关键词: 马铃薯, DIR蛋白, 基因家族, 生物信息学, 非生物胁迫, 表达模式

Abstract:

Objective All members of the DIR gene family in potato (Solanum tuberosum) were identified by the latest potato genome information. Bioinformatic techniques and transcriptome data were used to predict and analyze the phylogenetic relationship, gene structures, promoter elements and expression profiles of DIR gene family members. These results will lay a foundation for further study on the function of DIR genes in potate growth and development as well as their responses to stresses. Method Based on the protein sequences of Arabidopsis DIR gene and the model file of Dirigent domain, the whole genome identification of potato DIR family members was carried out. The physicochemical characteristic, chromosome localization, collinearity analysis, conserved motif, gene structure and cis-acting elements of potato DIR genes were analyzed by bioinformatics tools such as ExPASy, MEME, MCScanX, GSDS, PlantCARE, and TBtools, respectively. Transcriptome data and RT-qPCR were based to understand the expression patterns of DIR genes in different tissues and under stress treatment, and to explore the candidate DIR genes related to growth and development and stress responses. Result A total of 34 DIR genes were identified from the potato genome and unevenly distributed on 11 chromosomes. Phylogenetic analysis showed that 34 StDIR genes were divided into three subgroups. The conserved motifs and gene structures of StDIR members in the same subgroup were relatively consistent. Most of the StDIR genes contained only one exon. Analysis of cis-acting elements indicated that the StDIR genes had diverse hormone-related elements and abiotic stress response elements. Synteny analysis revealed that 5, 13 and 18 DIR genes in potato were collinear with 3, 15 and 16 DIR genes in rice, Arabidopsis and eggplant, respectively. The expression analysis of StDIR gene showed that the StDIR genes had relatively high expressions in the leaves, roots, stolons, and callus. However, the transcript abundance of the StDIR genes was lower in sepals, carpels, stamens, and petals. Furthermore, StDIR genes had different expressions under salt, drought, heat, and cold stresses, indicating that StDIR genes play important roles in abiotic stress responses. Conclusion A total of 34 DIR genes are identified in potato and divided into three subgroups. The conserved motif and gene structure in the same subgroup are basically consistent. The expression pattern of StDIR genes vary in different tissues and significantly respond to drought and high temperature stresses.

Key words: potato, DIR protein, gene family, bioinformatics, abiotic stress, expression profile