Integrative genomic and transcriptomic analyses reveal potential gene regulatory network associated with berry size and early- ripening caused by bud sport in grapes

Abstract Background Berry size and early-ripening are considered as crucial traits for grape production and breeding. However, the underlying molecular mechanisms regulating berry size and early-ripening caused by bud sport in grapes remain unknown. Results In this study, whole-genome resequencing was performed for the cultivars ‘Himord Seedless’, ‘Thompson Seedless’ and their larger berries and early-ripening bud sports, ‘Jinzao Wuhe’ and ‘Dawuhebai’. Consequently, 1,548 SNPs, 379 InDels and 481 SVs, corresponding to 1,440 target genes, were identified in both bud sports compared to their maternal plants. Transcriptome analysis for ‘Jinzao Wuhe’/‘Himord Seedless’ at four time-points, including full-flowering, berry expansion, véraison and maturity stages, generated 2,984 differential expression genes (DEGs). Of these, 121 DEGs comprise genetic variations which might play potential roles in controlling berry growth and maturity development. Furthermore, weighted gene co-expression network analysis (WGCNA) was carried out, which revealed 48 candidate genes with previously discovered SNPs, InDels and SVs, including MADS, NAC, WRKY, UDP-glycosyltransferases, cytochromes P450, and genes involved in cell wall modification, ethylene synthesis and plant resistance. Finally, a conceivable regulatory network was constructed by integrating entire clues about the function of target genes. Conclusions Combined with the whole-genome resequencing and RNA-seq, DEGs with genetic variations associated with early ripening and berry size were identified in ‘Himord Seedless’ and its bud variant ‘Jinzao Wuhe’. Our results gave new insights into the field of bud mutation and contributed to future grape breeding and genetic improvement.