Genome-Wide Identification and Expression Analysis of GA2ox, GA3ox, and GA20ox Are Related to Gibberellin Oxidase Genes in Grape (Vitis vinifera L.)

Abstract

Gibberellin (GAs) plays the important role in the regulation of grape developmental and growth processes. The bioinformatics analysis confirmed the differential expression of GA2, GA3, and GA20 gibberellin oxidase genes (<i>VvGA</i>2<i>oxs</i>, <i>VvGA3oxs,</i> and <i>VvGA20oxs</i>) in the grape genome, and laid a theoretical basis for exploring its role in grape. Based on the Arabidopsis <i>GA2oxs</i>, <i>GA3oxs</i>, and <i>GA20oxs</i> genes already reported, the <i>VvGA2oxs</i>, <i>VvGA3oxs</i>, and <i>VvGA20oxs</i> genes in the grape genome were identified using the BLAST software in the grape genome database. Bioinformatics analysis was performed using software such as DNAMAN v.5.0, Clustalx, MapGene2Chrom, MEME, GSDS v.2.0, ExPASy, DNAsp v.5.0, and MEGA v.7.0. Chip expression profiles were generated using grape Affymetrix GeneChip 16K and Grape eFP Browser gene chip data in PLEXdb. The expression of <i>VvGA2oxs</i>, <i>VvGA3oxs</i>, and <i>VvGA20oxs</i> gene families in stress was examined by qRT-PCR (Quantitative real-time-PCR). There are 24 <i>GAoxs</i> genes identified with the grape genome that can be classified into seven subgroups based on a phylogenetic tree, gene structures, and conserved Motifs in our research. The gene family has higher codon preference, while selectivity is negative selection of codon bias and selective stress was analyzed. The expression profiles indicated that the most of <i>VvGAox</i> genes were highly expressed under different time lengths of ABA (Abscisic Acid) treatment, NaCl, PEG and 5 °C. Tissue expression analysis showed that the expression levels of <i>VvGA2oxs</i> and <i>VvGA20oxs</i> in different tissues at different developmental stages of grapes were relatively higher than that of <i>VvGA3oxs</i>. Last but not least, qRT-PCR (Real-time fluorescent quantitative PCR) was used to determine the relative expression of the <i>GAoxs</i> gene family under the treatment of GA3 (gibberellin 3) and uniconazole, which can find that some <i>VvGA2oxs</i> was upregulated under GA3 treatment. Simultaneously, some <i>VvGA3oxs</i> and <i>VvGA20oxs</i> were upregulated under uniconazole treatment. In a nutshell, the <i>GA2ox</i> gene mainly functions to inactivate biologically active GAs, while <i>GA20ox</i> mainly degrades C20 gibberellins, and <i>GA3ox</i> is mainly composed of biologically active GAs. The comprehensive analysis of the three classes of <i>VvGAoxs</i> would provide a basis for understanding the evolution and function of the <i>VvGAox</i> gene family in a grape plant.