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Transcriptome sequencing and de novo analysis of a recessive genic male sterile line in cabbage (Brassica oleracea L. var. capitata)

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Abstract

Recessive genic male sterility (RGMS) is common in plants and has been widely applied as an effective and economic system for hybrid seed production in many crops. However, little is known regarding the molecular mechanisms of RGMS in cabbage (Brassica oleracea L. var. capitata) due to limited transcriptomic and genomic data. Comparative transcriptomic analyses were performed on the sterile (RGMS632-MS) and fertile plants (RGMS632-SF) of a RGMS line (RGMS632) using second-generation Illumina sequencing to identify critical genes and pathways associated with male sterility. A total of approximately 109 million sequencing reads was obtained using RNA-seq. Abundance analysis identified a total of 5107 unigenes that showed significant differences between the two kinds of plants. Among these, 1558 genes were upregulated while 3549 genes were downregulated by more than twofold in RGMS632-MS compared to RGMS632-SF. KEGG pathway enrichment analysis revealed changes in the transcript abundance of genes involved in the metabolism and signal transduction of various phytohormones. The majority of hormone signalling pathways were downregulated in RGMS632-MS. Furthermore, a set of potential candidate genes involved in the formation or abortion of pollen were investigated. These results increased our understanding of the molecular mechanisms and biological processes in RGMS plants.

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Acknowledgments

This study is supported by the National Science and Technology pillar program during the twelfth 5-year plan period (2012BAD02B01), the science and technology program of Shaanxi, China (2013K02-05), and the basic scientific research fund of Northwest A&F University (Z109021423).

Authors’ contributions

ZX, YZ conceived, designed, and performed the experiments. MH, JG analysed the data.YC, EZ contributed reagents/materials/analysis tools. JG wrote the paper. All authors read and approved the manuscript.

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Authors and Affiliations

  1. College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Jia Guo, Yanfeng Zhang, Maixia Hui, Yongan Cheng, Enhui Zhang & Zhongmin Xu

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  1. Jia Guo
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  2. Yanfeng Zhang
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  3. Maixia Hui
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Correspondence to Zhongmin Xu.

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Electronic supplementary material

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Supplementary material 1 (DOCX 22 kb)

Table S2.

Differentially expressed unigenes between RGMS632-SF and RGMS632-MS. (XLS 4038 kb)

Table S4.

List of other candidate male fertility-related genes. (XLS 110 kb)

Fig. S1

The length distribution of Unigenes from RGMS632-MS and RGMS632-SF plants. The horizontal coordinates are Unigene lengths and the vertical coordinates are numbers of Unigenes. (PDF 92 kb)

Fig. S2

Unigene homology searches against NR database. (A) The E-value distribution of the result of NR annotation. (B) The similarity distribution of unigene similarities against the NR database based on the best BLAST hits (E-value ≤ 1.0E − 5). (C) Proportional homology distribution among other plant species based on the best BLAST hits against the NR database (E-value ≤ 1.0 E-5). (PDF 63 kb)

Fig. S3

COG functional classification of the transcriptome of anthers of Cabbage (Brassica oleracea L. var. capitata). A total of 35,822 unigenes with significant homologies in the COG database (E-value ≤ 1.0 E-5) were classified into 25 COG categories. (PDF 66 kb)

Fig. S4

Comparison of transcript abundance levels between RGMS632-SF and RGMS632-MS. Red and green genes are up- and downregulated in RGMS632-MS compared to RGMS632-SF, respectively, while blue indicates genes that were not differentially expressed genes between the two plants. (PDF 95 kb)

Fig. S5

Gene Ontology (GO) classification for the differently expressed genes between RGMS632-SF and RGMS632-MS. All the differently expressed unigenes were classified into three main GO categories (biological process, cellular component and molecular function) and 52 sub-categories. The left y-axis indicates the percentage of a specific category of genes in each main category. The right y-axis indicates the number of genes in the same category. (PDF 150 kb)

Fig. S6

Number of differently expressed unigenes in each clade of the KEGG pathway maps. All of the differently expressed unigenes were assigned 124 KEGG pathways within 20 clades. In each category, the clades are listed according to their abundancies of unigenes. (PDF 125 kb)

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Guo, J., Zhang, Y., Hui, M. et al. Transcriptome sequencing and de novo analysis of a recessive genic male sterile line in cabbage (Brassica oleracea L. var. capitata). Mol Breeding 36, 117 (2016). https://doi.org/10.1007/s11032-016-0542-3

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