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 (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, 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 NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing NAC18.1 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. NAC18.1 encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). We introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.

Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

“…Further, each variable in PCA should ideally capture an independent biological feature of apples. However, some phenotypes analysed here are correlated, such as harvest date and firmness [ 23 ], and their variation may be driven by the same biological feature [ 27 ]. Therefore, interpreting our PCA as a quantification of the degree of phenotypic differentiation between cultivated and wild apples should take these caveats into consideration.…”

“…Similarly, selection for firm apples may explain why cultivated apples were harvested 15 days later than wild apples, since harvest date and firmness are strongly correlated [ 23 , 29 ]. It is well established that harvest date is a reliable predictor of fruit firmness, and these two phenotypes may be regulated by a common molecular pathway [ 27 ]. Thus, preference for firm fruit could be directly impacting the selection for apples with later harvest dates.…”

NAC Transcription Factor Family Regulation of Fruit Ripening and Quality: A Review

“…When MdNAC18.1, a homolog of SlNOR in tomato, was overexpressed in the nor mutant, the expression of the key ethylene biosynthesis gene SlACS2 was enhanced, the non-ripening phenotype of nor fruit could be partially restored, and MdNAC18.1 was suggested to be an indicator of apple harvest date, and fruit firmness at harvest and after harvest. Therefore, MdNAC18.1 may control apple fruit ripening in a conserved way, by regulating ethylene production [73].…”

Editorial: Improvement for Quality and Safety Traits in Horticultural Plants

“…For example, a locus strongly associated with firmness and harvest date of fruit was identified in apple by GWAS and the causal gene was found to encode the transcription factor NAC18.1 . Single nucleotide polymorphisms (SNPs) were found in both the CDS and promoter regions of NAC18.1 , leading to the differential ripening programs among the apple accessions (Migicovsky et al, 2021 ). Another interesting example reported the identification of a non-bitter allele fixed in C. lanatus by genome resequencing, which helped understand the domestication history of watermelons and their improvement (Guo et al, 2019 ).…”