Identification of quantitative trait loci (QTL) and development of markers associated with fruit quality traits in strawberry (Fragaria × ananassa Duch.)

Abstract Significant breeding targets in Fragaria species are improvement of the fruit quality traits that the bright red color of these fruits, attributed to anthocyanins, due to its appeal and nutritional value. To reveal the inheritance of the fruit quality traits, we performed quantitative trait loci (QTL) analysis using segregating populations derived from female ‘Fortuna’ and male ‘Rubygem’ cultivars. Entire plants with parents were evaluated for nine phenotypic features in the 2021 and 2022 production years. A total of 28 QTLs were detected for nine (9) quality traits. QTLs controlling regions corresponding to Fana_SNP and iStraw35 arrays were recorded for whole associated loci in each trait. The highest associated locus with phenotypic variation was detected as 26.1% and 10.50 LOD score in LG16 corresponding to Fvb6-1 around 13.3 Mb in the chroma value of the fruit. Linked loci were validated using designed HRM primers, and confirmative results were exhibited from extreme phenotypic plants. Ax-184476583 marker has a major QTL with a 5.24 LOD score and 13.3% phenotypic variance (PV) for xylose, it was located near the 5.2 Mb of Fvb2-3. A marker associated with the lightness value of fruit flesh color was produced in a range of 5.6 and 25.3% PV. Ax-184139018 marker for chroma value of fruit flesh color separated accessions according to phenotype. Markers were pointed on LG2, LG5, LG16 and LG18 corresponding to chr1, chr3, chr6 and chr7, respectively. These markers have been validated for the first time in strawberry breeding, and they could be used to be evaluated in marker-assisted selection for future strawberry breeding programs.