Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (17): 3443-3454.doi: 10.3864/j.issn.0578-1752.2020.17.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of F-Box Gene Family Based on Salt-Stressed Transcriptome Sequencing in Vicia faba L.

HAO ShuLin1(),CHEN HongWei2,LIAO FangLi3,LI Li2,LIU ChangYan2,LIU LiangJun2,WAN ZhengHuang2(),SHA AiHua1()   

  1. 1College of Agriculture, Yangtze University/Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, Hubei
    2Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064
    3Seed Authority of Jingzhou, Jingzhou 434020, Hubei
  • Received:2019-12-19 Accepted:2020-03-05 Online:2020-09-01 Published:2020-09-11
  • Contact: ZhengHuang WAN,AiHua SHA E-mail:shulinlin6@163.com;zhwan168@163.com;aihuasha@163.com

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Abstract:

【Objective】The distribution structure and evolution of F-box gene family members in Vicia faba were analyzed by bioinformatics method to study the expression patterns of family members and their responses to salt stress under different treatment times. It can provide a reference for the study of the biological function and the mechanism of F-box genes.【Method】Based on the salt-stressed transcriptome sequencing (RNA-seq) data, the NR, Swiss-Prot, PFAM and NCBI websites were used at the same time to screen and annotate the F-box genes of Vicia faba. The softwares including Web Logo 3, Prot Comp 9.0, MEGA-X and MEME were also applied to analyze the bioinformatics of conserved domain, subcellular localization, phylogenetic tree and Motif. Based on salt stress transcriptome data, the differential expression patterns of F-box gene family in Vicia faba (yz17134 salt tolerance and yz17078 salt intolerance) under salt stress were analyzed, and real-time fluorescence quantitative PCR (qRT-PCR) was used to verify the specific expression of part family members at 16 h and 24 h.【Result】Based on salt-stressed transcriptome sequencing (RNA-seq) data, 161 Vicia faba F-box genes were annotated and all contain F-box conserved domain. According to different C-terminal domains, they were divided into 11 subfamilies (FBX, FBXFBA, FBXLRR, FBXPP2, FBXKelch, FBXTUB, FBXFBD, FBXDUF, FBXACTIN, FBXWD40, and FBO). The analysis of the conserved domain showed that the F-box conserved Motif contained an extremely conserved tryptophan residue. By comparing and analyzing the evolutionary tree constructed by the F-box family of Vicia faba and the F-box family of Arabidopsis thaliana, it was found that most of the genes in the same C-terminal domain were clustered together. The results of subcellular localization prediction showed that 124 F-box genes were located outside the cell, and 37 F-box genes were located in the nucleus. The analysis of gene structure showed that there were no introns in the DNA sequences of the F-box family genes of Vicia faba, and all of them were composed of UTR zone and CDS zone. Analysis of F-box differential expression patterns based on salt-stressed transcriptome data showed that F-box gene expression in Vicia faba was diverse from each other at two different processing time points, the expression was more obvious at 16 hours after salt treatment. The results of qRT-PCR analysis showed that there were five different genes in the F-box family. The expressions of Vf056266.1, Vf062764.1 and Vf024236.1 were all up-regulated at 16 hours after salt treatment, Vf060904.1 and Vf045761.1 were both down-regulated at 16 hours after salt treatment.【Conclusion】161 Vicia faba F-box genes were identified by family annotation, and they were identified by family annotation, which were Evolutionarily divided into 11 subfamilies. 5 important genes were obtained through a series of bioinformatics analysis. What’s more, there exist difference among the expressions in diverse salt treatment time.

Key words: Vicia faba L., RNA-seq, F-box gene family, salt stress, expression pattern

Table 1

Primers for real-time quantitative PCR"

基因Gene 正向引物序列Forward primer sequence (5′-3′) 反向引物序列Reverse primer sequence (5′-3′)
Vf056266.1 CACGCCCAAAATCTCAAGGT AAGTTGCTAGGCCTTCCAGT
Vf060904.1 TGAACGAAACTGGCTTGA CGATGGTGCGATAGAGGA
Vf062764.1 TTACCAATAACCCTTCCAC TCAATACGATTAGCACCCT
Vf024236.1 CTGCTGCTGTTGTGAAGA AACCAAACGGGAGAAGAT
Vf045761.1 CCGTCTCATACTATCGTCTGTT GGGTCGGCTTGGGAGGAAT
VfNADHD4 AGGGTTAGTGAGCACCATGC ATAGCCAAAGGGAATACGCC

Fig. 1

Conserved Motif of Vicia faba L.F-box protein"

Fig. 2

Phylogenetic analysis of F-box protein in Vicia faba L. and Arabidopsis thaliana"

Fig. 3

Sub-cellular localization of F-box gene family in Vicia faba L."

Fig. 4

Family structure and Motif analysis of F-box gene in Vicia faba L."

Fig. 5

The pattern of expression of F-box family in salt stress of Vicia faba L. The heat map was generated based on the calculation of sequencing data of salt stress of Vicia faba L.. Each kind of color represents the value of the corresponding relative expression. The higher the value, the higher the expression"

Fig. 6

F-box genes of Vicia faba L.for salt stress based on qRT-PCR"

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