Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was exceptionally evolved in pineapple, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between the fan-shaped inflorescence and the wild-shaped inflorescence pineapples were analyzed in three tissues, i.e., the flower stem apex, the base of the inflorescence, and the inflorescence axis. The weight (i.e., individual yield) of fan-shaped fruit is 4.5 times that of wild-shaped fruit；and non-significant difference in soluble solids, soluble sugar, titratable acid, and Vitamin C was found. Between the fan-shaped inflorescence and wild-shaped inflorescence, a total of 5370 differentially expressed genes were identified across the three tissues. Of these genes, there were 489 overlapping differentially expressed genes in all three tissue comparisons. Between the two pineapples, functional analysis indicated that 444 transcription factors and 206 inflorescence development-related genes were differentially expressed in at least one tissue comparison, while 45 transcription factors and 21 inflorescence development-related genes were overlapped across three tissues. Among the 489 overlapping differentially expressed genes in the three tissue comparisons, excluding the inflorescence development-related genes and transcription factors, 80 of them revealed a higher percentage of involvement in the biological processes relating to response to auxin, and reproductive processes. RNA-seq value and real-time quantitative PCR analysis exhibited the similar gene expression patterns in the three tissues. Our result provided novel cues for understanding the molecular mechanisms of the formation of the fan-shaped inflorescence in pineapple, making a valuable resource for the study of plant breeding and the speciation of pineapple.

菠萝植物通常有一个头状花序。然而，在菠萝中异常进化出扇形的花序，具有多个冠芽。为揭示扇形花序形成的分子机制，分析了花茎尖、花茎顶端、花茎顶端和野生花序菠萝三个组织中的果实性状以及扇形花序与野生花序的转录差异。花序基部和花序轴。扇形果实的重量（即单株产量）是野生形果实的4.5倍；可溶性固形物、可溶性糖、可滴定酸和维生素C的差异不显着。在扇形花序和野生形花序之间，三种组织共鉴定出5370个差异表达基因。在这些基因中，在所有三个组织比较中有 489 个重叠的差异表达基因。在两个菠萝之间，功能分析表明，444 个转录因子和 206 个花序发育相关基因在至少一个组织比较中差异表达，而 45 个转录因子和 21 个花序发育相关基因在三个组织中重叠。在三个组织比较中的 489 个重叠差异表达基因中，不包括花序发育相关基因和转录因子，其中 80 个显示参与与生长素反应和生殖过程相关的生物过程的百分比更高。RNA-seq 值和实时定量 PCR 分析在三种组织中表现出相似的基因表达模式。我们的研究结果为了解菠萝扇形花序形成的分子机制提供了新的线索，为植物育种和菠萝的物种形成研究提供了宝贵的资源。