QTL mapping of phenolic compounds and fruit colour in sweet cherry using a 6+9K SNP array genetic map

Abundant phytochemical content in sweet cherry (Prunus avium L.) has health-promoting properties and contributes to fruit quality traits. To identify QTLs associated with sweet cherry phenolic compounds (phenolic acids and flavonoids), an F-1 sweet cherry population ('Vic' x 'Cristobalina', N = 161) was phenotyped by HPLC-DAD/FLD. Three hydroxycinnamic acids (neochlorogenic acid, p-coumaroylquinic acid, and p-coumaric acid) and four anthocyanins (cyanidin 3-O-glucoside, cyanidin 3-O-rutinoside, peonidin 3-O-glucoside, and peonidin 3-O-rutinoside) were identified and quantified. The same population was also phenotyped for skin and flesh fruit colour for 3 years using two methods. The population was genotyped with the Illumina RosBREED Cherry 6+9K SNP array, which allowed constructing high-density linkage maps ('Vic': 910 SNPs, 636.7 cM; 'Cristobalina': 789 SNPs, 666.0 cM), and saturating previously developed SNP maps for the same parental cultivars. QTL analyses revealed major QTLs associated to hydroxycinnamic acids content on a narrow region of linkage group (LG) 1, at very high significance (percentage of variance explained > 60%; LOD > 20). Thus, revealing that hydroxycinnamic acids content regulation is determined by a major gene. Candidate gene rho-coumarate 3-hydroxylase (C3H) was found to co-localize within these major LG1 QTLs, and next to QTL cofactor SNPs. Therefore, C3H is a strong candidate for hydroxycinnamic acid content regulation in sweet cherry, and probably in other Prunus species. For anthocyanins content and skin and flesh colour, major QTLs were found overlapping on LG3. These findings validate the previous colour QTLs reported in sweet cherry and the genetic model of a major gene regulating fruit coloration. PavMYB10, previously reported as a candidate gene of colour regulation in sweet cherry, co-localized in major anthocyanin content and colour QTLs, thus confirming is the candidate gene for these traits regulation in sweet cherry. Additionally, other anthocyanins content and colour QTLs detected on LGs 4 and 7 may be also relevant in colour regulation in sweet cherry.