College of Horticulture, China Agricultural University, Beijing, China.
Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
PLoS One. 2021 Nov 18;16(11):e0260017. doi: 10.1371/journal.pone.0260017. eCollection 2021.
Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.
花芽发育是核桃的一个重要特征，它影响核仁产量、产量稳定性、果实品质和商品价值。然而，关于核桃花芽发育的机制知之甚少。本研究通过组织学观察将核桃雌花芽发育分为五个时期（P01-05），并通过 PacBio Iso-Seq 和 RNA-seq 分析进行了进一步研究。因此，我们获得了 52875 条全长转录本，其中 4579 条是新转录本，3065 条是新基因，1437 条是保守 lncRNA，20813 条是可变剪接异构体。这些转录本极大地改进了当前的基因组注释，并增强了我们对核桃转录组的理解。接下来，对五个时期的雌花芽进行 RNA 测序，发现随着花芽发育梯度，昼夜节律-植物普遍富集。共鉴定到 14 个差异表达基因（DEGs），其中 6 个通过实时定量分析得到验证。此外，还检测到 6 个和 2 个差异表达的生物钟基因分别受到 AS 事件和 lncRNAs 的调控。所有这些检测到的植物生物钟基因形成一个复杂的相互关联的网络来调节花芽发育。因此，研究与生物钟相关的关键基因可以阐明核桃花芽发育的过程。
