Biology subjects

Callipo, P.

Publications and source records attributed to Callipo, P..

3 recordsLinked to original sources

bioRxiv2026

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

Genotype-by-environment interaction (GEI) challenges selection in clonally propagated perennial crops by reducing the consistency of clone performance across years. In perennial crops, both genetic and epigenetic variation are likely to contribute to complex trait variation among clones. However, the extent to which each molecular source contribute to GEI remains poorly understood. Here, we used UMR-seq, an assay that recovers SNPs and unmethylated-region (UMR; DNA methylation) profiles from a single library, to generate paired genomic and epigenomic profiles for 206 Riesling (Vitis vinifera L.) clones phenotyped for yield and juice quality traits across nine growing seasons. We then partitioned the contribution of each omic layer to clonal variation and GEI, and examined the genomic distribution of their effects. In models without explicit GEI, environmental and residual effects were the largest source of phenotypic variance and the clonal main effect was modest. Genomic relationships accounted for most of the clonal variance in four of five traits, and adding an epigenomic relationship matrix (ERM) to the genomic relationship matrix (GRM) had little effect. In contrast, when GEI effects were modelled using factor-analytic covariance structures, the epigenomic layer captured a substantial proportion of GEI variance and exceeded the genomic contribution in four of five traits. The two omic layers differed not only in the amount of GEI captured, but also in the pattern of clone re-ranking across years. When back-solved effects were aggregated into genomic windows, the largest genomic and epigenomic effects tended to fall in different regions, with overlap no greater than expected by chance. Together, these results show that genomic and epigenomic relationships capture complementary components of year-to-year variation in clone performance, with the epigenomic contribution expressed primarily through GEI. These findings provide a basis for investigating the molecular drivers of GEI and for testing whether genomic and epigenomic information can inform selection for stable clonal performance across variable environments.

genetics↗

bioRxiv2026

Leaf and cluster spectral signatures reveal trait-dependent prediction performance for grapevine cluster architecture and juice quality

Grapevine cluster architecture is a key selection target in breeding programs because it influences disease susceptibility, yield stability and juice quality. High-throughput phenotyping offers a rapid and non-destructive approach to capture biochemical and structural variation in these traits, yet the influence of plant organ reflectance and data partitioning strategies on trait prediction remains poorly understood. In this study, we evaluated how hyperspectral reflectance from different grapevine organs contributes to the prediction of cluster architecture and juice quality traits in two clonal populations of Riesling and Pinot. Using partial least squares regression (PLSR), we assessed the prediction accuracy of eight cluster architecture and six juice quality traits under two data partitioning strategies. Models based on cluster reflectance outperformed those using dry leaf reflectance for most traits, except for pH. Partitioning the dataset by cluster type increased trait variance and improved predictions for number of berries (R{superscript 2} = 0.53), berry diameter (R{superscript 2} = 0.79), and total acidity (R{superscript 2} = 0.48). Visible, red-edge and NIR spectra were most informative regions to predict the traits studied. Together, our results highlight the importance of organ-specific data and appropriate calibration strategies to improve phenomic models for the development of scalable proxies for grapevine improvement. HighlightSpectral phenomics reveals that prediction accuracy in grapevine depends on organ spectral signatures and traits, with cluster reflectance outperforming leaves, informing new phenotyping strategies for breeding improvement.

plant biology↗

bioRxiv2026

A dual genomic-epigenomic map of clonal evolution in grapevine

Grapevine is one of the worlds oldest and most economically important perennial crops and has been vegetatively propagated for centuries to millennia. This long history of clonal propagation has generated substantial intra-varietal diversity, but its molecular basis has remained difficult to resolve with short-read sequencing, which misses large structural variation and DNA base modifications. Here, we generated a high-quality, phased diploid reference genome for the elite cultivar Pinot noir and integrate it with Oxford Nanopore sequencing of 23 distinct clones to build an integrated, genome-wide map of clonal genetic and epigenetic variation in Vitis vinifera. The genome assembly reveals a deep history of ancient inbreeding, with approximately 12% of the genome occurring in extended runs of homozygosity. Across molecular layers, we observe contrasting evolutionary dynamics. Somatic genetic variation (67,277 SNPs and 4,037 SVs) is dominated by rare variants and strongly depleted from coding regions, consistent with strong purifying selection. A substantial fraction of the structural variation among clones is mechanistically linked to instability in repetitive DNA, particularly centromeric repeats. In contrast, CG context epigenetic variation is abundant (250,382 differentially methylated cytosines) and strongly enriched within gene bodies, highlighting it as a major source of clonal divergence. Most importantly, CG methylation patterns alone reconstruct clonal phylogenetic relationships with high fidelity, closely mirroring the SNP-based lineages. This congruence, absent in transient non-CG methylation, indicates that stable CG epialleles are mitotically inherited and preserve a persistent record. Together, our results show that clonal identity in grapevine is jointly encoded by genome and methylome, with stable CG methylation capturing propagation history at near-genetic resolution.

plant biology↗