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Analysis of differentially expressed genes and pathways associated with male sterility lines in watermelon via bulked segregant RNA-seq

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Abstract

Genic male sterility (GMS) is a common and important trait, which is widely used for the production of hybrid seeds. However, the molecular mechanism of GMS in watermelon remains poorly understood. In this study, we comparatively analyzed the transcriptome profiles of sterile and fertile floral buds using the bulked segregant analysis (BSA) and transcriptome sequencing (RNA-seq). A total of 2507 differentially expressed genes (DEGs) including 593 up-regulated and 1914 down-regulated, were identified to be related to male sterility in watermelon line Se18. Gene ontology (GO) analysis showed that 57 GO terms were significantly enriched, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed plant hormone signal transduction, glycolysis/gluconeogenesis, starch and sucrose metabolism, plant–pathogen interaction, phenylpropanoid biosynthesis pathways were obviously enriched. Furthermore, the efficiency of the RNA-seq analysis was validated by quantitative real-time PCR (qRT-PCR). Among the DEGs, some valuable candidate genes involved in pollen development were identified, such as gene Cla000029, a bHLH transcription factor and homologous to MS1 in Arabidopsis. Moreover, other DEGs including MYB gene Cla012590 (MYB26), Cla017100 (MYB21), etc., also provide useful information for further understanding the function of key genes involved in pollen development. This study provides new insights into the global network of male sterility in watermelon.

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Acknowledgements

This study was supported by the Modern Agro-industry Technology Research System of China (No. CARS-25), the Scientific Startup Foundation for Doctors of Northwest A&F University (No. Z109021604), the Basal Research Foundation of Northwest A&F University (No. Z109021612), the Science and Technological of Shaanxi Province (No. 2015KTTSNY03-04) and the Key Project of Shaanxi Province (2017ZDXM-NY-025).

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Author notes

  1. Yongqi Wang and Xiaozhen Yang contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China

    Yongqi Wang, Xiaozhen Yang, Vivek Yadav, Ruimin Zhang, Zhongyuan Wang, Jingjing Chang, Hao Li, Yong Zhang, Jianxiang Ma, Chunhua Wei & Xian Zhang

  2. Hanzhong City Agro-Technology Extension Center, Hanzhong, 723000, China

    Yongqi Wang

  3. Yangtze Normal University, Fuling, 408100, China

    Yanling Mo

  4. Cash Crop Research Institute, Wenshan Academy of Agricultural Sciences, Wenshan, 663099, China

    Yongchao Yang

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Contributions

YW, CW and XZ conceived and designed the experiments. YW and XY sequenced data analysis, and qPCR validation of gene expression. YW wrote the paper. ZW, RZ, JC and YY participated in the data analysis. HL, YZ, JM and VY provided helpful advice on data analysis. YM and CW revised the paper. XZ provided the materials, revised the paper and supervised the research.

Corresponding authors

Correspondence to Chunhua Wei or Xian Zhang.

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The authors declare that they have no conflict of interest.

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Wang, Y., Yang, X., Yadav, V. et al. Analysis of differentially expressed genes and pathways associated with male sterility lines in watermelon via bulked segregant RNA-seq. 3 Biotech 10, 222 (2020). https://doi.org/10.1007/s13205-020-02208-2

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  • DOI: https://doi.org/10.1007/s13205-020-02208-2

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