Identification and Characterization of DAMs Mutations Associated With Early Blooming in Sweet Cherry, and Validation of DNA-Based Markers for Selection

Abstract

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.

Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry

“…Marker-assisted identification/selection (MAS) is an active way to get DNA markers associated with valuable traits that accelerate the breeding process by replacing the selection with a phenotype to the selection at the DNA or gene level, which has been widely employed in fruit trees [10,11]. SSRs, or microsatellites, are short tandem repeats of one to six nucleotides, which are widely distributed in coding and non-coding regions of the whole genome [12,13].…”

A chromosome-scale assembly for tetraploid sour cherry (Prunus cerasusL.) ‘Montmorency’ identifies three distinct ancestralPrunusgenomes

“…We next carried out a phylogenetic analysis of all 18 and 12 DAM genes in ‘Montmorency’ and P. fruticosa , respectively, with manually annotated DAM genes from P. avium ( Figure 6b ) (30). All gene numbers and NCBI identifiers associated with this analysis can be found in Supplementary Table 4 .…”

“…To demonstrate the utility of the genome, we identified, manually annotated, and assigned progenitor subgenomes to two sets of genes present in the Prunus lineage. The first set includes the Dormancy-Associated MADS box genes (DAMs): highly conserved genes initially discovered in peach ( P. persica ) with major effects on dormancy transitions and flowering time in Prunus species (23–30). The second set includes the self-incompatibility S -allele genes that make up the S -haplotype, S -ribonuclease ( S -RNase) and S -locus F-box (SFB) (31–41).…”

Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus

“…In this region of the evergrowing ( EVG ) peach mutant, which does not enter dormancy [ 103 ], four of these DAM genes are deleted [ 72 ]. In sweet cherry, mutations in DAM family genes were identified in an early-blooming cultivar: a large deletion (694 bp) upstream of PavDAM1 , and various INDELs and SNPs in PavDAM4/5 UnTranslated Regions (UTRs) [ 92 ]. Additionally, the transformation of Arabidopsis thaliana with peach and P. mume MADS-box genes produced early-flowering [ 73 , 74 ].…”