Understanding water stress signaling mechanisms and screening for tolerant cocoa cultivars are major challenges when facing prolonged dry and rainy seasons in cocoa-producing areas. While abscisic acid (ABA) and proline are supposed to enhance drought tolerance in cocoa, the role of polyamines remains unclear. The aim of this study was to investigate the biochemical response and phenological adaptation of cocoa (Theobroma cacao) on different soil moisture conditions, with a focus on short-term (20 days) and long-term (89 days) stress conditions, and to compare the performance of three cocoa cultivars. In a split plot design with four blocks, cocoa seedlings of an international high-yielding cultivar (TSH-565) and two locally selected cultivars (IIa-22 and III-06) from the drought-exposed Alto Beni region, Bolivia, were arranged in pots under a roof shelter (cultivar: three levels). The seedlings were exposed to strong (VERY DRY) and moderate (DRY) soil moisture deficits, water logging (WET) and regular irrigation (MOIST) that served as a control (moisture: four levels). We examined the growth performance and the levels of ABA, proline, and polyamines in the leaves. Growth was reduced already at a moderate drought, while severe drought enhanced seedling mortality. Severe drought increased the levels of ABA by 453% and of proline by 935%, inducing a short-term stress response; both compounds were degraded over the long-term period. The polyamine concentration was unrelated to soil moisture. The cocoa cultivars did not differ in their biochemical response to soil moisture stress (proline: p-value = 0.5, ABA: p-value = 0.3), but the local cultivar III-06 showed a stronger height growth increment than the international cultivar TSH-565 (237%, p-value = 0.002) under drought conditions.

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