Chimeras in Merlot grapevine revealed by phased assembly

Abstract

Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren’t identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on ‘Merlot’ grapevine cultivar. Sequencing of cv. ‘Magdeleine Noire des Charentes’ and ‘Cabernet Franc’, the parents of cv. ‘Merlot’, allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 ‘Merlot’ specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.

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“…Our dataset revealed that the number of somatic mutations within one grapevine plant, when comparing distinct shoots (Merlot WT shoots and Merlot WB shoots), is similar to those found between grapevine clones (Table 1 ), with between 351,018 and 356,754 shoot-specific SNVs being identified in Merlot (Additional file 16: Table S6 ). The counts of shoot-specific SNVs in Merlot is higher than the number of intra-organisms SNVs that have been identified in grapevine (3.2-3.7k) [ 62 ] and other plant systems (4.9k SNVs in Zostera marina and 44-152k SNVs in Populus trichocarpa ) [ 63 , 64 ]. This is likely in large part due to the differences in methods used between our study and previous studies due to the differences in the aims of the studies.…”

“…This is likely in large part due to the differences in methods used between our study and previous studies due to the differences in the aims of the studies. Given that the main goal of this study was to identify putative causal variants of WB, we did not apply stringent filtering that these previous studies have applied [ 62 – 64 ].…”