光周期是调控开花和影响植物生长发育非常关键的环境因子。模式植物中已报道了光周期调控开花的分子机制，然而光周期对梨等蔷薇科木本果树的影响尚不明确。本研究以‘砀山酥梨’为材料，结合基因组学、生物信息学和分子生物学等方法，鉴定出梨的核心生物钟基因。其次，对核心生物钟基因所在的RVE和PRR基因家族进行成员鉴定和进化分析，进一步解析了光周期途径调控梨开花时间的关键基因PbLHY、PbPRR59a和PbPRR59b的功能。主要研究结果如下:

1. 探明了梨叶片响应光周期变化的转录组特征。分别在长日照（16 h光照/8 h黑暗）和短日照（8 h光照/16 h黑暗）条件下每隔4 h进行梨叶片取样。通过48 h连续时间序列转录组研究，发现梨叶片中有31.9%（13677/42812）的基因表达呈现昼夜节律性，其中，4674个基因在长日照和短日照下表达模式有显著差异。结合同源序列比对和转录组数据分析，鉴定了梨基因组中的生物钟核心振荡器基因，包括PbLHY、PbRVE8、PbPRRs、PbELF3、PbELF4、PbLUX、PbGI和PbLNK等，以上基因与多个生物过程相关，包括光合作用、胁迫反应、激素反应和次级代谢。特别是光合作用相关过程在节律分析和差异表达分析中有显著富集。该研究明确了光周期对梨基因表达和重要生理过程具有调控作用。

2. 分析了蔷薇科RVE基因家族的特征，明确了梨PbLHY基因调控成花的功能。在黑树莓、草莓、甜樱桃、苹果、梨、桃和梅等7个蔷薇科物种中共鉴定到51个RVE基因，梨基因组中包括10个成员。根据系统发育树结果，51个RVE基因被分为2个亚家族。7个蔷薇科物种中超过60%基因对的复制事件类型为分散复制。所有RVE基因对的Ka/Ks值均小于1，表明纯化选择是蔷薇科物种RVE基因家族进化的主要驱动力。在12 h光照/12 h黑暗下，所有PbRVEs基因的表达都具有昼夜节律性；在持续光照条件下PbLHY、PbRVE1a、PbRVE7和PbRVE8的表达受生物钟调控。结合梨叶片的转录组数据发现，包括PbLHY在内的多数PbRVEs基因的表达受光周期诱导。与对照植株相比，PbLHY转基因过表达株系开花时间显著延迟。这些结果说明梨生物钟关键基因PbLHY有调控成花的作用。

3. 鉴定了蔷薇科PRR基因家族，明确了PbPRR59a和PbPRR59b的表达特性和基因功能。PRR基因是生物钟核心振荡器的重要组分，参与植物开花调控。

本研究从7个蔷薇科物种中鉴定到43个PRR家族成员，构建进化树将其划分为3个亚家族，其中梨基因组中包含8个成员。系统分析表明，PRR基因结构和基序在各个亚家族内部高度保守。顺式作用元件预测结果显示PRR基因的启动子区域都包含G-box等光响应元件和脱落酸响应元件。不同梨PRR基因的组织表达模式存在差异，多数基因在根中具有高表达。PbTOC1a和PbTOC1b在子房的表达量高于其他器官。在持续光照条件下，除了PbPRR3，7个PbPRRs基因的表达都受生物钟调控。PbPRR59a和PbPRR59b均定位于细胞核。PbPRR59a和PbPRR59b转基因拟南芥开花时间延迟。与对照相比，在PbPRR59a和PbPRR59b过表达株系中AtGI、AtCO和AtFT的表达水平显著降低。

综上所述，本研究基于梨叶片转录组数据，比较分析不同光周期对梨叶片中基因表达的影响，挖掘梨生物钟核心振荡器基因，通过功能验证明确了PbLHY、PbPRR59a和PbPRR59b等生物钟关键基因调控开花时间的功能，为梨成花调控研究提供了重要参考。

