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Comparative transcriptome analysis of fertile and sterile buds from a genetically male sterile line of Chinese cabbage

  • Developmental Biology
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Abstract

In this study, we compared the transcriptome profiles of fertile versus sterile buds of a stably inherited genic male sterile AB line of Chinese cabbage using the Illumina high-throughput sequencing platform. Based on the analysis of gene expression levels, we detected 1013 differentially expressed genes (DEGs), including 907 that were upregulated and 106 that were downregulated in fertile buds. In addition, 481 genes were specifically differentially expressed. Among these, some DEGs were previously shown to play important roles in pollen and anther development, including AMS, MS2, ms35/myb26, and so on. We also performed gene ontology (GO) analysis to reveal the main biological functions of the DEGs. Only 19 GO terms were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed to uncover significantly enriched metabolic pathways and signal transduction pathways involving the DEGs, revealing five significantly enriched KEGG pathways that are pentose and glucuronate interconversions; alanine, aspartate, and glutamate metabolism; cysteine and methionine metabolism; ascorbate and aldarate metabolism; and starch and sucrose metabolism. These results could potentially explain the difference between fertile and sterile buds. Finally, we analyzed the expression patterns of 31 DEGs using qRT-PCR, which verified the reliability of the transcriptome sequencing results. Analysis of the transcriptome data provides valuable information for in-depth analysis of the molecular mechanism underlying pollen development, and it lays the foundation for clarifying the functions of these crucial genes and elucidating the sterility mechanism in Chinese cabbage.

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References

  • Aarts MG, Hodge R, Kalantidis K, Florack D, Wilson ZA, Mulligan BJ, Stiekema WJ, Scott R, Pereira A (1997) The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes. Plant J 12(3):615–623

    Article  CAS  PubMed  Google Scholar 

  • An H, Yang Z, Yi B, Wen J, Shen J, Tu J, Ma C, Fu T (2014) Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus. BMC Genomics 15:258

    Article  PubMed  PubMed Central  Google Scholar 

  • Ariizumi T, Hatakeyama K, Hinata K, Inatsugi R, Nishida I, Sato S, Kato T, Tabata S, Toriyama K (2004) Disruption of the novel plant protein NEF1 affects lipid accumulation in the plastids of the tapetum and exine formation of pollen, resulting in male sterility in Arabidopsis thaliana. Plant J 39:170–181

  • Ariizumi T, Toriyama K (2011) Genetic regulation of sporopollenin synthesis and pollen exine development. Annu Rev Plant Biol 62:437–60

    Article  CAS  PubMed  Google Scholar 

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995

    CAS  PubMed  Google Scholar 

  • Bosch M, Hepler PK (2005) Pectin methylesterases and pectin dynamics in pollen tubes. Plant Cell 17(12):3219–3226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao J (2012) The pectin lyases in Arabidopsis thaliana evolution, selection and expression profiles. PLoS One 7(10), e46944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang L, Zhiyong L, Xueling Y, Yiheng W, Qian M, Hui F (2014) Transcriptome analysis of the Chinese cabbage (Brassica rapa ssp. pekinensis) petal using RNA-Seq. J Hortic 1:114

    Google Scholar 

  • Chapple RM, Chaudhury AM, Blomer KC, Farrell LB, Dennis ES (1996) Construction of a YAC contig of 2 megabases around the MS1 gene in Arabidopsis thaliana. Aust J Plant Physiol 23(4):453–465

    Article  CAS  Google Scholar 

  • Chaudhury AM (1993) Nuclear genes controlling male fertility. Plant Cell 5(10):1277–1283

    Article  PubMed  PubMed Central  Google Scholar 

  • Coimbra S, Costa M, Jones B, Mendes MA, Pereira LG (2009) Pollen grain development is compromised in Arabidopsis agp6 agp11 null mutants. J Exp Bot 60(11):3133–3142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong X, Feng H, Xu M, Lee J, Kim YK, Lim YP, Piao Z, Park YD, Ma H, Hur Y (2013) Comprehensive analysis of genic male sterility-related genes in Brassica rapa using a newly developed Br300K oligomeric chip. PLoS One 8, e72178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fengying W, Lianjiu S, Yulong W, Xiaohui L, Bing Z, Yuxiu Q (2001) Breeding of nuclear male sterile line in qingmaye type of Chinese cabbage. Acta Hortic Sin 28(2):133–138

    Google Scholar 

  • Francis KE, Lam SY, Copenhaver GP (2006) Separation of Arabidopsis pollen tetrads is regulated by QUARTET1, a pectin methylesterase gene. Plant Physiol 142:1004–1013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guilan K, Zhiya Z, Yanzhi S, Lugang Z, Limin Z (1992) Breeding of alloplasmic male sterile line CMS3411-7 in Chinese cabbage (Brassica campestris L. ssp. pekinensis (Lour.) Olsson) and its application. Acta Hortic Sin 19(4):333–340

    Google Scholar 

  • Havey MJ (2004) The use of cytoplasmic male sterility for hybrid seed production. Molecular Biology and Biotechnology of Plant Organelles, Springer Netherlands, pp 623–634

  • Huang L, Cao J, Ye W, Liu T, Jiang L, Ye Y (2008) Transcriptional differences between the male-sterile mutant bcms and wild-type Brassica campestris ssp. chinensis reveal genes related to pollen development. Plant Biol (Stuttg) 10(3):342–55

    Article  CAS  Google Scholar 

  • Huang L, Ye Y, Zhang Y, Zhang A, Liu T, Cao J (2009) BcMF9, a novel polygalacturonase gene, is required for both Brassica campestris intine and exine formation. Ann Bot 104:1339–1351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hui F, Yutang W, Suning Z (1995) Inheritance of and utilization model for genic male sterility in Chinese cabbage (Brassica pekinensis Rupr.). Acta Hortic Sin 402:133–140

