RNA-seq of Cranberry Hybrids

Cranberry (Vaccinium macrocarpon) is an important North American fruit crop with vulnerability to temperature extremes and a relatively recent domestication history. Hybridization with a cold-adapted crop wild relative (CWR), V. oxycoccos, offers a strategy for improving temperature stress tolerance.We conducted RNA sequencing (RNA-seq) on V. macrocarpon and F1 hybrids between V. macrocarpon and V. oxycoccos subjected to acute heat and cold stress, capturing early transcriptional responses up to 30 minutes (heat) and 95 minutes (cold) after treatment onset. We then evaluated differences in responses across genotypes and stress conditions.Differential expression analysis and functional profiling revealed cold-induced differences in pathways related to photosynthesis, ribosomes, defense, and hormone signaling during cold stress. No subgenome-specific functional specialization was observed. Two F1 hybrids exhibited suggestive cold resilience, with expression changes elevated at 60 minutes but declining by 95 minutes. Hybrids also displayed substantial regulatory variation and transgressive downregulation of photosynthesis genes.These findings suggest that V. oxycoccos introgression holds promise for breeding cold-tolerant or disease-resistant cranberry cultivars. Variation observed between F1 hybrids reflects the diversity introduced through CWR germplasm and provides opportunities for selection. However, reduced photosynthetic function may indicate cytonuclear incompatibilities or differing thermal optima. Conservation of V. oxycoccos and other CWRs remains critical for future crop improvement.