Allelic variations at two functional gene loci are associated with aroma and texture in peach fruit

Aroma and texture are two key factors determining peach fruit quality. However, the specific gene loci that coordinately regulate both traits simultaneously remain largely unclear. In this study, a multi-omics strategy integrating GC–MS, RNA sequencing (RNA-seq) and genome re-sequencing was used to identify differentially accumulated volatile metabolites and differentially expressed genes (DEGs) between two peach cultivars with contrasting fruit texture at six ripening stages. Allelic variations were further validated in a panel of 54 peach accessions. The objectives were to identify novel genes and their regulatory interactions related to the above traits, and to uncover useful allelic variations or haplotype that can be developed as molecular markers for peach breeding. Phenotypic analysis showed that fruit firmness in the slow-ripening cv. ‘SAAS 030′ significantly decreased during late ripening stages, whereas that in the stony hard cv. ‘BRY’ remained relatively stable. Targeted metabolomics analysis quantified 39 VOCs and 37 non-VOCs, among which lactone contents were positively correlated with d -galacturonic acid. All six lactones significantly increased during the ripening in ‘SAAS 030′, but showed little change in ‘BRY’. Similarly, transcript level of 23 DEGs increased gradually during ripening in ‘SAAS 030′, but remained relatively constant in ‘BRY’. Comparative analysis of resequencing data from 54 peach accessions identified five SNP loci (SNP_14092032_A/G, SNP_14092292_T/C, SNP_18844192_G/T, SNP_18854859_C/T, SNP_18857454_T/C) distributed across two functional genes, PpYUC11 and PpACX2 . These SNPs formed into six haplotype patterns that were simultaneously associated with both lactone content and fruit texture. These results provide valuable molecular resources for developing breeding tools to improve the efficiency and precision of peach quality breeding.