Transcriptomic reads of prickle and prickless F1 individuals (Rosa chinensis 'Old Blush' x Rosa wichurana)

Prickles are sharp appendages of plants that was thought to be a defense against insect and mammalian herbivores. In the agricultural production process, prickles are an undesirable trait because the crops with prickle are more difficult to handle, harvest, transport and also bring safety hazards for workers. Roses are among the most popular and economically important horticultural crops. In the Rosa genus, prickles are largely present with a great diversity in terms of form and density. With the recent development of genetic and genomic resources, rose can be a good model to study the molecular and genetic bases of prickle initiation and development. To mine new regulators of prickle initiation and development, we used a mixed pool of F1 individuals with or without NGPs, we presented the transcriptomic changes during prickle initiation and development by comparing the transcriptome of rose stems with and without prickles and a detailed time-course transcriptomic analysis of prickle development. We developed two unusual transcriptomic analyses methods to optimize the candidate genes pool. The precisely detailed analyses allow us to detect important regulators of prickle initiation and development. We highlighted the best potential regulators of prickle initiation by combining the transcriptomic results with genetic studies.

皮刺（prickle）是植物的尖锐附属结构，此前被认为是抵御昆虫与哺乳类植食动物的防御结构。在农业生产流程中，皮刺属于不受欢迎的性状：携带皮刺的作物更难开展操作、采收与运输工作，还会为作业人员带来安全隐患。玫瑰是最具人气且经济价值突出的园艺作物之一。在蔷薇属植物中，皮刺广泛存在，且其形态与密度具有丰富的多样性。随着近年来遗传学与基因组学研究资源的发展，玫瑰可成为研究皮刺起始与发育的分子及遗传基础的优良模式物种。为挖掘皮刺起始与发育的新型调控因子，我们构建了携带与不携带NGPs的F1代个体混合池；通过对比有皮刺与无皮刺玫瑰茎的转录组（transcriptome），并针对皮刺发育开展详细的时间序列转录组分析，阐明了皮刺起始与发育过程中的转录组变化规律。我们开发了两种非常规的转录组分析方法，以优化候选基因集。这些精准细致的分析使我们得以识别出皮刺起始与发育的关键调控因子。我们结合转录组分析结果与遗传学研究，筛选出了皮刺起始过程中最具潜力的调控因子。