Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. Here we explore the evolutionary history of peach using a large-scale SNP data set generated from 58 high-coverage genomes of cultivated peach and closely related relatives, including 44 newly re-sequenced accessions and 14 accessions from a previous study. Our analyses suggest that peach originated about 2.47 Mya in southwest China in glacial refugia generated by the uplift of the Tibetan plateau. Our exploration of genomic selection signatures and demographic history supports the hypothesis that frugivore-mediated selection occurred several million years before the eventual human-mediated domestication of peach. We also identify a large set of SNPs and/or CNVs, and candidate genes associated with fruit texture, taste, size, and skin color, with implications for genomic-selection breeding in peach. Collectively, this study provides valuable information for understanding the evolution and domestication of perennial fruit tree crops.

Background: Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.Results: Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of thePpOFP2gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes thatPpOFP2is causal for flat-fruit shape.Conclusions: Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.

A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.

This study performed physiological, transcriptome, and metabolite analyses of peach fruit under different nitrogen (N) conditions at different growth stages. Nitrogen management directly affected the yield, fruit quality, and metabolites of peach in different growth stages. Different fertilizing time influenced yield and leaf N concentration. RNA-Seq was used to analyze the influence of N levels at the fruit pit hardening (PH) and fruit expansion (FE) stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed differentially expressed genes (DEGs) related to carbon and nitrogen metabolite processes. Metabolome analysis shows that applying different nitrogen fertilizers at different growth stages of peach mainly affected metabolites related to carbon and amino acids. This research provides insight into the metabolic processes underlying different N responses during different growth stages and provides a foundation to improve the efficiency of N use in peach.

Pre-harvest nitrogen (N) application has been proven effective for improving fruit yield and quality. However, a full understanding of how differences in N availability/plant N status influence the transcriptome and metabolism underlying yield formation and quality remains elusive. Here, a combined analysis of the morpho-physiological qualities, transcriptome, and metabolite of peach plants was performed under different nitrogen levels at fruit pit hardening (PH) and fruit expansion (FE). Nitrogen fertilizer directly affected the yield, fruit quality, and metabolites of peach at different growth stages. RNA-Seq was used to analyze the influence of N levels at PH and FE in peach. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the differentially expressed genes (DEGs) focused on flavonoid biosynthesis and secondary metabolite biosynthetic processes. The differential metabolites among the different treatments were mainly involved in flavonoid metabolism. Transcriptome analysis showed that applying different nitrogen fertilizers at different growth stages of peach mainly affected the synthesis of flavonoids in fruit. Overall, these results suggest that the impacts of pre-harvest N application on fruit yield and quality differ between developmental stages. This research provides a full understanding of the metabolic processes underlying fruit growth and development in peach, providing a theoretical basis for the improvement of nitrogen use efficiency in peach trees.