In sweet cherry (Prunus avium L.), quantitative trait loci have been identified for fruit maturity, colour, firmness, and size to develop markers for marker-assisted selection. However, resolution is usually too low in those analyses to directly target candidate genes, and some associations are missed. In contrast, genome-wide association studies are performed on broad collections of accessions, and assemblies of reference sequences from Tieton and Satonishiki cultivars enable identification of single nucleotide polymorphisms after whole-genome sequencing, providing high marker density.
Two hundred and thirty-five sweet cherry accessions were sequenced and phenotyped for harvest time and fruit colour, firmness, and size. Genome-wide association studies were used to identify single nucleotide polymorphisms associated with each trait, which were verified in breeding material consisting of 64 additional accessions. A total of 1,767,106 single nucleotide polymorphisms were identified. At that density, significant single nucleotide polymorphisms could be linked to co-inherited haplotype blocks (median size ~10 kb). Thus, markers were tightly associated with respective phenotypes, and individual allelic combinations of particular single nucleotide polymorphisms provided links to distinct phenotypes. In addition, yellow-fruit accessions were sequenced, and a ~90-kb-deletion on chromosome 3 that included five MYB10 transcription factors was associated with the phenotype.
Overall, the study confirmed numerous quantitative trait loci from bi-parental populations using high-diversity accession populations, identified novel associations, and genome-wide association studies reduced the size of trait-associated loci from megabases to kilobases and to a few candidate genes per locus. Thus, a framework is provided to develop molecular markers and evaluate and characterize genes underlying important agronomic traits.
The sweet cherry plant (Prunus avium L.) is primarily self-incompatible, with so-called S-alleles responsible for the inability of flowers to be pollinated not only by their own pollen grains but also by pollen from other cherries having the same S-alleles. This characteristic has wide-ranging impacts on commercial growing, harvesting, and breeding. However, mutations in S-alleles as well as changes in the expression of M locus-encoded glutathione-S-transferase (MGST) can lead to complete or partial self-compatibility, simplifying orchard management and reducing possible crop losses. Knowledge of S-alleles is important for growers and breeders, but current determination methods are challenging, requiring several PCR runs. Here we present a system for the identification of multiple S-alleles and MGST promoter variants in one-tube PCR, with subsequent fragment analysis on a capillary genetic analyzer. The assay was shown to unequivocally determine three MGST alleles, 14 self-incompatible S-alleles, and all three known self-compatible S-alleles (S3′, S4′, S5′) in 55 combinations tested, and thus it is especially suitable for routine S-allele diagnostics and molecular marker-assisted breeding for self-compatible sweet cherries. In addition, we identified a previously unknown S-allele in the ’Techlovicka´ genotype (S54) and a new variant of the MGST promoter with an 8-bp deletion in the ´Kronio´ cultivar.
Non-invasive flesh firmness prediction using near infrared spectroscopy has been perfected and validated on three apple varieties. Three novel calibration models were developed following three year's of repeated large-scale sampling of stored commercial apple varieties ‘Gala’, ‘Red Jonaprince’ and ‘Jonagored’. The spectroscopic results were compared directly with those obtained using the invasive method. Increased accuracy of calibration models was achieved with the newly established data collection model. The results exhibited coefficient of determination for calibration, R2, and ratio of prediction to deviation (RPD) in excess of 0.91 and 2.3, respectively, thus enabling excellent prediction of flesh firmness via a non-invasive and fast spectroscopic approach. The highest R2 obtained was 0.94, RPD 2.6 root mean square error of calibration 5.87 N, and root mean square error of cross-validation (internal) 6.75 N were found for variety ‘Red Jonaprince’. Our complex long-term study provided excellent external validated calibration models and the approach can help developing calibration models for commercial sorting lines using near infrared spectroscopy.
The cropping of six sweet cherry cultivars that originated in the Research and Breeding Institute of Pomology at Holovousy, and a standard one, ‘Burlat’, were evaluated on three rootstocks in the period of 2007–2017. Trees planted in a spacing of 1.5 m × 5.0 m were trained as tall spindle axes utilising their natural tendency to develop a central leader. On the standard rootstock, P-TU-2, ‘Tim’ was the most productive with a mean total harvest of 47.6 kg per tree. ‘Sandra’ yielded the most on the PHLC rootstock with 56.2 kg per tree and ‘Helga’ yielded the most on Gisela 5 with a mean total harvest of 55.9 kg per tree. The mean impact of the rootstock on the tree vigour, measured upon the trunk cross section area, ranged from 148.4 cm2 on the standard rootstock P-TU-2 to 114.1 cm2 on the PHLC and 125.2 cm2 on Gisela 5 . On the standard rootstock P-TU-2, the most vigorous one according to this criterion was ‘Jacinta’ (178.0 cm2) whereas ‘Justyna’ (109.7 cm2) was the least vigorous. On the PHLC, the most vigorous was ‘Sandra’ (147.2 cm2) and the least was ‘Amid’ (94.0 cm2). The other tree characteristics were mainly dependant on the cultivar and minimally, or not at all, influenced by the rootstock vigour.
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