Transcriptome and Metabolome Based Mechanisms Revealing the Accumulation and Transformation of Sugars and Fats in <i>Pinus armandii</i> Seed Kernels during the Harvesting Period

<i>Pinus armandii</i> seed kernel is a nutrient-rich and widely consumed nut whose yield and quality are affected by, among other things, harvesting time and climatic conditions, which reduce economic benefits. To investigate the optimal harvesting period of <i>P. armandii</i> seed kernels, this study determined the nutrient composition and seed kernel morphology and analyzed the gene expression and metabolic differences of <i>P. armandii</i> seed kernels during the harvesting period by transcriptomics and metabolomics. The results revealed that during the maturation of <i>P. armandii</i> seed kernels, there was a significant increase in the width, thickness, and weight of the seed kernels, as well as a significant accumulation of sucrose, soluble sugars, proteins, starch, flavonoids, and polyphenols and a significant decrease in lipid content. In addition, transcriptomic and metabolomic analyses of <i>P. armandii</i> seed kernels during the harvesting period screened and identified 103 differential metabolites (DEMs) and 8899 differential genes (DEGs). Analysis of these DEMs and DEGs revealed that <i>P. armandii</i> seed kernel harvesting exhibited gene-metabolite differences in sugar- and lipid-related pathways. Among them, starch and sucrose metabolism, glycolysis, and gluconeogenesis were associated with the synthesis and catabolism of sugars, whereas fatty acid degradation, glyoxylate and dicarboxylic acid metabolism, and glycerophospholipid metabolism were associated with the synthesis and catabolism of lipids. Therefore, the present study hypothesized that these differences in genes and metabolites exhibited during the harvesting period of <i>P. armandii</i> seed kernels might be related to the accumulation and transformation of sugars and lipids. This study may provide a theoretical basis for determining the optimal harvesting time of <i>P. armandii</i> seed kernels, changes in the molecular mechanisms of nutrient accumulation, and quality directed breeding.