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Background <p>The auxin response factor (ARF) is a key regulator involved in plant growth, development, and stress response. In this study, we systematically identified the ARF gene family using a pan-genomic approach based on 47 high-quality potato genomes.</p> Results <p>Among the 28 members of the potato ARF pan-gene family, no core or private genes were identified. Only one gene was classified as near-core, while the remaining genes were considered non-essential. Ka/Ks analysis indicated that a single gene was under positive selection, whereas the rest of the family members were subject to purifying selection. Structural variations across the 21 potato genomes did not significantly alter the expression of ARF pan-gene family members, and no notable expression differences were detected. However, these structural variations did lead to changes in conserved domains in certain strains. RNA-seq analysis revealed differential expression of ARF family members under drought stress compared to control conditions, with variation in expression levels among different genes. Further investigation suggested that transcription factors are involved in regulating the expression of ARF gene family members.</p> Conclusions <p>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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月22日

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  • Quancai Man,
  • Wei Li,
  • Shunjuan Gao,
  • Fangming Liu,
  • Shuo Sun,
  • Xiaojing Liu,
  • Baisong Lin,
  • Lei Wang,
  • Mingya Ding,
  • Xiaotian Chen,
  • Jianghui Cui

摘要

Background

The auxin response factor (ARF) is a key regulator involved in plant growth, development, and stress response. In this study, we systematically identified the ARF gene family using a pan-genomic approach based on 47 high-quality potato genomes.

Results

Among the 28 members of the potato ARF pan-gene family, no core or private genes were identified. Only one gene was classified as near-core, while the remaining genes were considered non-essential. Ka/Ks analysis indicated that a single gene was under positive selection, whereas the rest of the family members were subject to purifying selection. Structural variations across the 21 potato genomes did not significantly alter the expression of ARF pan-gene family members, and no notable expression differences were detected. However, these structural variations did lead to changes in conserved domains in certain strains. RNA-seq analysis revealed differential expression of ARF family members under drought stress compared to control conditions, with variation in expression levels among different genes. Further investigation suggested that transcription factors are involved in regulating the expression of ARF 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.