Apple Ripening Is Controlled by a NAC Transcription Factor

Abstract

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 pre-harvest ripening and associated textural changes following harvest are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (<i>Malus domestica</i>) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, <i>NAC18.1</i>, may 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 a genetic marker within <i>NAC18.1</i> to markers targeting three other firmness-related genes currently used by breeders (<i>ACS1</i>, <i>ACO1</i>, and <i>PG1</i>), and found that the <i>NAC18.1</i> marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing <i>NAC18.1</i> across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. <i>NAC18.1</i> encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (<i>Solanum lycopersicum</i>). We introduced both <i>NAC18.1</i> transgene haplotypes into the tomato <i>nor</i> mutant and showed that both haplotypes complement the <i>nor</i> ripening deficiency. Taken together, these results indicate that polymorphisms in <i>NAC18.1</i> may underlie substantial variation in apple firmness through modulation of a conserved ripening program.