Sunflower, a major edible oil crop producing a high-quality and healthful oil for human consumption and also recycled for use as feedstock to produce biodiesel fuel, is recently being cultivated in rotation with rice in the paddy field. The oil of cultivars with a high oleic acid content has higher oxidation stability and better nutritional properties than the standard cultivars, which have a high linoleic acid content. In this study, we evaluated the effects of excess water on plant growth, seed yield, and oil quality. Seed yield, the major yield components, the oleic acid content and the total oil content were negatively affected by a shallow water table. In particular, waterlogging at the establishment stage decreased the growth and seed yield severely. In addition, waterlogging during the flowering and maturation stages tended to decrease the oleic acid content and to increase the linoleic acid content. These results will be useful for improving management practices to increase the seed yield and improve the oil quality of sunflower in rotation with upland paddy rice.

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