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Background <p>Plant height (PH) is a key agronomic trait influencing Maize yield and environmental adaptability. An optimal plant height can improve lodging resistance, planting density, and harvest index, thereby promoting stable and increased Maize yield. To investigate the genetic basis of plant height regulation, a multi-parent population comprising 917 F<sub>8</sub> recombinant inbred lines (RILs) was developed by crossing five tropical, subtropical, and temperate inbred lines (YML32, CML171, TML418, NK40-1, and Chang7-2) with the dwarf inbred line Ye107.</p> Results <p>Phenotypic analysis revealed wide variation in plant height and high heritability among the RILs. Using 6,389,682 high-quality SNPs generated through whole-genome resequencing (WGS), 147 significant SNPs and 22 QTLs associated with plant height were identified by genome-wide association studies (GWAS) and linkage analysis, respectively. Integration of these results revealed co-localization of a significant SNP (1–25,296,496) and a major QTL (<i>qPH1-1</i>), confirming a key locus on chromosome 1. This integrative approach, combined with functional annotation, led to the identification of four key candidate genes (<i>Zm00001eb008340</i>, <i>Zm00001eb038680</i>, <i>Zm00001eb038690</i> and <i>Zm00001eb038700</i>) potentially involved in plant height regulation, which encode ubiquitin carboxy-terminal hydrolase 26, the putative kinase-like protein TMKL1, exocyst complex component EXO84C, and the zinc finger protein Bud20, respectively.</p> Conclusions <p>Functional annotation suggested these candidate genes are likely involved in auxin-mediated pathways. This hypothesis was supported by qRT-PCR analysis, which showed high expression of the candidate genes in internode tissues at the V14 rapid growth stage. Notably, <i>Zm00001eb038700</i> is located upstream of BR2, a well-characterized gene involved in plant height regulation in maize, implicating its potential role in a conserved regulatory network. This study elucidates novel genetic components underlying plant height in maize and provides valuable genomic resources for breeding compact, high-yielding hybrids.</p>

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A multi-parent population approach to reveal the genetic basis of plant height in maize

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月6日

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  • Tao Dai,
  • Xiaoli Hong,
  • Fuyan Jiang,
  • Babar Ijaz,
  • Ranjan K. Shaw,
  • Xingfu Yin,
  • Xingming Fan

摘要

Background

Plant height (PH) is a key agronomic trait influencing Maize yield and environmental adaptability. An optimal plant height can improve lodging resistance, planting density, and harvest index, thereby promoting stable and increased Maize yield. To investigate the genetic basis of plant height regulation, a multi-parent population comprising 917 F8 recombinant inbred lines (RILs) was developed by crossing five tropical, subtropical, and temperate inbred lines (YML32, CML171, TML418, NK40-1, and Chang7-2) with the dwarf inbred line Ye107.

Results

Phenotypic analysis revealed wide variation in plant height and high heritability among the RILs. Using 6,389,682 high-quality SNPs generated through whole-genome resequencing (WGS), 147 significant SNPs and 22 QTLs associated with plant height were identified by genome-wide association studies (GWAS) and linkage analysis, respectively. Integration of these results revealed co-localization of a significant SNP (1–25,296,496) and a major QTL (qPH1-1), confirming a key locus on chromosome 1. This integrative approach, combined with functional annotation, led to the identification of four key candidate genes (Zm00001eb008340, Zm00001eb038680, Zm00001eb038690 and Zm00001eb038700) potentially involved in plant height regulation, which encode ubiquitin carboxy-terminal hydrolase 26, the putative kinase-like protein TMKL1, exocyst complex component EXO84C, and the zinc finger protein Bud20, respectively.

Conclusions

Functional annotation suggested these candidate genes are likely involved in auxin-mediated pathways. This hypothesis was supported by qRT-PCR analysis, which showed high expression of the candidate genes in internode tissues at the V14 rapid growth stage. Notably, Zm00001eb038700 is located upstream of BR2, a well-characterized gene involved in plant height regulation in maize, implicating its potential role in a conserved regulatory network. This study elucidates novel genetic components underlying plant height in maize and provides valuable genomic resources for breeding compact, high-yielding hybrids.