Genome-wide identification of grape PLATZ family genes and expression analysis during seed development

Abstract: 【Objective】PLATZ is a plant-specific zinc finger transcription factor and has important functions in many processes of plant growth and development. It has also been reported to be involved in the development of seeds in other plants, but the regulatory mechanism in the seed of grape berry development is still unclear. By identifying the structure and expression of the grapevine PLATZ gene family, this study aimed to lay a foundation for further understanding the role of PLATZ family genes in various plant growth and developmental processes especially in seed development.【Methods】Based on the grape genome data, basic local alignment search tool (BLAST) and Hidden Markov Models (HMM) profiles were used to identify the members of the grape PLATZ family. Online websites including Pfam, NCBI, SMART, Ex PASy, PSORT, GSDS 2.0, MEME and bioinformatics analysis software including SPDE, MEGA-X and TBtools were used to predict the physicochemical properties, gene structure, protein subcellular localization, phylogenetic relationship and distribution of cis-acting elements of grapePLATZ gene family. qRT-PCR was used to analysis the expression level of the VvPLATZ genes during seed development and in response to exogenous IAA.【Results】A total of 13 PLATZ members were identified in the whole grape genome, which were distributed on 9 chromosomes. The amino acid sequence length of family members was between 115 and 306 aa. The maximum molecular mass was 34 700.11 u and the minimum was 12 703.00 u. The isoelectric points were between 8.20 and 10.12, the instability factor was between 36.88 and 71.24, and the aliphatic index was between 62.37 and 85.96. The subcellular localization prediction results showed that 9 of the 13 grape PLATZ family members were localized in the nucleus, 2 in the cytoplasmic, 1 in the chloroplast, and 1 in the peroxisome. The phylogenetic analysis showed that grape PLATZ protein members were divided into four groups (A, B, C, D), subgroups A, B, C, and D contain 2, 3, 6, and 2 grape PLATZ members, respectively, and subgroup did not contain any grape PLATZ members, showing some evolutionary loss. The protein conservation motif analysis showed that grape PLATZ protein had strong conservation, while intron- exon distribution analysis suggested evolutionary diversity in grape PLATZ genes. The syntenic analysis found that VvPLATZ7- VvPLATZ8 and VvPLATZ5- VvPLATZ11 were segmental duplicated genes. In addition, the analysis of cis-acting elements found that there were 24 elements in PLATZ family, which were divided into 4 categories according to their functions: hormone response, light response, stress response, plant developmental regulation. Except for the VvPLATZ6 gene, all other genes have hormone- responsive elements. Except for the VvPLATZ11 and VvPLATZ5, most grape PLATZ genes contain stress-responsive cis-elements. The transcriptome data showed that the VvPLATZ5, VvPLATZ11 and VvPLATZ12 were significantly up- regulated during ovule development of the seedless progeny compared with the seeded progeny, while the VvPLATZ2 was up-regulated in the seed progeny. The expression levels of the VvPLATZ2 and VvPLATZ6 were significantly higher in the seeded varieties than that in the seedless varieties, suggesting that they might play a role in the seed development. Compared with the seeded varieties, the expression level of the VvPLATZ5 was significantly higher in the seed development of the two seedless grape varieties than that in the seeded varieties, suggesting that it might be related to ovule abortion. It was worth noting that the differential expression patterns of the VvPLATZ2 and VvPLATZ5 genes covered almost the entire developmental period, and the differential fold changes were quite large. The expression levels of the VvPLATZ4/13, VvPLATZ11 and VvPLATZ12 were significantly higher in the seedless varieties at the early stage of the seed development (20 and 30 DAF) than those in the seeded varieties. All 8 VvPLATZ genes were in response to IAA treatment, the expression levels of the VvPLATZ5 and VvPLATZ12 genes significantly increased 6 h post treatment. 【Conclusion】A total of 13 PLATZ genes were identified in the grape genome, and the VvPLATZ genes showed differential expression during the process of the seed development, and it significantly responded to IAA treatment. Our result enriched the understanding of grape PLATZ gene, laid a theoretical foundation for further research on the function of grape PLATZ gene, and was conducive to provide highquality genetic resources for grape molecular breeding.