Bloom time in sweet cherry (Prunus avium L.) is a highly heritable trait that varies between genotypes and depends on the environmental conditions. Bud-break occurs after chill and heat requirements of each genotype are fulfilled, and dormancy is released. Bloom time is a critical trait for fruit production as matching cultivar adaptation to the growing area is essential for adequate fruit set. Additionally, low chilling cultivars are of interest to extend sweet cherry production to warmer regions, and for the crop adaptation to increasing winter and spring temperatures. The aim of this work is to investigate the genetic control of this trait by analyzing multiple families derived from the low chilling and extra-early flowering local Spanish cultivar 'Cristobalina' and other cultivars with higher chilling requirements and medium to late bloom times. Bloom time evaluation in six related sweet cherry populations confirmed a high heritability of this trait, and skewed distribution toward late flowering, revealing possible dominance of the late bloom alleles. SNP genotyping of the six populations (n = 406) resulted in a consensus map of 1269 SNPs. Quantitative trait loci (QTL) analysis using the Bayesian approach implemented by FlexQTL™ software revealed two major QTLs on linkage groups 1 and 2 (qP-BT1.1m and qP-BT2.1m) that explained 47.6% of the phenotypic variation. The QTL on linkage group 1 was mapped to a 0.26 Mbp region that overlaps with the DORMANCY ASSOCIATED MADS-BOX (DAM) genes. This finding is consistent with peach results that indicate that these genes are major determinants of chilling requirement in Prunus. Haplotype analysis of the linkage group 1 and 2 QTL regions showed that 'Cristobalina' was the only cultivar tested that contributed early bloom time alleles for these two QTLs. This work contributes to knowledge of the genetic control of chilling requirement and bloom date and will enable marker-assisted selection for low chilling in sweet cherry breeding programs.

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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.

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The Spanish local cultivar 'Ambrunés' stands out due to its high organoleptic quality and fruit firmness. These characteristics make it an important parent for breeding cherries with excellent fresh and post-harvest quality. In this work, an F1 sweet cherry population (n=140) from 'Ambrunés' × 'Sweetheart' was phenotyped for two years for fruit diameter, weight and firmness and genotyped with the RosBREED cherry Illumina Infinium ® 6K SNP array v1. These data were used to construct a linkage map and to carry out QTL mapping of these fruit quality traits. Genotyping of the parental cultivars revealed that 'Ambrunés' is highly heterozygous, and its genetic map is the longest reported in the species using the same SNP array. Phenotypic data analyses confirmed a high heritability of fruit size and firmness and a distorted segregation towards softer and smaller fruits. However, individuals with larger and firmer fruits than the parental cultivars were observed, revealing the presence of alleles of breeding interest. In contrast to other genetic backgrounds in which a negative correlation was observed between firmness and size, in this work, no correlation or low positive correlation was detected between both traits. Firmness, diameter and weight QTLs detected validated QTLs previously found for the same traits in the species and major QTLs for the three traits were located on a narrow region of LG1 of 'Ambrunés'.Haplotype analyses of these QTLs revealed haplotypes of breeding interest in coupling phase in 'Ambrunés', which can be used for the selection of progeny with larger and firmer fruits.

Dormancy release and bloom time of sweet cherry cultivars depend on the environment and the genotype. The knowledge of these traits is essential for cultivar adaptation to different growing areas, and to ensure fruit set in the current climate change scenario. In this work, the major sweet cherry bloom time QTL qP-BT1.1m (327 Kbs; Chromosome 1) was scanned for candidate genes in the Regina cv genome. Six MADS-box genes (PavDAMs), orthologs to peach and Japanese apricot DAMs, were identified as candidate genes for bloom time regulation. The complete curated genomic structure annotation of these genes is reported. To characterize PavDAMs intra-specific variation, genome sequences of cultivars with contrasting chilling requirements and bloom times (N = 13), were then mapped to the ‘Regina’ genome. A high protein sequence conservation (98.8–100%) was observed. A higher amino acid variability and several structural mutations were identified in the low-chilling and extra-early blooming cv Cristobalina. Specifically, a large deletion (694 bp) upstream of PavDAM1, and various INDELs and SNPs in contiguous PavDAM4 and -5 UTRs were identified. PavDAM1 upstream deletion in ‘Cristobalina’ revealed the absence of several cis-acting motifs, potentially involved in PavDAMs expression. Also, due to this deletion, a non-coding gene expressed in late-blooming ‘Regina’ seems truncated in ‘Cristobalina’. Additionally, PavDAM4 and -5 UTRs mutations revealed different splicing variants between ‘Regina’ and ‘Cristobalina’ PavDAM5. The results indicate that the regulation of PavDAMs expression and post-transcriptional regulation in ‘Cristobalina’ may be altered due to structural mutations in regulatory regions. Previous transcriptomic studies show differential expression of PavDAM genes during dormancy in this cultivar. The results indicate that ‘Cristobalina’ show significant amino acid differences, and structural mutations in PavDAMs, that correlate with low-chilling and early blooming, but the direct implication of these mutations remains to be determined. To complete the work, PCR markers designed for the detection of ‘Cristobalina’ structural mutations in PavDAMs, were validated in an F2 population and a set of cultivars. These PCR markers are useful for marker-assisted selection of early blooming seedlings, and probably low-chilling, from ‘Cristobalina’, which is a unique breeding source for these traits.

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Bloom date (BD) in peach is determined by the dynamic relationship between chilling (CR) and heat requirement (HR) fulfilment during dormancy. Understanding these thermal requirements would enable breeders to adapt new cultivars to variable climates. Among the three traits, HR is the least investigated, with the genetic variability in peach germplasm and interaction between HR, CR and BD still mostly unknown. Therefore, we investigated the HR of 136 peach cultivars over 8 growing seasons (2014–2021) by calculating the growing degree hours (GDH) from the moment their CR was satisfied until full bloom. The HR ranged from 1362 to 10,348 GDH across years and cultivars, with cultivar HR eight-year having the best linear unbiased prediction (BLUP) values from 4808 to 7721 GDH. In addition, a high positive correlation between BD and CR, a negative correlation between CR and HR and a seasonal effect on the correlation between BD and HR were observed. Moreover, simulating HR with different threshold base temperatures (Tb) revealed different trends of GDH accumulation, suggesting that genotype-specific Tb should be determined to allow precise discrimination of this requirement. Peach germplasm showed high variation in HR that could be used in breeding for bloom delay to adapt to different environments and climate change.