Comparative transcriptomic and hormone analyses reveal the molecular mechanisms regulating almond flowering stages

Almond (Prunus dulcis) is cultivated worldwide and is valued for its flavourful seeds, which have significant economic value. In China, domestically cultivated almonds are primarily found in Shache County, Kashgar, Xinjiang. However, in this region, the flowering stages generally begin too early, such that almond blooms are vulnerable to low spring temperatures, which can damage or kill flower organs and severely affect fruit yield. To date, there have been no studies on the regulatory mechanisms involved in almond flowering. Therefore, we conducted transcriptomic and hormone analyses on six flower developmental stages in two almond cultivars-the primary Chinese cultivar Wanfeng and the primary American cultivar Nonpareil-to determine the molecular mechanisms regulating flowering. In Shache County, Wanfeng almond completed its entire flowering stage in just 16 days, whereas Nonpareil required 43 days. The results of the GO and KEGG enrichment analyses of the differentially expressed genes revealed that Nonpareil almond requires more photosynthesis and more nutrients to complete the flowering process. The photoperiod pathway and time-ordered gene coexpression network revealed that four flowering time genes, CDFs, GA2ox8, IAA7, and WNK1, exhibited temporal expression patterns during the FP5 stage, which inhibited the development time needed for the two almond cultivars. Cytokinin-type hormones presented stronger differential accumulation patterns between the flowering stages of the two almond cultivars. We cloned a pair of PdSVP and PdAGL15 genes that interact in the nucleus and may regulate the developmental progress of the two cultivars during the bud stage. Finally, we integrated several key findings to construct a flowchart depicting the delayed flowering development of almond cultivars. Changes in environmental conditions significantly influence the delayed flowering of Nonpareil almond. This study employed multiomics strategies to reveal the complex differential molecular mechanisms of flowering development in two almond cultivars, providing a reference for the subsequent breeding of high-quality late-flowering almond cultivars in Xinjiang.