Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (<em>Cerasus humilis</em>) Using a High-Density Genetic Map

Background/Objectives: The Chinese dwarf cherry (Cerasus humilis) is an endemic shrub fruit tree species in China. Its fruit are flavorful, nutrient-rich, and have considerable research and utilization potential. However, most currently-cultivated varieties of Cerasus humilis are highly acidic and primarily used for processing. Consumer-preferred, low-acid, fresh-eating varieties are scarce, limiting industrial development. We used 208 F₁ individuals derived from a cross between high-acid “Nongda 4” and the low-acid “DS-1.” Methods: Restriction site-associated DNA-sequencing (RAD-seq) was used to develop single nucleotide polymorphism (SNP) markers and construct a high-density genetic linkage map. Using two years of fruit titratable acidity phenotypic data, quantitative trait locus (QTL) mapping and candidate gene screening were performed. Results: The genetic map contained 2491 SNP markers, assigned to eight linkage groups. The total genetic distance was 672.71 cM, with an average distance of 0.27 cM between markers, indicating high map quality. QTL mapping identified 18 loci associated with fruit titratable acidity, including 11 major-effect QTLs (logarithm of odds, LOD ≥3.5). These major-effect QTLs were concentrated on linkage groups LG2 and LG5, with an explained phenotypic variation of 8.6–31.13%. Two candidate genes were identified within QTL intervals: phosphoester phosphatase and MATE transmembrane transporter. The phosphatase gene’s expression showed a strong correlation with titratable acid content (P &lt; 0.01, correlation coefficient 0.93), suggesting that it plays an important role regulating fruit acidity in Cerasus humilis. Conclusions: This study supports marker-assisted breeding of low-acid, fresh-eating varieties, aiding commercial promotion of Cerasus humilis.