under deficit irrigation. To explore the molecular basis of these contrasting seed coat colors under water deficit, we combined targeted phenolic profiling with RNA-seq analysis of seed coat tissue from plants grown under deficit irrigation. Four differentially expressed genes (Phvul.007G206000, Phvul.002G079300, Phvul.010G090300 and Phvul.009G040700) were identified as candidate genes potentially associated with flavan-3-ols production and accumulation. In addition, 962 and 483 differentially expressed genes were detected at stages R8 and R9, respectively, reflecting extensive transcriptional reprogramming during late grain filling. Among the candidates, Phvul.002G079300, annotated as a short hypocotyl 1-like gene involved in light signaling, showed coherent differential expression between landraces in RNA-seq and significant up-regulation in 'Peumo' at R9 by RT-qPCR, whereas the remaining genes displayed non-significant but biologically suggestive expression trends. Altogether, these results support a working model in which seed coat color differences between 'Peumo' and 'Tórtola' arise from the combined effects of phenylpropanoid-derived flavan-3-ol accumulation, and the differential expression of regulatory genes linked to light and stress signaling under water deficit, and they highlight the need for broader germplasm coverage and functional studies to establish causal relationships.