<i>De novo</i> and comparative transcriptome analysis of genetic male sterile and fertile lines in radish <i>(</i><i>Raphanus sativus)</i>

In radish, male sterility studies mainly focus on cytoplasmic male sterility (CMS) while genetic male sterility (GMS) has received less attention. To explore global gene expression profiles and identify genes associated with GMS, we performed de novo and comparative transcriptome analyses of flower buds from a GMS line and maintainer (fertile) line. Our study produced approximately 700 million paired-end reads, which were assembled into 115,284 unigenes with an average length of 1,196 bp and N50 of 1,729 bp. These unigenes were extensively annotated, with nearly 60% of them having homologs in the databases and 50% assigned with Gene Ontology (GO) terms. A total of 3,390 differentially expressed genes (DEGs) between the GMS line and the maintainer line were identified, with 2,645 down-regulated and 745 up-regulated in the GMS line. GO analyses showed biological processes related to plant reproductive development such as gametophyte development, pollen wall assembly, pollen development and pollen exine formation, as well as those related to cell wall development such as cell wall oganization and cell wall biogenesis, were significantly different in these two lines. The transcriptome assembly and comparative transcriptome analysis provides novel insights into the GMS in radishfacilitating the application of GMS in radish hybrid breeding. <b>Abbreviation:</b> 136S, the male sterile line in this article; 136F, the corresponding maintainer line(fertile); AGL, AGAMOUS-LIKE gene; CMS, cytoplasmic male sterility while; COG, Clusters of Orthologous Groups; DEGs, differentially expressed genes, FPKM, Fragments Per Kilobase of transcript per Million mapped reads; GMS, genetic male sterility; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes, NPGs, non-pollen genes在萝卜中，雄性不育相关研究主要聚焦于细胞质雄性不育（cytoplasmic male sterility, CMS），而遗传型雄性不育（genetic male sterility, GMS）的相关研究则较少受到关注。为探究全局基因表达谱并鉴定与GMS相关的基因，本研究对GMS材料与保持系（可育系）的花蕾进行了从头转录组组装与比较转录组分析。本研究共获得约7亿条双端测序读段，经组装得到115284条单基因簇（unigene），其平均长度为1196 bp，N50值为1729 bp。这些单基因簇得到了广泛注释：近60%的单基因簇在数据库中存在同源序列，50%被注释到基因本体论（Gene Ontology, GO）条目下。本研究共鉴定出GMS材料与保持系间的3390个差异表达基因（differentially expressed genes, DEGs），其中在GMS材料中下调表达的有2645个，上调表达的有745个。GO富集分析显示，两类材料在与植物生殖发育相关的生物学过程（如配子体发育、花粉壁组装、花粉发育及花粉外壁形成）以及与细胞壁发育相关的生物学过程（如细胞壁组织、细胞壁生物发生）中均存在显著差异。本转录组组装与比较转录组分析为萝卜GMS研究提供了全新视角，有助于推动GMS在萝卜杂交育种中的应用。**缩写说明：** 136S：本文所用雄性不育系；136F：对应的可育保持系；AGL：AGAMOUS类基因（AGAMOUS-LIKE gene）；CMS：细胞质雄性不育（cytoplasmic male sterility）；COG：直系同源簇（Clusters of Orthologous Groups）；DEGs：差异表达基因（differentially expressed genes）；FPKM：每百万映射读段中每千碱基转录本的片段数（Fragments Per Kilobase of transcript per Million mapped reads）；GMS：遗传型雄性不育（genetic male sterility）；GO：基因本体论（Gene Ontology）；KEGG：京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes）；NPGs：非花粉基因（non-pollen genes）