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Apple fruit quality depends heavily on traits such as firmness, flavor, and color, which are regulated by complex genetic networks. Among them, firmness is particularly important because it affects storage, transportability, and marketability. Previous efforts to map firmness-related genes faced challenges due to apple's long juvenile period and complex genome. Although several QTLs and candidate genes like MdACS1 and MdERF3 have been identified, the specific genetic factors driving natural variations in firmness remain unclear. Based on these challenges, there is a strong need to conduct high-resolution genetic mapping and functional validation studies to dissect the molecular basis of apple fruit firmness and ripening.

A research team from Northwest A&F University, in collaboration with Yale University, published a on October 8, 2024, in . The team resequenced the genomes of 294 apple hybrids derived from 'Fuji' and 'Cripp’s Pink' and identified a critical SNP mutation in the MdNAC5 gene that influences apple firmness and ripening. By combining high-density genetic mapping with functional assays, the study provides a detailed molecular framework linking MdNAC5 variation to ethylene biosynthesis and fruit texture, offering valuable tools for apple breeding programs.

In this study, researchers constructed a high-density genetic map using 5014 bin markers covering 17 apple chromosomes. They identified 60 QTLs associated with fruit-related traits, among which a major locus on chromosome 3 stood out. Within this region, they pinpointed a nonsynonymous A-to-T SNP in MdNAC5 that alters the encoded amino acid from methionine to leucine. Functional analysis revealed that the MdNAC5A variant (A allele) accelerates ripening and reduces fruit firmness, while the MdNAC5T variant (T allele) delays ripening and maintains firmness. Overexpression studies in apple calli and tomato fruit showed that MdNAC5A led to higher production of methionine and ACC, key precursors in ethylene biosynthesis, compared to MdNAC5T. Further experiments demonstrated that both variants directly bind to the promoters of MdACS1 and MdERF3, two ethylene-related genes, but MdNAC5A exhibited stronger regulatory activity. This dual regulation by MdNAC5 and its interaction with MdERF3 modulate ethylene levels, ultimately controlling fruit firmness and ripening pace. These findings shed light on the fine-tuned genetic mechanisms behind apple fruit quality traits.

"Identifying MdNAC5 as a major genetic regulator of apple firmness is a milestone in fruit crop genomics," said Dr. Yazhou Yang, one of the study's corresponding authors. "Our findings not only deepen the understanding of ripening control in climacteric fruits but also provide a direct molecular target for apple breeding programs aiming to improve storage and consumer qualities. By manipulating MdNAC5 alleles, we could tailor apples to meet specific market demands, extending shelf life without compromising taste."

This discovery opens up exciting possibilities for precision breeding in apples. By selecting specific MdNAC5 variants, breeders can engineer cultivars with tailored firmness levels and ripening times, optimizing apples for longer storage, better transport resilience, and enhanced consumer appeal. Additionally, the study highlights how fine-scale genetic mapping and functional validation can accelerate the development of superior fruit crops. Beyond apples, similar strategies could be applied to other climacteric fruits where texture and ripening are key commercial traits, ultimately contributing to reducing food loss and enhancing agricultural sustainability.

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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).

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 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.