Allelic diversity of NAC18.1 is a major determinant of fruit firmness and harvest date in apple ( Malus domestica )

Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of ripening and associated textural changes are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple () using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, , cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ~800 apple accessions. In this population, we compared to three other ripening-related markers currently used by breeders (, , and ), and found that the effect of the genotype on both traits greatly exceeded that observed for the other markers. By sequencing across 18 accessions, we revealed two predominant haplotypes containing the SNP previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. encodes a protein with high similarity to the NON-RIPENING (NOR) transcription factor, an early regulator of ripening in tomato (). To test whether these genes are functionally orthologous, we introduced transgenes into the tomato mutant and showed that both haplotypes complement the ripening deficiency. Taken together, these results indicate that polymorphisms in underlie substantial variation in apple firmness and harvest time through modulation of a conserved ripening program.