, 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


Main conclusion

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.


Simple sequence repeats Transcription factor Transcriptome Vernalization Vicia faba 



Differentially expressed gene


False discovery rate


Gene ontology


Simple sequence repeats


Transcription factor


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.

Supplementary material

425_2019_3308_MOESM1_ESM.pdf (1.3 mb)
Supplementary material 1 (PDF 1288 kb)
425_2019_3308_MOESM2_ESM.pdf (902 kb)
Supplementary material 2 (PDF 901 kb)
425_2019_3308_MOESM3_ESM.pdf (1.6 mb)
Supplementary material 3 (PDF 1632 kb)
425_2019_3308_MOESM4_ESM.xlsx (118 kb)
Supplementary material 4 (XLSX 117 kb)
425_2019_3308_MOESM5_ESM.xlsx (69 kb)
Supplementary material 5 (XLSX 68 kb)
425_2019_3308_MOESM6_ESM.xlsx (99 kb)
Supplementary material 6 (XLSX 98 kb)
425_2019_3308_MOESM7_ESM.xlsx (190 kb)
Supplementary material 7 (XLSX 190 kb)
425_2019_3308_MOESM8_ESM.xlsx (292 kb)
Supplementary material 8 (XLSX 291 kb)
425_2019_3308_MOESM9_ESM.xlsx (10 kb)
Supplementary material 9 (XLSX 9 kb)


