‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the ‘Shanghai Shuimi’ landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.

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