Transcriptomic stress responses in <i>Vaccinium</i> spp. F1 hybrids: Implications for temperature‐resilient cranberry breeding using a crop wild relative

Societal Impact Statement Climate extremes threaten the sustainability of cranberry production, a culturally and economically important North American crop. This study demonstrates that wild cranberries ( Vaccinium oxycoccos ) harbor genetic variation that may enhance cold stress resilience when introduced into cultivated cranberry through hybridization. By identifying gene expression patterns associated with temperature tolerance, this research supports the development of climate‐resilient cranberry varieties and highlights the importance of conserving crop wild relatives. These insights advance sustainable agriculture and food security by informing breeding strategies that can help protect berry production in the face of increasing environmental stress. Summary 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), Vaccinium 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 min (heat) and 95 min (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. No subgenome‐specific functional specialization was observed. Two F1 hybrids exhibited suggestive cold resilience, with expression changes elevated at 60 min but declining by 95 min. Hybrids also displayed substantial regulatory variation under stress and transgressive downregulation of photosynthesis genes under ambient conditions. These findings suggest that V. oxycoccos introgression could be utilized in breeding cold‐tolerant cranberry cultivars. Variation observed between F1 hybrids reflects the diversity introduced through CWR germplasm and provides opportunities for selection. Conservation of V. oxycoccos and other CWRs remains critical for future crop improvement.