Genome-wide Identification Of Rice VQ Gene Family And Its Expression Profiles In Rice

VQ proteins are unique to plant kindom.In recent years,it has been found that the interaction of VQ proteins and WRKY transcription factors is involved in plant growth,metabolism and stress resistance.However,systematic studies on expression profiles of rice VQ gene family in response to biotic,abiotic stresses and hormone treatments are still rare.In this study,sequence identification,domain or motif search,multiple sequence alignment and phylogenetic tree construction of rice VQ family were performed by bioinformatics tools such as MEGA6.0,Clustalx1.83,IBS1.0 and MapInspect.Quantitative real-time PCR(qRT-PCR)was used to analyze the expression profiles of rice VQ genes rice after treatment of hormones such as salicylic acid(SA),jasmonic acid(JA),ethylene(ET)and abscisic Acid(ABA),Riziocotinia solani inoculation and abiotic stresses such as polyethyleneglycol(PEG)simulated drought,high sality and cold(4℃).Moreover,the effect of nitric oxide(NO)on the expression of VQ genes was investigated and the similarity of VQ and WRKY genes was analyzed based on microarry hybridization data in the previous study of our lab.The results are summarized as follows:1.The rice genome contained 40 VQ genes distributed unevenly in 12 chromosomes.Only 3 VQ genes contained introns.Different VQ motifs,such as FxxxVQxFTG,FxxxVQxVTG,FxxxVQxITGand FxxxVHxVTG,were found in rice.Among them,FxxxVQxLTG was the predominant forms.Phylogenetic analysis indicated that the VQ proteins of rice and Arabidopsis were categorized into 8 groups.Most of rice VQ proteins were clustered into individual groups which are distinct with Arabidopsis VQ proteins,suggesting obvious divergences between them.2.The expression levels of most of rice VQ genes(except for VQ1,3,5,8,11,13,24,25 and 30)were relatively low in different tissues during different develpoment stages.Moreover,the expression of most of rice VQ genes(except for VQ5,7,10 and 24)had no evident tissue-specific and development-specific characteristics.3.qRT-PCR analysis indicated that the numbers of differentially expressed VQ genes were different in response to various hormones(Genes with significant difference(p<0.05)in expression levels at least one time point were defined as differentially expressed genes compared with those of 0 h).The maximum numbers(28)were registered under JA treatment.Arranged in descending order were ET(12),ABA(10)and SA(5)treatments.Additionally,20,9,11 and 12 rice VQ genes were responsive to high sality,PEG,cold and R.solani infection,respectively.These findings suggest that a portion of rice VQ genes may be involved in the responses to biotic and abiotic stresses through one or more signal pathways mediated by hormones.4.Microarray analysis showed that 14 VQ genes were differentially expressed after NO treatment.Most of them were upregulated.The promoter regions of these VQ genes were enriched with W-box or W-box like elements(specific binding sites of WRKY proteins).The average frequency of 5.4 was much higher statistically expected.Clustering analysis indicated that the differentially expressed VQ genes shared similar exprerssion patterns of some WRKY genes upon NO triggering.These observations suggest that rice VQ and WRKY may interact with each other,and their interaction may play regulatory roles in NO signaling pathway.