Pan-genome identification and expression analysis of the auxin response gene family in potato

Background The auxin response factor plays an important role in plant growth and development, and stress resistance. In this study, the auxin response factor family was identified based on 47 high-quality potato pan-genomes. Results There were no core or private genes among the 28 members of the potato pan-gene family, with only one being a near-core gene, while the rest were non-essential genes. The Ka/Ks ratio values showed that only one gene was under positive selection, while the remaining family members were under purifying selection. Structural variations in the 21 potato genomes did not significantly affect the expression of the pan-gene family members, nor were any significant differences observed. Structural variations led to changes in conserved domains in some strains. RNA-seq data analysis showed that auxin response-factor family members were differentially expressed under drought stress relative to control conditions; moreover, the expression of the various gene family members differed under drought stress. Further analysis revealed that transcription factors were involved in regulating the expression of auxin response-factor gene family members. Conclusions Our findings revealed the function of the auxin response-factor family members in biological processes in potato, and provide a new theoretical reference for drought resistance-breeding in this important crop species.