Lemon is a healthy fruit with high medicinal value.

Bud dormancy is crucial for winter survival and is characterized by the inability of the bud meristem to respond to growth-promotive signals before the chilling requirement (CR) is met. However, our understanding of the genetic mechanism regulating CR and bud dormancy remains limited. This study identified PpDAM6 (DORMANCY-ASSOCIATED MADS-box) as a key gene for CR using a genome-wide association study analysis based on structural variations in 345 peach (Prunus persica (L.) Batsch) accessions. The function of PpDAM6 in CR regulation was demonstrated by transiently silencing the gene in peach buds and stably overexpressing the gene in transgenic apple (Malus × domestica) plants. The results showed an evolutionarily conserved function of PpDAM6 in regulating bud dormancy release, followed by vegetative growth and flowering, in peach and apple. The 30-bp deletion in the PpDAM6 promoter was substantially associated with reducing PpDAM6 expression in low-CR accessions. A PCR marker based on the 30-bp indel was developed to distinguish peach plants with non-low and low CR. Modification of the H3K27me3 marker at the PpDAM6 locus showed no apparent change across the dormancy process in low- and non-low- CR cultivars. Additionally, H3K27me3 modification occurred earlier in low-CR cultivars on a genome-wide scale. PpDAM6 could mediate cell–cell communication by inducing the expression of the downstream genes PpNCED1 (9-cis-epoxycarotenoid dioxygenase 1), encoding a key enzyme for ABA biosynthesis, and CALS (CALLOSE SYNTHASE), encoding callose synthase. We shed light on a gene regulatory network formed by PpDAM6-containing complexes that mediate CR underlying dormancy and bud break in peach. A better understanding of the genetic basis for natural variations of CR can help breeders develop cultivars with different CR for growing in different geographical regions.

Sugar content is a key determinant of peach (Prunus persica) fruit quality, influencing taste, consumer preferences, and market value. However, the roles of Major Facilitator Superfamily (MFS) transporters in sugar metabolism and regulation remain largely unexplored. This study employed a combination of spatial metabolomics, quantitative genetics, transcriptomics, comparative genomics, and functional genomics to investigate the role of 67 MFS members in balancing sugar metabolism during peach fruit development. Spatial metabolomics revealed dynamic sugar distribution patterns, with ERD6-like transporters (PpERDL16-1) and tonoplastic sugar transporters 1 (PpTST1) promoting sucrose accumulation and polyol/monosaccharide transporters 5 (PpPMT5-1) and sucrose transporters 4 (PpSUT4) reducing sucrose transport during fruit ripening. Functional studies confirmed these roles: PpERDL16-1 overexpression enhanced sucrose transport, and PpPMT5-1 or PpSUT4 silencing reduced sugar levels in peach fruit. Quantitative trait locus (QTL) mapping identified a major locus on chromosome 5, upstream of PpTST1, forming distinct haplotypes (Hap1 and Hap2). Hap1 was associated with lower PpTST1 expression and higher sugar and soluble solids content (SSC), while Hap2 was linked to higher PpTST1 expression and lower sugar content. This inverse relationship suggests that upstream genetic variants fine-tune PpTST1 expression in a context-dependent manner, potentially through interactions with transcription factors or epigenetic modifiers. Notably, PpTST1 overexpression increased sugar content but did not alter SSC, indicating compensatory mechanisms such as changes in organic acid metabolism or water content. These results illuminate the molecular mechanisms regulating sugar homeostasis in peach fruits, providing valuable targets for the genetic improvement of fruit quality through breeding programs.

Peach (Prunus persica) landrace has typical regional characteristics, strong environmental adaptability, and contains many valuable genes that provide the foundation for breeding excellent varieties. Therefore, it is necessary to assemble the genomes of specific landraces to facilitate the localization and utilization of these genes. Here, we de novo assembled a high-quality genome from an ancient blood-fleshed Chinese landrace Tianjin ShuiMi (TJSM) that originated from the China North Plain. The assembled genome size was 243.5 Mb with a contig N50 of 23.7 Mb and a scaffold N50 of 28.6 Mb. Compared with the reported peach genomes, our assembled TJSM genome had the largest number of specific structural variants (SVs) and long terminal repeat-retrotransposons (LTR-RTs). Among the LTR-RTs with the potential to regulate their host genes, we identified a 6688 bp LTR-RT (named it blood TE) in the promoter of NAC transcription factor-encoding PpBL, a gene regulating peach blood-flesh formation. The blood TE was not only co-separated with the blood-flesh phenotype but also associated with fruit maturity date advancement and different intensities of blood-flesh color formation. Our findings provide new insights into the mechanism underlying the development of the blood-flesh color and determination of fruit maturity date and highlight the potential of the TJSM genome to mine more variations related to agronomic traits in peach fruit.