Adjustment of Respiration Strategies in Roots Contributes to the Waterlogging Resistance in Actinidia valvata ‘Shuixiu’

Soil hypoxia caused by waterlogging severely restricts kiwifruit growth, and screening waterlogging-tolerant rootstocks and analyzing their mechanisms are of great significance for industrial development. In this study, waterlogging-tolerant Actinidia valvata ‘Shuixiu’ was used as the test material and Actinidia chinensis ‘Hongyang’ as the control. Waterlogging stress was simulated artificially, and physiological measurements combined with transcriptome sequencing were used to explore its waterlogging tolerance regulatory characteristics based on respiratory metabolism. The results showed that the waterlogging tolerance of ‘Shuixiu’ was significantly better than that of ‘Hongyang’. It upregulated sucrose synthase and α/β-amylase genes and inhibited the continuous up-regulation of trehalose-6-phosphate synthase genes, leading to significant accumulation of glucose-6-phosphate, a key glycolytic substrate. Some members of glycolytic key gene families, such as glucose-6-phosphate isomerase and phosphofructokinase, were upregulated in ‘Shuixiu’, which increased phosphoglycerate kinase activity and accumulated 3-phosphoglyceric acid and pyruvate, ensuring efficient conversion of carbon sources to ATP. Some members of core tricarboxylic acid cycle gene families, such as pyruvate dehydrogenase and citrate synthase, were upregulated in ‘Shuixiu’, with significantly higher pyruvate dehydrogenase activity and acetyl coenzyme A content, maintaining partial aerobic respiration capacity. Some members of the alanine transaminase gene family were upregulated in ‘Shuixiu’ to enhance alanine fermentation, resulting in a significant reduction in root ethanol accumulation. This study clarified the core respiratory metabolic regulatory characteristics of kiwifruit in response to waterlogging and provided key targets and a theoretical basis for molecular breeding of waterlogging-tolerant rootstocks.