为了探究甜菊(Stevia rebaudiana Bertoni)自交不亲和的生理和分子机制，以甜菊自交不亲和无性系‘B4’及自交亲和无性系‘Z8-42’为研究对象，对2个无性系的自花授粉柱头进行荧光显微观察和转录组分析。荧光显微观察结果显示：‘B4’自花授粉柱头无花粉附着，而‘Z8-42’自花授粉柱头有花粉附着。2个无性系自花授粉柱头转录组整体测序质量较高，共获得43.84 Gb clean data。在组装的51 819个unigene中，表达unigene有49 214个；注释到NR数据库的表达unigene最多（29 523）；并且，在NR数据库中，注释到向日葵（Helianthus annuus Linn.）同源序列的unigene最多（20 117）。在2个无性系中共筛选到7 560个差异表达unigene；以‘B4’为对照，‘Z8-42’自花授粉柱头中表达量上调的差异表达unigene有3 122个，表达量下调的差异表达unigene有4 438个。GO功能注释和富集分析结果表明：甜菊差异表达unigene的功能包括生物过程、细胞组分和分子功能3个大类47个小类，其中，生物过程大类中富集到信号转导的差异表达unigene最多（225），细胞组分大类中富集到膜部分、膜固有成分和膜组成成分的差异表达unigene非常多（分别为1 700、1 665和1 664），分子功能大类中富集到离子结合的差异表达unigene最多（1 650）。共有1 605个差异表达unigene被注释到KEGG代谢通路的6个大类中，其中，注释到代谢大类的差异表达unigene最多（882），占比为55.0%，分布在10个二级分类的91条代谢通路中。单个代谢通路中，植物-病原体互作通路的差异表达unigene最多（81）。综合上述研究结果，初步判定甜菊自交不亲和可能发生在柱头与花粉互作的起始阶段，如识别、黏附过程；差异表达unigene引起的柱头细胞信号转导、膜成分、离子结合等功能和结构改变可能是导致供试的2个无性系自交亲和性不同的原因，并且植物-病原体互作通路可能参与柱头和花粉的识别过程，与自交不亲和性密切相关。

 In order to explore the physiological and molecular mechanisms of self-incompatibility of Stevia rebaudiana Bertoni, taking self-incompatible clone ‘B4’ and self-compatible clone ‘Z8-42’ of S. rebaudiana as research objects, fluorescence microscopy and transcriptome analysis were conducted for self-pollinated stigmas of the two clones. The fluorescence microscopy result shows that there are no pollens attached to the self-pollinated stigmas of ‘B4’, while there are pollens attached to the self-pollinated stigmas of ‘Z8-42’. The overall transcriptome sequencing quality of self-pollinated stigmas of the two clones is relatively good, and a total of 43.84 Gb clean data are obtained. There are 49 214 expressed unigenes among 51 819 assembled unigenes; the expressed unigenes annotated in NR database are the most (29 523); and in NR database, the unigenes annotated to homologous sequences of Helianthus annuus Linn. are the most (20 117). A total of 7 560 differentially expressed unigenes are screened out from the two clones; when taking ‘B4’ as the control, there are 3 122 differentially expressed unigenes with up-regulated expression and 4 438 differentially expressed unigenes with down-regulated expression in self-pollinated stigmas of ‘Z8-42’. The GO functional annotation and enrichment analysis results show that the functions of differentially expressed unigenes of S. rebaudiana contain three categories of biological process, cellular component and molecular function and 47 subcategories, in which, differentially expressed unigenes enriched into signal transduction in biological process category are the most (225), a large number of differentially expressed unigenes are enriched into membrane part, intrinsic component of membrane, and integral component of membrane (1 700, 1 665, and 1 664, respectively) in cellular component category, and differentially expressed unigenes enriched into ion binding in molecular function category are the most (1 650). A total of 1 605 differentially expressed unigenes are annotated into six categories of KEGG metabolic pathways, in which, differentially expressed unigenes annotated into metabolism category are the most (882), accounting for 55.0%, and are distributed in 91 metabolic pathways of 10 secondary classifications. In single metabolic pathway, differentially expressed unigenes in plant-pathogen interaction pathway are the most (81). Taken together, it can be preliminarily concluded that self-incompatiblility of S. rebaudiana may occur at the initial stage of stigma-pollen interaction, such as recognition and adhesion processes; functional and structural variations including stigma cell signal transduction, membrane part, ion binding, etc. caused by differentially expressed unigenes may be the reason of different self-compatibilities of the two test clones, and plant-pathogen interaction pathway may be involved in stigma-pollen recognition process, which is closely associated with self-incompatibility.