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, 251:22 | Cite as

Comprehensive transcriptome analysis of faba bean in response to vernalization

  • Bei Gao
  • Xiao-Chun Bian
  • Feng Yang
  • Mo-Xian Chen
  • Debatosh Das
  • Xiu-Ru Zhu
  • Yong Jiang
  • Jianhua Zhang
  • Yun-Ying CaoEmail author
  • Chun-Fang WuEmail author
Original Article

Abstract

Main conclusion

This study unravels the transcriptional response of a highly productive faba bean cultivar under vernalization treatment.

Abstract

Faba bean (Vicia faba L.) is a member of the Leguminosae family and an important food crop worldwide providing valuable nutrients for humans. However, genome-wide studies and comprehensive sequencing resources of faba bean remain limited. Vernalization is crucial for enhanced yields in a number of winter-sown crops. However, the effects of vernalization on faba bean remain unknown. In this study, we generated a high-quality transcriptome assembly and functional annotation source for vernalized faba bean (Vicia faba L.) cv. Tongxian-2, a domesticated cultivar from southern China. A total of 369.9 million clean Illumina paired-end RNA-Seq reads were generated, and the transcriptome was assembled into 68,683 unigene sequences, with an average length of 1018 bp and an N50 of 1652 bp. Comprehensive functional annotation provided putative functional descriptions for more than 70% of the faba bean transcripts. We annotated a total of 1560 faba bean transcripts encoding transcription factors (TFs) belonging to 55 distinct TF families. The bHLH (168 transcripts), ERF (123 transcripts) and WRKY (105 transcripts) contained the largest number of TFs in response to vernalization. Genome-wide transcript changes comparing vernalized and unvernalized seedlings were investigated using bioinformatics approaches, which revealed a strong repression of photosynthesis and carbon metabolism, while genes participating in ‘response to stress’ were significantly induced. We also specifically identified vernalization-induced twenty-two ‘pollen–pistil interaction’ genes. A detailed functional annotation and expression profile analyses unveiled a number of protein kinases, which were specifically induced in vernalized seedlings. We also identified a total of 6852 simple sequence repeats (SSRs) in 6552 transcripts, representing a valuable genomic molecular marker resource for faba bean. In summary, this study provides new insights into the vernalization process in this economically valuable crop. The transcriptome data obtained provides us with a valuable candidate gene resource for future functional and molecular breeding studies. These data will contribute to the genome annotation for ensuing genome projects.

Keywords

Simple sequence repeats Transcription factor Transcriptome Vernalization Vicia faba 

Abbreviations

DEG

Differentially expressed gene

FDR

False discovery rate

GO

Gene ontology

SSR

Simple sequence repeats

TF

Transcription factor

VRN

Vernalization response gene

Notes

Acknowledgements

This work was supported by Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX18_2416), Science and Technology Program of Nantong (MS12018099), Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX18_2416), the Shenzhen Virtual University Park Support Scheme to CUHK Shenzhen Research Institute (YFJGJS1.0), the Natural Science Foundation of Hunan Province (2019JJ50263) and Hong Kong Research Grant Council (AoE/M-05/12, AoE/M-403/16, GRF14160516, 14177617, 12100318).

Compliance with ethical standards

Conflict of interests

The authors declare that they have no competing interests.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Bei Gao
    • 1
    • 2
    • 3
  • Xiao-Chun Bian
    • 1
  • Feng Yang
    • 4
  • Mo-Xian Chen
    • 4
  • Debatosh Das
    • 4
  • Xiu-Ru Zhu
    • 2
  • Yong Jiang
    • 5
  • Jianhua Zhang
    • 6
  • Yun-Ying Cao
    • 2
    Email author
  • Chun-Fang Wu
    • 1
    Email author
  1. 1.Jiangsu Yanjiang Institute of Agricultural SciencesNantongChina
  2. 2.College of Life SciencesNantong UniversityNantongChina
  3. 3.School of Life SciencesThe Chinese University of Hong KongHong KongChina
  4. 4.Shenzhen Research InstituteThe Chinese University of Hong KongShenzhenChina
  5. 5.National Oceanographic CenterQingdaoChina
  6. 6.Department of Biology, Hong Kong Baptist University and State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongHong KongChina

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