Genome-wide association mapping in a sweet cherry germplasm collection(Prunus avium L.)reveals candidate genes for fruit quality traits

In sweet cherry(Prunus avium L.),large variability exists for various traits related to fruit quality.There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands.With this objective,a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years,and characterized using a genotyping-by-sequencing approach.The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes.We identified numerous SNP-trait associations for global fruit size(weight,width,and thickness),fruit cracking,fruit firmness,and stone size,and we pinpointed several candidate genes involved in phytohormone,calcium,and cell wall metabolisms.Finally,we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations.This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality,and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.

Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

The timing of fruit maturity is an important trait in sweet cherry production and breeding.Phenotypic variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control,but that control might be complicated by phenotypic instability across environments.Although such genotype-by-environment interaction(G×E)is a common phenomenon in crop plants,knowledge about it is lacking for fruit maturity timing and other sweet cherry traits.In this study,1673 genome-wide SNP markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA,thus sampling eight‘environments’.The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic predictions.Linkage disequilibrium among marker loci declined rapidly with physical distance,and ordination of the relationship matrix suggested no strong structure among germplasm.The most parsimonious G×E model allowed heterogeneous genetic variance and pairwise covariances among environments.Narrow-sense genomic heritability was very high(0.60–0.83),as was accuracy of predicted breeding values(>0.62).Average correlation of additive effects among environments was high(0.96)and breeding values were highly correlated across locations.Results indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new environments.Limited G×E for this trait indicated that phenotypes of individuals will be stable across similar environments.Equivalent analyses for other sweet cherry traits,for which multiple years of data are commonly available among breeders and cultivar testers,would be informative for predicting performance of elite selections and cultivars in new environments.

Multi-year analyses on three populations reveal the first stable QTLs for tolerance to rain-induced fruit cracking in sweet cherry (Prunus avium L.)

Rain-induced fruit cracking is a major problem in sweet cherry cultivation.Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon,whereas genetic studies have lagged behind.The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking.We hypothesized that a large genetic variation would be revealed,by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance.Three populations were evaluated over 7–8 years by estimating the proportion of cracked fruits for each genotype at maturity,at three different areas of the sweet cherry fruit:pistillar end,stem end,and fruit side.An original approach was adopted to integrate,within simple linear models,covariates potentially related to cracking,such as rainfall accumulation before harvest,fruit weight,and firmness.We found the first stable quantitative trait loci(QTLs)for cherry fruit cracking,explaining percentages of phenotypic variance above 20%,for each of these three types of cracking tolerance,in different linkage groups,confirming the high complexity of this trait.For these and other QTLs,further analyses suggested the existence of at least two-linked QTLs in each linkage group,some of which showed confidence intervals close to 5 cM.These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars.Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals,allowing the exploration of underlying candidate genes.