Glutamate metabolic correlation analysis reveals CnP5CS1 contributes to 2-acetyl-1-pyrroline accumulation in aromatic coconut

Flavor quality, a key sensory attribute of coconut, has consistently been a central breeding objective throughout long-term domestication and varietal improvement efforts. Developing high-aroma varieties requires a clear understanding of their underlying molecular genetic mechanisms. However, research on the metabolic regulatory enzymes involved remains limited, particularly those linked to 2-acetyl-1-pyrroline (2AP), a volatile compound that primarily contributes to the unique scent of aromatic coconuts. We developed contrasting populations and systematically evaluated the role of CnP5CS in 2AP accumulation by examining enzyme activity, metabolic flux, population-level genetic variation, and transcriptional regulatory networks. In the aromatic coconut population, the selected genomic regions were enriched in pathways associated with amino acid metabolism and stress responses. Conspicuously, glutamate (Glu) and its derivatives showed significant correlations within the differentiated populations. The Glu metabolic enzyme P5CS was subjected to strong purifying selection, and haplotype-phenotype association analysis further identified the dominant CnP5CS1 allele genotype. Moreover, we established metabolic marker indicators to assess relative 2AP levels, based on the metabolic profiles of CnP5CS and the substrates and products of its catalyzed reactions. The Y1H assay identified the key transcription factor CnYAB2, which exhibited a strongly correlated expression pattern with CnP5CS1 and major markers of 2AP metabolism. The identification of CnP5CS1 offers a novel perspective on the genetic regulation of 2AP metabolism in aromatic coconuts and establishes a theoretical foundation for developing molecular markers to support the breeding of high-aroma varieties.