Correspondence between maturity date and molecular variations in a NAC transcription factor of diploid and polyploid Prunus species

Abstract

The maturity date (MD) of Prunus stone fruit has been long known to be a quantitatively inherited trait. A NAC -type gene indicated as PpNAC1 (ppa008301m) has been found recently to be a strong candidate of a major gene influencing MD in peach. A 9-bp insertion in this gene resulted in earlier MD in two segregating peach populations. This study was carried out to test whether this mutation in the PpNAC1 gene can be used as a reliable functional marker for MD in a wide range of peach cultivars of various origins and phenotypic characters. A total of 125 peach cultivars were examined using a 3 × 3 custom chi-square contingency table according to their NAC genotype and MD (early, midseason, and late). Cramer's V equaled 0.478 and the Goodman-Kruskal index (l) was 0.37, indicating an extremely strong correlation between MD and NAC genotype. In addition, we determined 15 sequences from 10 cultivars of five Prunus species including peach, almond, apricot, sour cherry, and European plum with E-values ranging from 9e-88 to 2e-74, supporting their homology to PpNAC1 . A total of 69 single nucleotide polymorphisms and two insertion/deletions were detected in the coding region of the partial NAC domain sequences with three mutations putatively inducing nonconservative amino acid replacements and a nonsense mutation in specific alleles of early ripening apricot and sour cherry cultivars. The results are discussed with focus on the putative molecular mechanisms of mutations in the NAC genes, crop evolutionary perspectives, and the opportunities for designing cost-efficient markers to predict MD in Prunus breeding programs.