Flooding-induced transcriptomic responses and yield stability in oil palm (Elaeis guineensis)

Flooding response in oil palm involves a subtle or broad transcriptional strategy, each associating differently to yield stability across flooding depths. ADH1 baseline expression discriminates these response types. Oil palm is among the world's most productive oil crops, yet information on its response to flooding is limited despite increasing flooding frequency associated with climate change. In this study, leaf transcriptomes from oil palms in the field sampled under non-flooding, low-flooding, and high-flooding conditions revealed two distinct transcriptomic response types, designated as Group 1 and Group 2. Group 1 displayed a subtle transcriptional response, exhibiting fewer differentially expressed genes with predominantly low-magnitude changes, whereas Group 2 displayed a broad transcriptional response, with a higher proportion of genes exhibiting large-magnitude changes. Expression trends for cell wall modification genes (XTH) and stress-associated transcription factors (DREB) were consistent between field-flooded palms and submerged young plantlets. Notably, baseline expression of the hypoxia marker, ALCOHOL DEHYDROGENASE 1 (ADH1), discriminated the two transcriptome groups under non-flooded conditions. Group 1 displayed low baseline levels that were strongly inducible upon flooding, but Group 2 exhibited elevated baseline levels that were sustained under flooding. Mediation analysis showed that the negative association between flood depth and fresh fruit bunch yield operates primarily through suppression of frond architectural traits (rachis length, leaf width, petiole cross-sectional area) in Group 2, while Group 1 displayed better yield stability through frond production, a trait likely insensitive to flood depth. These findings highlight that flood-resilient transcriptional strategies, distinguishable by ADH1 baseline expression, may exist in oil palm, with implications for breeding or stress priming programs targeting flood-prone areas.