Multiple-population QTL mapping of maturity and fruit-quality traits reveals LG4 region as a breeding target in sweet cherry (Prunus avium L.)

Abstract

Sweet cherry maturity date and fruit quality are relevant traits for its marketability, transport, and consumer acceptance. In this work, sweet cherry fruit development time, maturity date, and commercial fruit-quality traits (size, weight, firmness, soluble solid content, and titratable acidity) were investigated to improve the knowledge of their genetic control, and to identify alleles of breeding interest. Six sweet cherry populations segregating for these traits were used for QTL analyses. These populations descend from cross- and self-pollinations of local Spanish sweet cherries 'Ambrunés' and 'Cristobalina', and breed cultivars ('Brooks', 'Lambert', or 'Vic'). The six populations (n = 411), previously genotyped with RosBREED Cherry 6 K SNP array, were phenotyped for 2 years. QTL analyses were conducted using a multifamily approach implemented by FlexQTL^™. Fruit development time, soluble solid content, and titratable acidity QTLs are first reported in sweet cherry in this work. Significant QTLs were detected for all the traits. Eighteen were more stable as they were detected for 2 years. Of these, nine are first reported in this work. The major QTLs for fruit development time, maturity date, firmness, and soluble solid content were identified on the same narrow region of linkage group 4. These traits also showed significant positive correlation (long fruit development time associated with late maturity, high firmness, and high SSC). NAC transcription factor genes identified on this LG4 region may be candidate genes for the regulation of these traits in sweet cherry, as previously described in syntenic regions of other Rosaceae species. Haplotypes of breeding interest on this LG4 genomic region were identified and will be useful for sweet cherry breeding from this and related plant material.

Keywords: Plant breeding.

Fig. 1

Violin-plot distribution and phenotype individual values (dots) of fruit development time (FD), maturity date (MD), fruit size (FS), fruit weight (FW), fruit firmness (FF), soluble solid content (SSC), and titratable acidity (TA) per population, in years 2017 (purple) and 2018 (blue). Black lines indicate median values. Red lines indicate ‘Cristobalina’ phenotypic values (female parental values in F₁s) and yellow lines indicate male parental values

Fig. 2

Spearman correlation coefficient among traits, trait distribution histograms, and correlation plots in 2017 (a) and 2018 (b). Asterisks indicate correlation significance (*p < 0.01; **p < 0.001; ***p < 0.0001). Positive and negative correlations at p < 0.0001 are marked in blue and orange, respectively

Fig. 3

Genetic positions on the consensus linkage map of QTLs detected both years. QTL interval overlapping both years is shown in bold, intervals detected only 1 year are shown with diagonal bars. All QTLs detected, including each year interval, are shown in Supplementary Fig. 1. Bloom-time QTLs shown were previously published and correspond to data from the same plant material and same years

Fig. 4

Haplotypes of LG4 major QTLs for fruit development period (FD), maturity date (MD), and firmness (FF) QTLs (qP-FD4.2^m/qP-MD4.2^m/qP-FF4.1^m; LG4: 50–54 cM) in parental and ancestor cultivars, and in each population. Mean phenotype values of both years of each segregating class detected in each population are shown. Values for these haplotypes are also shown for SSC. Means significant differences between segregating classes are identified by different letters (p < 0.05)