Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple

Abstract

Fruit firmness is an important trait for characterizing the quality and value of apple. It also serves as an indicator of fruit maturity, as it is a complex trait regulated by multiple genes. Resequencing techniques can be employed to elucidate variations in such complex fruit traits. Here, the whole genomes of 294 F₁ hybrids of ‘Fuji’ and ‘Cripp's Pink’ were resequenced, and a high-density binmap was constructed using 5014 bin markers with a total map distance of 2213.23 cM and an average map distance of 0.44 cM. Quantitative trait loci (QTLs) of traits related to fruit were mapped, and an A-T allele variant identified in the coding region of MdNAC5 was found to potentially regulate fruit firmness and ripening. The overexpression of MdNAC5^A resulted in higher production of methionine and 1-aminocyclopropanecarboxylic acid compared to MdNAC5^T, leading to reduced fruit firmness and accelerated ripening in apples and tomatoes. Furthermore, the activities of MdNAC5^A and MdNAC5^T were enhanced through their differential binding to the promoter regions of MdACS1 and MdERF3. Spatial variations in MdNAC5^A and MdNAC5^T caused changes in MdACS1 expression following their interaction with MdERF3. Ultimately, utilizing different MdNAC5 alleles offers a strategy to manipulate fruit firmness in apple breeding.

Acknowledgements

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). We thank Dr. Xinzhong Zhang (China Agricultural University, Beijing) for advising on map construction. We are very grateful to Dr. Ce Liu and Yuhui Xu for his advice and help in data analysis. We thank Dr. Jing Zhang and Yangang Yuan, Miss Mingrong Luo, and Wenjing Cao (Horticulture Science Research Center, Northwest A&F University, Yangling, China) for their assistance with LC-MS and technical support in this work. We thank all the graduate students in our team for helping with the phenotypic data collection.

Author contributions

Z.Z., Y.Y., and L.L. designed the project; L.L., Y.W., J.Y., and H.G. collected samples and performed phenotyping; L.L., J.Y., J.G., Z.H., and K.Y. performed experiments; L.L., H.C., and Y.W. analyzed data; L.L., Z.Z., and Y.W. wrote and modified the manuscript; all authors read and approved the contents of this paper.

Data availability

Sequencing raw reads are deposited in the NCBI under the following accession numbers: resequencing data of 294 hybrids and their parents (PRJNA816648), the data of BSA-seq (PRJNA1143202), and transcriptome data of fruit calli (PRJNA1141185). The transcriptome data of the parents ‘Fuji’ and ‘Cripp's Pink’ during the development stage were obtained from Liu et al. [64] (PRJNA728501).

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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