  1. Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25(12):1263–1274PubMedCrossRefGoogle Scholar
  2. Arun-Chinnappa KS, McCurdy DW (2015) De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research. Front Plant Sci 6:217. CrossRefPubMedPubMedCentralGoogle Scholar
  3. Aubry S, Kelly S, Kumpers BM, Smith-Unna RD, Hibberd JM (2014) Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS Genet 10(6):e1004365PubMedPubMedCentralCrossRefGoogle Scholar
  4. Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167PubMedCrossRefGoogle Scholar
  5. 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
  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120PubMedPubMedCentralCrossRefGoogle Scholar
  7. Bouche F, Lobet G, Tocquin P, Perilleux C (2016) FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucleic Acids Res 44(D1):D1167–D1171PubMedCrossRefGoogle Scholar
  8. Brunner AM, Evans LM, Hsu CY, Sheng XY (2014) Vernalization and the chilling requirement to exit bud dormancy: shared or separate regulation? Front Plant Sci 5:732. CrossRefPubMedPubMedCentralGoogle Scholar
  9. Cao YY, Bian XC, Chen MX, Xia LR, Zhang J, Zhu FY, Wu CF (2017) iTRAQ-based quantitative proteomic analysis in vernalization-treated faba bean (Vicia faba L.). PLoS One 12(11):e0187436PubMedPubMedCentralCrossRefGoogle Scholar
  10. Chouard P (1960) Vernalization and its relations to dormancy. Annu Rev Plant Physiol 11(1):191–238CrossRefGoogle Scholar
  11. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676CrossRefGoogle Scholar
  12. Diel MI, Pinheiro MVM, Cocco C, Thiesen LA, Altíssimo BS, Fontana DC, Caron BO, Testa V, Schmidt D (2017) Artificial vernalization in strawberry plants: phyllochron, production and quality. Aust J Crop Sci 11(10):1315CrossRefGoogle Scholar
  13. Ding F, Cui P, Wang Z, Zhang S, Ali S, Xiong L (2014) Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. BMC Genomics 15:431PubMedPubMedCentralCrossRefGoogle Scholar
  14. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. P Natl Acad Sci USA 95(25):14863–14868CrossRefGoogle Scholar
  15. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(2):W29–W37PubMedPubMedCentralCrossRefGoogle Scholar
  16. Gao B, Zhang D, Li X, Yang H, Wood AJ (2014) De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis. BMC Res Notes 7:490PubMedPubMedCentralCrossRefGoogle Scholar
  17. Gao B, Zhang D, Li X, Yang H, Zhang Y, Wood AJ (2015) De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration. BMC Genomics 16:416PubMedPubMedCentralCrossRefGoogle Scholar
  18. Gao B, Li X, Zhang D, Liang Y, Yang H, Chen M, Zhang Y, Zhang J, Wood AJ (2017) Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum. Sci Rep 7:7571PubMedPubMedCentralCrossRefGoogle Scholar
  19. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36(10):3420–3435PubMedPubMedCentralCrossRefGoogle Scholar
  20. Greenup AG, Sasani S, Oliver SN, Walford SA, Millar AA, Trevaskis B (2011) Transcriptome analysis of the vernalization response in barley (Hordeum vulgare) seedlings. Plos One 6(3):e1790010CrossRefGoogle Scholar
  21. Guy B, Vasyl P, Susmita D, Somnath D (2008) clValid: an R package for cluster validation. J Stat Softw 25:1–22Google Scholar
  22. 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
  23. Jensen ES, Peoples MB, Hauggaard-Nielsen H (2010) Faba bean in cropping systems. Field Crops Res 115(3):203–216CrossRefGoogle Scholar
  24. Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G (2017) PlantTFDB 40: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45(D1):D1040–D1045PubMedPubMedCentralCrossRefGoogle Scholar
  25. Kim DH, Doyle MR, Sung S, Amasino RM (2009) Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 25:277–299PubMedCrossRefGoogle Scholar
  26. Landry EJ, Coyne CJ, Hu JG (2015) Agronomic performance of spring-sown faba bean in Southeastern Washington. Agron J 107(2):574–578CrossRefGoogle Scholar
  27. Lee BH, Henderson DA, Zhu JK (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell 17(11):3155–3175PubMedPubMedCentralCrossRefGoogle Scholar
  28. Li X, Zhang S, Bai J, He Y (2016) Tuning growth cycles of Brassica crops via natural antisense transcripts of BrFLC. Plant Biotechnol J 14(3):905–914PubMedCrossRefGoogle Scholar
  29. Liu Q, Donner E, Yin Y, Huang RL, Fan MZ (2006) The physicochemical properties and in vitro digestibility of selected cereals, tubers and legumes grown in China. Food Chem 99(3):470–477CrossRefGoogle Scholar
  30. Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B (2014) Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ 37(5):1250–1258PubMedCrossRefGoogle Scholar
  31. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550PubMedPubMedCentralCrossRefGoogle Scholar
  32. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21(16):3448–3449PubMedCrossRefGoogle Scholar
  33. Mahfoozi S, Limin AE, Ahakpaz F, Fowler DB (2006) Phenological development and expression of freezing resistance in spring and winter wheat under field conditions in north-west Iran. Field Crop Res 97(2–3):182–187CrossRefGoogle Scholar
  34. Meaden PG, Arneborg N, Guldfeldt LU, Siegumfeldt H, Jakobsen M (1999) Endocytosis and vacuolar morphology in Saccharomyces cerevisiae are altered in response to ethanol stress or heat shock. Yeast 15(12):1211–1222PubMedCrossRefGoogle Scholar
  35. Mutasa-Göttgens ES, Joshi A, Holmes HF, Hedden P, Göttgens B (2012) A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics 13(1):99PubMedPubMedCentralCrossRefGoogle Scholar
  36. Ocana S, Seoane P, Bautista R, Palomino C, Claros GM, Torres AM, Madrid E (2015) Large-scale transcriptome analysis in faba bean (Vicia faba L.) under Ascochyta fabae infection. PLoS One 10(8):e0135143PubMedPubMedCentralCrossRefGoogle Scholar
  37. O’Sullivan DM, Angra D (2016) Advances in faba bean genetics and genomics. Front Genet 7:150PubMedPubMedCentralGoogle Scholar
  38. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19(5):651–652PubMedCrossRefGoogle Scholar
  39. 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/
  40. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140PubMedPubMedCentralCrossRefGoogle Scholar
  41. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T (2012) A travel guide to Cytoscape plugins. Nat Methods 9(11):1069–1076PubMedPubMedCentralCrossRefGoogle Scholar
  42. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20(17):3246–3248PubMedCrossRefGoogle Scholar
  43. Shavrukov Y, Kurishbayev A, Jatayev S, Shvidchenko V, Zotova L, Koekemoer F, de Groot S, Soole K, Langridge P (2017) Early flowering as a drought escape mechanism in plants: How can it aid wheat production? Front Plant Sci 8:1950PubMedPubMedCentralCrossRefGoogle Scholar
  44. Shea DJ, Itabashi E, Takada S, Fukai E, Kakizaki T, Fujimoto R, Okazaki K (2018) The role of FLOWERING LOCUS C in vernalization of Brassica: the importance of vernalization research in the face of climate change. Crop Pasture Sci 69(1):30–39CrossRefGoogle Scholar
  45. Singh P, Jatav A, Singh P, Singh A, Sharma SK, Chaudhary US (2017) Effect of vernalization and fungicidal seed treatment on yield and quality of wheat (Triticum aestivum L.). Int J Curr Microbiol App Sci 6(9):20–26CrossRefGoogle Scholar
  46. Sun M, Qi X, Hou L, Xu X, Zhu Z, Li M (2015) Gene expression analysis of Pak Choi in response to vernalization. PloS One 10(10):e0141446PubMedPubMedCentralCrossRefGoogle Scholar
  47. Sung SB, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nat 427(6970):159–164CrossRefGoogle Scholar
  48. Trevaskis B, Hemming MN, Dennis ES, Peacock WJ (2007) The molecular basis of vernalization-induced flowering in cereals. Trends Plant Sci 12(8):352–357PubMedCrossRefGoogle Scholar
  49. Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, maize. Plant Cell Environ 32(9):1211–1229PubMedCrossRefGoogle Scholar
  50. Varet H, Brillet-Gueguen L, Coppee JY, Dillies MA (2016) SARTools: a DESeq2- and EdgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data. PLoS One 11(6):e0157022PubMedPubMedCentralCrossRefGoogle Scholar
  51. Winfield MO, Lu CG, Wilson ID, Coghill JA, Edwards KJ (2010) Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol J 8(7):749–771PubMedCrossRefGoogle Scholar
  52. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39(2):W316–W322PubMedPubMedCentralCrossRefGoogle Scholar
  53. Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303(5664):1640–1644PubMedPubMedCentralCrossRefGoogle Scholar
  54. Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. P Natl Acad Sci USA 103(51):19581–19586CrossRefGoogle Scholar
  55. 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
  56. 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

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

Personalised recommendations