Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor

Abstract

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.

Molecular Insights of Fruit Quality Traits in Peaches, Prunus persica

“…Based on the acidity levels, peaches can be categorized as high-acid and low-acid favored by western and eastern consumers, respectively. Evidence suggests that both acidity cultivars were propagated through natural selection and quality improvement efforts by the breeders [ 18 , 19 , 20 , 21 , 22 ]. The content and composition of soluble sugars and organic acids determine the organoleptic peach flavor attributes.…”

“…Various GWAS studies narrowed the physical position of the D locus but with consistency might be located from 700 to 1000 kbp on Chr5. Though major QTLs for fruit acidity were identified on the D locus, few QTLs were also present in chromosomes 1,2, and 6 [ 22 , 26 , 27 ]. TA (titratable acidity) and pH were the commonly measured acid-related attributes, and low-acid phenotype is the dominant trait in peaches.…”

“…Five putative ALMT (aluminum-activated malate transporter 1) were implicated in increased malate content, of which one putative vacuolar malate transporter gene named PpALMT1 (Pp.LH.06G01819) was transiently overexpressed in peach mesocarp showed increased malate content than vector control mesocarp. PpALMT1 could be a candidate gene causing divergence in fruit acidity between cultivars [ 22 ]. GWAS analysis was performed for TA, pH, malate, and citrate content.…”

“…Sucrose (~75 to 76%) was found to be a major contributor, followed by fructose (9 to 10%), glucose (8 to 12%), and sorbitol (3 to 4%) [ 29 , 30 , 31 , 32 ]. GWAS identified a significant locus associated with sucrose (Chr5: 614,754–1,109,368 bp), fructose (Chr1: 11,738,129–12,006,040 bp), glucose (Chr4: 10,736,973–12,413,438 bp), and sorbitol (Chr6: 22,350,242–22,451,210 bp) [ 22 ]. Analysis of improved peach germplasm concluded an increase in the sweetness in improved germplasm than in wild peaches, and it is due to the accumulation of fructose.…”

“…Analysis of improved peach germplasm concluded an increase in the sweetness in improved germplasm than in wild peaches, and it is due to the accumulation of fructose. The candidate gene associated with fructose accumulation was searched, and PpERDL16 (early response to dehydration 6-like 16) was identified as the causal gene [ 22 ]. Comparative genome studies and biochemical analysis on peach flavor components of wild and modern peaches help to understand the molecular bases of new varieties.…”