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Title:           Regulatory structural variations upstream of a NAC transcription factor control fruit maturity timing in peach
Subject:         DOI: 10.1093/jxb/erag210; Journal of Experimental Botany, 77, 16, 2026-04-29.; Abstract: Fruit maturity date is a key developmental trait in fruit trees, as it determines the timing of when fruits enter the ripening phase, thereby shaping the harvest calendar and fruit quality. In peach, ripening time varies over several months, yet the genetic and regulatory basis underlying this extensive phenological diversity has remained largely unresolved. Here, we dissect the long-standing chromosome 4 maturity date locus (qMD4.1) and show that a multi-allelic series of structural variants in the upstream regulatory region of the transcription factor NAC1 explains most of the observed variation in ripening time in cultivated peach. Across multiple independent populations and diverse genetic backgrounds, these variants (collectively termed Md) stratify maturity date from ultra-early to late cultivars with largely additive and dosage-dependent effects. Using recombinant-based genetic dissection, long-read sequencing, transcriptomic analyses, and epigenomic data integration, we show that Md alleles are consistently associated with allele-dependent shifts in the temporal dynamics of NAC1 transcript accumulation, and that the affected region overlaps with chromatin features characteristic of regulatory activity. By resolving the genetic architecture of a major phenological locus, our results support a central role for cis-regulatory structural variation in modulating developmental timing in peach and provide biologically interpretable markers for predicting maturity date. More broadly, this work illustrates how non-coding structural variation can contribute to variation in fruit developmental trajectories, with implications for breeding strategies aimed at modulating harvest windows in peach and other stone fruit species.
Keywords:        Fruit trees; maturity date; peach; QTL; ripening; structural variants
Author:          Alessandro Giulio Tagliabue
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     Item: 
      Title: Regulatory structural variations upstream of a NAC transcription factor control fruit maturity timing in peach
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       Item: 
        Title: Introduction
        Destination: secerag210-s1
       Item: 
        Title: Materials and methods
        Destination: secerag210-s2
        Children: 
         Item: 
          Title: Plant materials and phenotyping
          Destination: secerag210-s2.1
         Item: 
          Title: Genotyping, linkage map construction, and quantitative trait locus mapping
          Destination: secerag210-s2.2
         Item: 
          Title: DNA extraction and resequencing
          Destination: secerag210-s2.3
         Item: 
          Title: Genomics analyses
          Destination: secerag210-s2.4
         Item: 
          Title: Validation and genotyping of Md alleles
          Destination: secerag210-s2.5
         Item: 
          Title: Fruit sampling and RNA sequencing analyses
          Destination: secerag210-s2.6
         Item: 
          Title: Epigenomic datasets and data processing
          Destination: secerag210-s2.7
       Item: 
        Title: Results
        Destination: secerag210-s3
        Children: 
         Item: 
          Title: Maturity date mapping in D×P progeny
          Destination: secerag210-s3.1
         Item: 
          Title: Genomic variation at the Md locus
          Destination: secerag210-s3.2
         Item: 
          Title: Association of Md alleles with maturity date across multiple segregating progenies
          Destination: secerag210-s3.3
         Item: 
          Title: Association of Md alleles with maturity date in germplasm collections
          Destination: secerag210-s3.4
         Item: 
          Title: Functional evidence of the effects of Md structural variants on NAC1 expression
          Destination: secerag210-s3.5
         Item: 
          Title: Origin and spread of Md alleles
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       Item: 
        Title: Discussion
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        Children: 
         Item: 
          Title: Allelic determinants of maturity date in peach
          Destination: secerag210-s4.1
         Item: 
          Title: Functional evidence and transcriptional dynamics of the Md locus
          Destination: secerag210-s4.2
         Item: 
          Title: Breeding implications and marker-assisted selection
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         Item: 
          Title: Conclusion
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       Item: 
        Title: Supplementary data
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       Item: 
        Title: Acknowledgements
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       Item: 
        Title: Author contributions
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       Item: 
        Title: Conflict of interest
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       Item: 
        Title: Funding
        Destination: secerag210-s8
       Item: 
        Title: Data availability
        Destination: secerag210-s9
       Item: 
        Title: References
        Destination: reflist
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    Title: Regulatory structural variations upstream of a NAC transcription factor control fruit maturity timing in peach
    Author: Alessandro Giulio Tagliabue
    Subject: DOI: 10.1093/jxb/erag210; Journal of Experimental Botany, 77, 16, 2026-04-29.; Abstract: Fruit maturity date is a key developmental trait in fruit trees, as it determines the timing of when fruits enter the ripening phase, thereby shaping the harvest calendar and fruit quality. In peach, ripening time varies over several months, yet the genetic and regulatory basis underlying this extensive phenological diversity has remained largely unresolved. Here, we dissect the long-standing chromosome 4 maturity date locus (qMD4.1) and show that a multi-allelic series of structural variants in the upstream regulatory region of the transcription factor NAC1 explains most of the observed variation in ripening time in cultivated peach. Across multiple independent populations and diverse genetic backgrounds, these variants (collectively termed Md) stratify maturity date from ultra-early to late cultivars with largely additive and dosage-dependent effects. Using recombinant-based genetic dissection, long-read sequencing, transcriptomic analyses, and epigenomic data integration, we show that Md alleles are consistently associated with allele-dependent shifts in the temporal dynamics of NAC1 transcript accumulation, and that the affected region overlaps with chromatin features characteristic of regulatory activity. By resolving the genetic architecture of a major phenological locus, our results support a central role for cis-regulatory structural variation in modulating developmental timing in peach and provide biologically interpretable markers for predicting maturity date. More broadly, this work illustrates how non-coding structural variation can contribute to variation in fruit developmental trajectories, with implications for breeding strategies aimed at modulating harvest windows in peach and other stone fruit species.
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  Checksum: 073c689c
   Type: CRC32
  Checksum: fd0fc481849ff04d736a9146d560d8d9
   Type: MD5
  Checksum: e234b54767b63f5317e228f0d4277b800f6cc16a
   Type: SHA-1
  Checksum: f8095edf207142c49fea45bea94845728d1f764fd1bc30dff04057f0ff4422fc
   Type: SHA-256