Apple firmness traced to single gene variant controlling ripening
image: A model showing the roles of MdNAC5 alleles associated with fruit firmness and ripening variation in apple.
Credit: Horticulture Research
Fruit firmness is one of the most critical traits influencing apple quality, consumer acceptance, and postharvest performance. A new study has uncovered how natural genetic variation in the transcription factor MdNAC5 directly determines differences in apple fruit firmness and ripening time. By comparing hybrids of ‘Fuji’ and ‘Cripp’s Pink,’ researchers found that a single A-to-T mutation in MdNAC5 changes amino acid composition, thereby altering ethylene production through regulation of MdACS1 and MdERF3. The MdNAC5A allele accelerates softening, while MdNAC5T maintains firmness for longer. These findings provide a molecular explanation for firmness divergence and offer breeders a promising genetic handle for tailoring fruit quality.
Apple is one of the world's most widely cultivated fruits, yet its quality traits—such as texture, flavor, and storability—are complex, being influenced by multiple genes and environmental factors. Among them, fruit firmness plays a pivotal role, dictating consumer preference and transportability. Breeding for improved firmness has long been challenging due to apple’s long juvenile period, high heterozygosity, and difficulty in precisely identifying causal genes. Past research has linked firmness variation to regions on several chromosomes and to ethylene-related regulators, but clear candidate genes remained elusive. Due to these challenges, there is a need to explore the molecular basis of firmness and ripening in greater depth.
A research team from Northwest A&F University, in collaboration with Yale University, has identified MdNAC5 as a critical gene governing apple fruit firmness and ripening. Their study, published (DOI: 10.1093/hr/uhae284) on October 8, 2024, in Horticulture Research, demonstrates that a single nucleotide variant within MdNAC5 drives divergent firmness outcomes in apples. The work shows how this transcription factor interacts with ethylene pathway genes, offering a breakthrough in understanding the genetic mechanisms underlying apple quality.
To dissect the genetic basis of firmness, the team resequenced 294 F1 hybrids of 'Fuji' and 'Cripp's Pink,' creating a high-density bin map of over 5,000 markers. Quantitative trait locus (QTL) analysis pinpointed MdNAC5 on chromosome 3 as a key regulator, with the strongest statistical signal among all mapped regions. Functional tests revealed that two alleles, MdNAC5A and MdNAC5T, differ by a single A-to-T substitution, resulting in a methionine-to-leucine change in the protein. Overexpression experiments in apple calli and tomato confirmed that MdNAC5A promotes higher levels of methionine and ACC (ethylene precursors), leading to softer, faster-ripening fruit. Conversely, MdNAC5T reduced ethylene synthesis and delayed softening. Molecular assays demonstrated that both alleles bind directly to the promoters of MdACS1 and MdERF3, but MdNAC5A showed stronger activation, enhancing ethylene signaling. Transgenic tomato lines carrying MdNAC5A ripened several days earlier than controls, confirming cross-species conservation of its effect. These findings establish MdNAC5 as a central switch that links natural genetic variation to fruit firmness and ripening divergence in apple, providing mechanistic insight into a long-standing question in fruit biology.
“Our results show that a single gene, MdNAC5, can tip the balance between firmness retention and rapid softening in apple,” said Dr. Hua Gao, corresponding author of the study. “This discovery not only clarifies the molecular basis of a key quality trait but also provides a genetic target for breeders. By selecting or editing the appropriate allele, it becomes possible to fine-tune fruit texture and shelf life, meeting diverse consumer and industry demands. The findings bridge fundamental biology with practical breeding applications.”
The discovery of natural allelic variation in MdNAC5 opens new avenues for breeding apples with tailored firmness and ripening profiles. Breeders could use MdNAC5 as a molecular marker to select for firmer, longer-lasting varieties suited to extended storage and global transport, or softer varieties optimized for immediate consumption. Beyond apples, the conservation of NAC transcription factors across species suggests similar strategies may be applied to other climacteric fruits such as tomato, peach, and melon. Ultimately, this knowledge provides a genetic toolkit for balancing fruit quality, consumer satisfaction, and supply chain efficiency in the horticultural industry.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae284
Funding information
This work was supported by the Earmarked Fund for the China Agriculture Research System (CARS-27), the National Natural Science Foundation of China (No. 32302683), the Project of Weinan Experimental demonstration Station of Northwest A&F University (2024WNXNZX-1), and the China Postdoctoral Science Foundation (2024 M752636).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.