Integrated Transcriptomic, Proteomic, and Metabolomic Analyses Reveal Mechanisms Underlying Day–Night Differences in Carbohydrate Metabolism between Diploid and Tetraploid Rice

Polyploidy plays a crucial role in plant evolution, as polyploid plants possess larger genomes compared to their diploid counterparts. This genomic expansion leads to changes in gene redundancy and interactions, which alter the physiological metabolism of polyploids. Carbohydrate metabolism is a crucial energy metabolism pathway in plants, significantly impacting plant growth and development. In this study, we employed multi-omics analysis to investigate the differences in carbohydrate metabolism between diploid and tetraploid flag leaves during both day and night periods at the grain-filling stage. Our results revealed significant differences in carbohydrate metabolism between diploid (GFD-2X) and autopolyploid (GFD-4X) rice during both day and night periods. Chromosome doubling resulted in GFD-4X exhibiting reduced sucrose catabolism during the daytime, while starch synthesis and catabolism were stronger in GFD-4X compared to GFD-2X during both daytime and nighttime. Additionally, the phosphorylation of monosaccharides was enhanced in GFD-4X, suggesting that changes in chromosome ploidy altered carbohydrate metabolism, thereby benefiting the regulation and redistribution of carbohydrates in tetraploid rice. Furthermore, analysis of respiration-related pathways indicated that tetraploid rice may have more vigorous respiratory activity. Specifically, GFD-4X exhibited enhanced glycolysis and TCA cycle activity at night, resulting in more efficient energy production, which in turn influenced growth and the developmental process. This study examined the regulatory networks of genes, proteins, and metabolites involved in carbohydrate metabolism in diploid and tetraploid rice during both day and night periods. Our findings offer insights into how chromosome ploidy affects carbohydrate metabolism and reveal the distinct growth and developmental mechanisms of tetraploid rice.