Chromosome-level genome assembly of a blood-fleshed peach ‘ZhongHuaXueTao’ provides new insights into fruit flesh color and maturation

Peach ( Prunus persica ) is an economically significant Rosaceae fruit. While the genome of the ‘Lovell’ reference has been previously released, genome-level variations remain underexplored. Here, we present a chromosome-level genome assembly of a blood-fleshed peach ‘ZhongHuaXueTao’ (‘ZHXT’), an ancient landrace primarily cultivated in central China. The ‘ZHXT’ genome spans 253.28 Mb with a scaffold N50 of 29.37 Mb. Genome comparison with the ‘Lovell’ reference genome uncovered 385 369 single nucleotide polymorphisms (SNPs), 103 395 insertions, 54 512 deletions, and 6 250 structural variants. Gene family analysis highlighted expansions in transmembrane transporter activity and immune response. RNA-seq analyses demonstrated distinct expression patterns of anthocyanin biosynthesis genes ( PpUFGT-1 , PpANS , PpPAL and PpGST) in ‘ZHXT’ compared with white- and yellow-fleshed peaches. Alignment of 338 peach accessions against the ‘ZHXT’ genome identified 11 513 248 SNPs and 1 539 000 InDels markers. Genome-wide association analysis (GWAS) pinpointed multiple genetic loci and candidate genes for five agronomic traits, including fruit flesh color, fruit shape, flesh color around the stone, fruit mature date, and fruit development period. PpMDL1 , PpCCD4 , and PpGTPase were identified as candidate genes for the blood-fleshed trait, while PpUVR8 and PpNAC5 genes were identified as candidates for the fruit mature date trait. Genotype frequency and expression analysis further confirmed the reliability of these trait loci. In general, these genomic resources will enhance our understanding of genetic diversity and facilitate functional genomics in peach breeding and improvement.