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Peer-reviewedCC BY 4.0Frontiers in Plant Science

Pan-genome analysis of the AP2/ERF gene family and its functional characterization in banana plant height

  • Zhiwei Lu1,2,3
  • Mingwei Li1,2,3
  • Shiyu Lu1,2,4
  • Weijun Xiao1,2,4
  • Zhiwei Jia1,2,3
  • Yulin Hu1,2,3
  • Yajie Duan1,2,3
  • Zhencai Pang1,2,3
  • Dequan Sun1,2,3
  • Xiaowan Hou1,2,3
  • Huigang Hu1,2,3
4 affiliations
  1. 1State Key Laboratory of Tropical Crop Breeding, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences
  2. 2Key Laboratory of Postharvest Physiology and Technology of Tropical Horticultural Products of Hainan Province
  3. 3Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products
  4. 4Chinese Academy of Agricultural Sciences
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Abstract

Introduction: Banana is a globally essential staple and industrial crop whose sustainable production is frequently challenged by excessive plant height and susceptibility to wind-induced lodging. Managing plant architecture is therefore critical for improving lodging resistance, yet the underlying genetic mechanisms governing plant height in banana remain poorly understood.

Methods: To elucidate the genetic basis of plant height, we performed a systematic pan-genome analysis of the AP2/ERF gene family across 18 diverse banana genomes. The identified genes were characterized for their duplication mechanisms and selective pressures. Furthermore, we integrated the pan-genomic dataset with published phenotypic data using a haplotype-based association study to uncover key candidate genes and analyze the geographic distribution of their associated alleles across accessions.

Results: A total of 4,732 MaAP2ERF genes were identified, yielding 468 non-redundant representative members. Dispersed duplication was the primary driver of family expansion (43.38%), whereas whole-genome duplication (WGD) established the conserved core foundation, accounting for all 42 core genes shared across all genomes. In contrast, dispersed duplication drove all 157 private genes, while the remaining 269 dispensable members arose from a combination of five duplication mechanisms. Evolutionary analysis indicated strong purifying selection on most members (K a /K s ratios between 0.2 and 0.5). Haplotype-based association identified MaAP2ERF144 and MaAP2ERF407 as key candidates for plant height, with MaAP2ERF407 demonstrating a dual association with stem elongation and lignin content for mechanical strength. Geographic analysis revealed that height-increasing alleles are mainly concentrated in Southeast Asia, Oceania, and East Africa, whereas dwarf alleles predominate in East Asian accessions.

Discussion: These findings provide a comprehensive genomic framework for the banana AP2/ERF gene family and elucidate the evolutionary mechanisms shaping its diversity. The identified functional candidate genes and key haplotype loci offer valuable genetic targets for precision molecular breeding to develop high-yielding, lodging-resistant banana cultivars with optimized plant architecture.

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Cite

BibTeXRIS
BibTeX
@article{lu2026pangenome,
  title = {{Pan-genome analysis of the AP2/ERF gene family and its functional characterization in banana plant height}},
  author = {Zhiwei Lu and Mingwei Li and Shiyu Lu and Weijun Xiao and Zhiwei Jia and Yulin Hu and Yajie Duan and Zhencai Pang and Dequan Sun and Xiaowan Hou and Huigang Hu},
  journal = {Frontiers in Plant Science},
  year = {2026},
  month = oct,
  doi = {10.3389/fpls.2026.1944831},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1944831/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Pan-genome analysis of the AP2/ERF gene family and its functional characterization in banana plant height
AU  - Zhiwei Lu
AU  - Mingwei Li
AU  - Shiyu Lu
AU  - Weijun Xiao
AU  - Zhiwei Jia
AU  - Yulin Hu
AU  - Yajie Duan
AU  - Zhencai Pang
AU  - Dequan Sun
AU  - Xiaowan Hou
AU  - Huigang Hu
PY  - 2026
DA  - 2026/10/19
JO  - Frontiers in Plant Science
DO  - 10.3389/fpls.2026.1944831
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2026.1944831/full
AB  - Introduction: Banana is a globally essential staple and industrial crop whose sustainable production is frequently challenged by excessive plant height and susceptibility to wind-induced lodging. Managing plant architecture is therefore critical for improving lodging resistance, yet the underlying genetic mechanisms governing plant height in banana remain poorly understood.  Methods: To elucidate the genetic basis of plant height, we performed a systematic pan-genome analysis of the AP2/ERF gene family across 18 diverse banana genomes. The identified genes were characterized for their duplication mechanisms and selective pressures. Furthermore, we integrated the pan-genomic dataset with published phenotypic data using a haplotype-based association study to uncover key candidate genes and analyze the geographic distribution of their associated alleles across accessions.  Results: A total of 4,732 MaAP2ERF genes were identified, yielding 468 non-redundant representative members. Dispersed duplication was the primary driver of family expansion (43.38%), whereas whole-genome duplication (WGD) established the conserved core foundation, accounting for all 42 core genes shared across all genomes. In contrast, dispersed duplication drove all 157 private genes, while the remaining 269 dispensable members arose from a combination of five duplication mechanisms. Evolutionary analysis indicated strong purifying selection on most members (K a /K s ratios between 0.2 and 0.5). Haplotype-based association identified MaAP2ERF144 and MaAP2ERF407 as key candidates for plant height, with MaAP2ERF407 demonstrating a dual association with stem elongation and lignin content for mechanical strength. Geographic analysis revealed that height-increasing alleles are mainly concentrated in Southeast Asia, Oceania, and East Africa, whereas dwarf alleles predominate in East Asian accessions.  Discussion: These findings provide a comprehensive genomic framework for the banana AP2/ERF gene family and elucidate the evolutionary mechanisms shaping its diversity. The identified functional candidate genes and key haplotype loci offer valuable genetic targets for precision molecular breeding to develop high-yielding, lodging-resistant banana cultivars with optimized plant architecture.
SN  - 1664-462X
ER  -