Herbaceous peony (Paeonia lactiflora Pall.) is a popular ornamental and medicinal plant. Taking approximately six to seven months, the seeds germination under natural conditions experiences dual dormancies, which seriously affects horticultural cultivation. Few studies have been conducted on exploring both biological and molecular mechanism that regulates dormancy removal process in hypocotyls double dormant plants. Here, we first measured ABA and GA₃ content changes at four key dormancy break stages, and then performed transcriptomic analyses to identify the differentially expressed genes (DEGs) using RNA-seq. We subsequently carried out Quantitative real-time PCR (qRT-PCR) to validate RNA-seq data. ABA content decreased during the whole dormancy removal process and GA₃ content exhibited decreasing slightly and then increasing trend. RNA sequencing de novo assembly generated a total of 99,577 unigenes. 20,344 unigenes were differentially expressed in the whole dormancy release process. The qPCR results of 54 selected unigenes were consistent with the FPKM values obtained from RNA-seq. Our results summarize a valuable collection of gene expression profiles characterizing the dormancy release process. The DEGs are candidates for functional analyses of genes affecting the dormancy release, which is a precious resource for the on-going physiological and molecular investigation of seeds dormancy removal in other perennial plants.

草本牡丹（Paeonia lactiflora Pall。）是一种流行的观赏和药用植物。自然条件下的种子萌发需要大约六到七个月的时间，因此会双重休眠，从而严重影响园艺种植。关于探索调节下胚轴双休眠植物中休眠去除过程的生物学和分子机制的研究很少。在这里，我们首先在四个关键的休眠中断阶段测量了ABA和GA ₃含量的变化，然后使用RNA序列进行了转录组分析，以鉴定差异表达的基因（DEG）。随后，我们进行了定量实时PCR（qRT-PCR）以验证RNA序列数据。在整个休眠去除过程和GA _3中ABA含量降低含量呈现先下降后上升的趋势。从头开始的RNA测序产生了总共99,577个单基因。在整个休眠释放过程中差异表达20,344个单基因。54个选定的单基因的qPCR结果与从RNA-seq获得的FPKM值一致。我们的结果总结了表征休眠释放过程的基因表达谱的有价值的集合。DEG是影响休眠释放基因功能分析的候选者，这是正在进行的其他多年生植物种子休眠去除的生理和分子研究的宝贵资源。