Chimeras in Merlot grapevine revealed by phased assembly

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.