Photoperiod is a key environment cue to regulate flowering and affect plant growth and development. Molecular mechanism of photoperiod regulation of flowering has been widely reported in model plants, yet the influence on woody fruit trees of the Rosaceae family remain unknown. In this study, the core clock genes of pear (Pyrus bretschneideri) were identified by using genomics, bioinformatics and molecular biology methods, with ‘Dangshansuli’ as the experimental material. Secondly, members identification and evolutionary analysis of the RVE and PRR families were carried out. The functions of clock genes PbLHY, PbPRR59a and PbPRR59b regulating flowering in pear by photoperiod pathway were further explored. The main findings are as follows:

1. The transcriptome characteristics of pear leaves in response to photoperiod were explored. Pear leaf samples were collected under long-day (16 h light/8 h light) and short-day (8 h light/16 h dark) conditions at 4 h intervals. Using continuous 48 h time-series transcriptome analyses, it was found that 31.9% (13,667/42,812) of the genes in pear leaves showed circadian rhythm. and 4,674 genes were differently expressed between long-day and short-day conditions. Combined with homologous sequence alignment and transcriptome date analysis, the candidate homologs of core oscillators in pear were identified, including PbLHY, PbRVE8, PbPRRs, PbELF3, PbELF4, PbLUX, PbGI and PbLNK. They were associated with multiple biological processes,such as photosynthesis, stress response, hormone response, and secondary metabolism. Strikingly, photosynthesis-related pathways were enriched in both the rhythmic and the differential expression analysis. This study clarified that photoperiod could regulate gene expression and physiological processes of pear.

2. The characteristics of the RVE gene family of Rosaceae were analyzed, and the function of PbLHY gene in controlling flowering was clarified. A total of 51 RVE genes were identified in seven Rosaceae species, including black raspberry, strawberry, sweet cherry, apple, pear, peach and Japanese apricot, of which ten members were included in the pear genome. Based on phylogenetic tree results, these genes were divided into two subfamilies. More than 60% of gene pairs in the seven Rosaceae species had a dispersed duplication event type. The Ka/Ks values of all RVE gene pairs were less than 1, indicating that purification selection was the main driving force of the RVE family in Rosaceae species. Under 12 h light/12 h dark, the expression of all PbRVE genes had circadian rhythm. The expression of PbLHY, PbRVE1a, PbRVE7 and PbRVE8 under continuous light conditions was regulated by the circadian clock. Combined with transcriptome data of pear leaves, the expression of most PbRVE genes, including PbLHY, was induced by photoperiod. Compared with the control, the flowering time of PbLHY transgenic lines was significantly delayed. These results indicated that PbLHY has an important function in controlling flowering.

3. The PRR families of Rosaceae species were identified, and the expression patterns and gene functions both PbPRR59a and PbPRR59b were studied. PRR genes are important components of circadian clock core oscillators and are involved in the regulation of plant flowering. 43 PRR family members were identified from seven Rosaceae species, which were divided into three subfamilies by the evolutionary tree, of which eight members were included in the pear genome. Systematic analysis showed that gene structure and motif of PRRs were highly conserved within three subfamilies. The cis-acting element prediction results showed that the promoter region of each PRR genes contained a variety of elements, such as G-box and abscisic acid response elements (ABRE). There were differences in the tissue expression patterns of PbPRR genes. Most genes had high expression level in roots. PbTOC1a and PbTOCb were expressed in ovary higher than in other organs. Under continuous light conditions, except for PbPRR3, the remaining PbPRR genes were regulated by the circadian clock. PbPRR59a and PbPRR59b were both localized to the nucleus, Flowering time was significantly delayed in PbPRR59a and PbPRR59b transgenic lines. The expression levels of AtGI, AtCO and AtFT were reduced in the PbPRR59a and PbPRR59b overexpression lines compared to the control.

In summary, this study comparatively analyzed the effects of photoperiod on gene expression based on the transcriptome data of pear leaves, mined the circadian clock core oscillators of pear, and elaborated the function of keyclock genes PbLHY, PbPRR59a and PbPRR59b in controlling flowering time through functional validation, providing a reference for flowering regulation research of pear.

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