Comprehensive transcriptome analysis of faba bean in response to vernalization
This study unravels the transcriptional response of a highly productive faba bean cultivar under vernalization treatment.
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.
KeywordsSimple sequence repeats Transcription factor Transcriptome Vernalization Vicia faba
Differentially expressed gene
False discovery rate
Simple sequence repeats
Vernalization response gene
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.
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57(1):289–300Google Scholar
- Guy B, Vasyl P, Susmita D, Somnath D (2008) clValid: an R package for cluster validation. J Stat Softw 25:1–22Google Scholar
- Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Prot 8(8):1494–1512CrossRefGoogle Scholar
- Ray H, Bock C, Georges F (2015) Faba bean: transcriptome analysis from etiolated seedling and developing seed coat of key cultivars for synthesis of proanthocyanidins, phytate, raffinose family oligosaccharides, vicine, and convicine. Plant Genome 8 (1). doi:org/ https://doi.org/10.3835/plantgenome2014.07.0028
- Zeng C, Chen Z, Xia J, Zhang K, Chen X, Zhou Y, Bo W, Song S, Deng D, Guo X, Wang B, Zhou J, Peng H, Wang W, Peng M, Zhang W (2014) Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in cassava. BMC Plant Biol 14(1):207PubMedPubMedCentralCrossRefGoogle Scholar
- Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, Yang JF, Cao YY, Zhang Y, Yoshida T, Fernie AR, Fan GY, Wen B, Zhou R, Liu TY, Fan T, Gao B, Zhang D, Hao GF, Xiao S, Liu YG, Zhang JH (2017) Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. Plant J 91(3):518–533PubMedCrossRefGoogle Scholar