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Updated: Jul 23, 2025

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Chimeras in Merlot grapevine revealed by phased assembly.

V Sichel1, G Sarah1,2, N Girollet3

  • 1UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France.

BMC Genomics
|July 14, 2023
PubMed
Summary

This study developed a new method to detect periclinal chimeras in grapevine using advanced sequencing and bioinformatics. This discovery aids in improving grapevine cultivars through better understanding of genetic variation.

Keywords:
ChimeraHifi sequencingPhased assemblyVitis viniferaWhole genome

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Area of Science:

  • Plant genetics
  • Viticulture
  • Genomics

Background:

  • Chimerism, where multiple genotypes exist within one individual, is valuable for plant ontogenesis and breeding, particularly in viticulture for traits like berry color.
  • Periclinal chimeras, with variants confined to a cell layer, are stable and propagable, yet crucial agronomic characters may be impacted by unidentified chimeras.
  • Grapevine leaf development involves L1 and L2 meristem layers, while lateral roots originate solely from L2, enabling chimera detection by comparing root and leaf DNA.

Purpose of the Study:

  • To develop and apply a novel method for detecting periclinal chimeras in the 'Merlot' grapevine cultivar.
  • To leverage high-resolution sequencing and bioinformatics for accurate chimera identification and characterization.
  • To explore the potential of chimera detection for improving grapevine cultivars via clonal selection and breeding.

Main Methods:

  • Utilized new generation Hifi long reads sequencing and trio-binning with parental sequences ('Magdeleine Noire des Charentes' and 'Cabernet Franc') for haplotype-resolved assembly of the 'Merlot' cultivar.
  • Constructed pseudomolecules from 33 to 47 contigs, enabling high-resolution haplotype comparison and annotation transfer from PN40024 VCost.v3.
  • Applied rigorous variant selection and validated findings using Molecular Inversion Probes (MIPseq) to confirm detected chimeras.

Main Results:

  • Detected 51 and 53 'Merlot' specific periclinal chimeras on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, with some located in coding regions.
  • Successfully performed haplotype-resolved assembly and pseudomolecule construction for the 'Merlot' grapevine.
  • Validated 69% of a subset of detected positions using MIPseq, with 25% being doubtful and 6% invalidated, demonstrating the method's efficacy.

Conclusions:

  • Established a robust method for periclinal chimera detection in grapevine using advanced sequencing and bioinformatics.
  • Identified numerous chimeras in the 'Merlot' cultivar, highlighting their potential impact on agronomic traits.
  • Opened new avenues for improving grapevine cultivars through precise chimera identification and utilization in breeding programs.