Transcriptome profiling of genotypes showing contrasting bunch compactness subtraits reveals differential expression of genes involved in cell wall organization and terpene metabolism

Abstract

Bunch compactness (BC) is a complex trait which can influence several aspects of fruit quality given its role in disease susceptibility, ripening heterogeneity and consumer acceptance (in the case of fresh grapes). It is determined by the simultaneous expression of severalattributes, many of which are influenced by seasonal effects. High throughput phenotyping methods has enabled the study of BC variation and opened new avenues for its study in a more precise fashion. At the same time, GWAS analyses helped to identify some candidate genes, related to growth regulators metabolism. In this work we characterized the transcriptional profiles at early developmental stagesand in two seasons, considering two genotypes (Dodrelyabi and Crimson seedless) with contrasting phenotypes for BC. Inflorescence samples were taken in 2024 and 2025 seasons at two stages: 10 leaves stage (E-L 16) and beginning of flowering (E-L 20). Then, RNAseq analyses were performed using EdgeR (FDR < 0.05, TREAT log2 fold-change:1) revealing that only a small portion of differentially expressed genes (DEGs) were common to both seasons (e.g. at E-L16 stage: 296 common genes of 1418 total DEGs and 271 common genes of 1250 total DEGs, for upregulated and downregulated genes, respectively). The gene set enrichment analysis of the DEGs displayed several significant Gene Ontology terms in each case, suggesting a strong response for cell wall organization inDodrelyabi and an elicited defense response along with redox-related processes in Crimson seedless, at both developmental stages. Infact, similar results are reported when applying weighted co-expression network analysis. Module identification with CEMiToolassembled a total of eight modules. Particularly, two modules (M2 and M4) were related to immune response and redox response, respectively. The M1 module was also enriched in several terms associated with pollen-based processes and cell wall, highlighting the importance of these processes within the developmental timeframe considered in this study. Finally, lists for the most expressed genesidentified by RNAseq analysis, and the hub genes and co-expressed modules, are presented. Overall, this is one of the few worksaddressing transcriptional variation over consecutive seasons with focus in BC trait/subtraits. More conditions should be explored toidentify conserved responses associated to BC, considering a larger set of grapevine cultivars.

Acknowledgements

This work was supported by ANID-FONDECYT from Chile, grant 1221410