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

ABSTRACT

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.

Abbreviation: 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

KEYWORDS:

• Radish breeding
• genetic male sterility (GMS)
• differentially expressed genes
• RNAseq
• Denovo transcriptome analysis

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary material

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Additional information

Funding

This work was supported by the Agricultural Elite Breeds Project of Shandong Province [2013LZ017; 2016LZGC035] and Natural Science Foundation of Shandong Province [ZR2015YL054].