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Comprehensive transcriptome analysis of faba bean in response to vernalization

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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.

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Data availability

All the sequencing data were deposited in the NCBI-SRA database and will be released to the public upon acceptance of the manuscript.

Abbreviations

DEG:

Differentially expressed gene

FDR:

False discovery rate

GO:

Gene ontology

SSR:

Simple sequence repeats

TF:

Transcription factor

VRN :

Vernalization response gene

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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).

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  1. Bei Gao, Xiao-Chun Bian and Feng Yang contributed equally to this work.

Authors and Affiliations

  1. Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China

    Bei Gao, Xiao-Chun Bian & Chun-Fang Wu

  2. College of Life Sciences, Nantong University, Nantong, China

    Bei Gao, Xiu-Ru Zhu & Yun-Ying Cao

  3. School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China

    Bei Gao

  4. Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China

    Feng Yang, Mo-Xian Chen & Debatosh Das

  5. National Oceanographic Center, Qingdao, China

    Yong Jiang

  6. Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China

    Jianhua Zhang

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  1. Bei Gao
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Gao, B., Bian, XC., Yang, F. et al. Comprehensive transcriptome analysis of faba bean in response to vernalization. Planta 251, 22 (2020). https://doi.org/10.1007/s00425-019-03308-x

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