Allelic variations of endopolygalacturonase genes associated with fruit softening in apricot (Prunus armeniaca)

Fruit of most apricot (Prunus armeniaca L.) cultivars becomes soft rapidly during ripening, and the loss of firmness causes postharvest deterioration that limits the shelf-life of the fruit. Fruit softening is largely associated with the breakdown of the cell walls in the fruit, and endopolygalacturonase is one of the most important enzymes involved in this process. To identify allelic variations in the PaPG gene (an endopolygalacturonase gene in apricots; GenBank accession no. HG540310), eight PaPG alleles were isolated from two firm-fleshed cultivars and two soft-fleshed cultivars of apricot. There were 67 single-nucleotide polymorphisms (SNPs) in the PaPG alleles; 50 were found in the non-coding region, whereas 17 were in the encoding region. This indicated that the introns of the PaPG alleles were more variable. A general comparison of the deduced amino acid sequences of the PaPG protein revealed six differing amino acids, indicating that only six SNPs induced codon alteration. According to the phenotype data, there were 16 allelic variations correlated with fruit softening in PaPG alleles. Phylogenetic analysis showed that PaPG alleles in firm-fleshed cultivars were clustered in one clade and PaPG alleles in soft-fleshed cultivars were clustered in another. The information generated by this study will contribute to marker-assisted selection (MAS) involved in the loss of fruit firmness in apricots and the development of functional markers for breeding apricots with a longer shelf-life.