    Article  Google Scholar 

  • Hui F, Yutang W, Shujuan J, Gang J, Jusheng J, Wenjun D (1996) Multiple allele model for genic male sterility in Chinese cabbage. Acta Hortic Sin 467:133–142

    Google Scholar 

  • Jiang L, Yang SL, Xie LF, Puah CS, Zhang XQ, Yang WC, Sundaresan V, Ye D (2005) VANGUARD1 encodes a pectin methylesterase that enhances pollen tube growth in the Arabidopsis style and transmitting tract. Plant Cell 17:584–596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang J, Zhang G, Bonnema G, Fang Z, Wang X (2008) Global analysis of gene expression in flower buds of Ms-cd1 Brassica oleracea conferring male sterility by using an Arabidopsis microarray. Plant Mol Biol 66:177–192

    Article  CAS  PubMed  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • Lou P, Kang J, Zhang G, Bonnema G, Fang Z, Wang X (2007) Transcript profiling of a dominant male sterile mutant (Ms-cd1) in cabbage during flower bud development. Plant Sci 172:111–119

    Article  CAS  Google Scholar 

  • Markovic O, Janecek S (2001) Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution. Protein Eng 14:615–631

    Article  CAS  PubMed  Google Scholar 

  • Mascarenhas JP (1989) The male gametophyte of flowering plants. Plant Cell 1:657–664

    Article  PubMed  PubMed Central  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  CAS  PubMed  Google Scholar 

  • Pacini E, Guarnieri M, Nepi M (2006) Pollen carbohydrates and water content during development, presentation, and dispersal: a short review. Protoplasma 228:73–77

    Article  CAS  PubMed  Google Scholar 

  • Palusa SG, Golovkin M, Shin SB, Richardson DN, Reddy AS (2007) Organ-specific, developmental, hormonal and stress regulation of expression of putative pectate lyase genes in Arabidopsis. New Phytol 174:537–550

    Article  CAS  PubMed  Google Scholar 

  • Shufang Z, Zhaohua S, Xueyun Z (1990) Breeding of interactive genic male sterile line in Chinese cabbage (Brassica pekinensis Rupr.) and utilization model. Acta Hortic Sin 17:117–125

    Google Scholar 

  • Sorensen AM, Kröber S, Unte US, Huijser P, Dekker K, Saedler H (2003) The Arabidopsis ABORTED MICROSPORES (AMS) gene encodes a MYC class transcription factor. Plant J 33:413–423

    Article  CAS  PubMed  Google Scholar 

  • Thorbly GJ, Shumukov L, Vizir IY, Yang CY, Mulligan BJ, Wilson ZA (1997) Fine-scale molecular genetic (RFLP) and physical mapping of a 8.9 cM region on the top arm of Arabidopsis chromosome 5 encompassing the male sterility gene, ms1. Plant J 12(2):471–479

    Article  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138

  • Wang Y, Yu X, Cao J (2004) Isolation and characterization of BcMF3, a gene expressed only in maintainer line in Chinese cabbage-pak-choi (Brassica campestris L. ssp. chinensis Makino var. communis Tsen et Lee). J Genet Genomics 31(11):1302–1308

    Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev 10(1):51–63

    Google Scholar 

  • Wei M, Song M, Fan S, Yu S (2013) Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling. BMC Genomics 14:97

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson ZA, Zhang DB (2009) From Arabidopsis to rice: pathways in pollen development. J Exp Bot 60:1479–1492

    Article  CAS  PubMed  Google Scholar 

  • Xie DX, Feys BF, James S, Manuela NR, Turner JG (1998) COl l: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science 280:1091–1094

    Article  CAS  PubMed  Google Scholar 

  • Xinke N, Feiyan W, Huihong Z, Xiusheng L (1980) The selection and utilization of Chinese cabbage (Brassica pekinensis Rupr.) of male sterile AB line. Acta Hortic Sin 7:25–32

    Google Scholar 

  • Yadav S, Yadav PK, Yadav D, Yadav D, Yadav KDS (2009) Pectin lyase: a review. Process Biochem 44:1–10

    Article  Google Scholar 

  • Yang C, Xu Z, Song J, Conner K, Vizcay Barrena G, Wilson ZA (2007) Arabidopsis MYB26/MALE STERILE35 regulates secondary thickening in the endothecium and is essential for anther dehiscence. Plant Cell 19:534–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Huang L, Liu T, Yu X, Cao J (2008) Functional analysis of a pollen-expressed polygalacturonase gene BcMF6 in Chinese cabbage (Brassica campestris L. ssp. chinensis Makino). Plant Cell Rep 27:1207–1215

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the National Natural Science Funds (31201625 and 31272157) and the earmarked fund for China Agriculture Research System (CARS-25-A-03).

Raw data and supplement data (Table S1 and Table S2) was uploaded to NCBI, and its number is GSE77427.

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    Authors and Affiliations

    1. College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China

      Chang Liu, Zhiyong Liu, Chengyu Li, Yun Zhang & Hui Feng

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    1. Chang Liu
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    2. Zhiyong Liu
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    3. Chengyu Li
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    5. Hui Feng
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    Correspondence to Hui Feng.

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    Editor: Ewen Mullins

    Chang Liu and Zhiyong Liu contributed equally to this work.

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    Liu, C., Liu, Z., Li, C. et al. Comparative transcriptome analysis of fertile and sterile buds from a genetically male sterile line of Chinese cabbage. In Vitro Cell.Dev.Biol.-Plant 52, 130–139 (2016). https://doi.org/10.1007/s11627-016-9754-9

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