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Key message <p>Eleven QTLs controlling maize ESL were identified via high-resolution QTL mapping of 866 maize–teosinte RILs and three promising candidate genes for <i>qESL1-1</i> were further screened through integrated RNA-seq and qRT-PCR.</p> Abstract <p>Ear shank length (ESL) represents a critical architectural trait in maize that significantly influences yield formation, kernel dehydration, and mechanical harvesting efficiency. To dissect the genetic architecture underlying ESL variation, we conducted a high-resolution quantitative trait locus (QTL) mapping using 866 maize–teosinte BC₂S₃ recombinant inbred lines genotyped with 19,838 single nucleotide polymorphism markers. Phenotypic evaluation across three environments revealed extensive ESL variation with values ranging from 9.9 to 18.7&#xa0;cm. Correlation analysis demonstrated that ESL showed positive correlations with most agronomic traits but negative correlations with most yield-related traits, while having relatively limited effects on nutritional traits. Multiple QTL mapping identified 11 QTLs distributed across eight chromosomes, collectively explaining 35.8% of phenotypic variation with individual effects ranging from 1.6% to 4.7%. Notably, 10 of 11 QTLs carried teosinte alleles that increased ESL values, indicating strong directional selection during the prolonged domestication and improvement process. The target QTL <i>qESL1-1</i> was validated using near-isogenic lines, confirming its significant effect on ESL and pleiotropic effects. RNA-sequencing (RNA-seq) transcriptome analysis using near-isogenic lines identified 773 differentially expressed genes, with three promising candidate genes within the <i>qESL1-1</i> locus: <i>Zm00001d028720</i> (phosphatidylinositol transfer protein), <i>Zm00001d028761</i> (chloroplast unusual positioning protein), and <i>Zm00001d028766</i> (asparagine synthetase). Gene ontology enrichment analysis revealed significant enrichment in terms related to floral organ development, while pathway analysis highlighted roles in amino acid metabolism and mitogen-activated protein kinase (MAPK) signaling. This study provides insights into the polygenic architecture of ESL and identifies genetic resources from teosinte for optimizing maize plant architecture in modern breeding programs.</p>

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Integrative QTL mapping and RNA-seq unravel the genetic architecture and candidate genes for ear shank length in a large maize–teosinte population

  • 期刊论文

  • 发表日期：

    2025年12月19日

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  • Mutian Gao,
  • Wei Jia,
  • Yanmei Xiao,
  • Zhijie Liao,
  • Haibin Tang,
  • Hongbing Luo,
  • Cheng Huang

摘要

Key message

Eleven QTLs controlling maize ESL were identified via high-resolution QTL mapping of 866 maize–teosinte RILs and three promising candidate genes for qESL1-1 were further screened through integrated RNA-seq and qRT-PCR.

Abstract

Ear shank length (ESL) represents a critical architectural trait in maize that significantly influences yield formation, kernel dehydration, and mechanical harvesting efficiency. To dissect the genetic architecture underlying ESL variation, we conducted a high-resolution quantitative trait locus (QTL) mapping using 866 maize–teosinte BC₂S₃ recombinant inbred lines genotyped with 19,838 single nucleotide polymorphism markers. Phenotypic evaluation across three environments revealed extensive ESL variation with values ranging from 9.9 to 18.7 cm. Correlation analysis demonstrated that ESL showed positive correlations with most agronomic traits but negative correlations with most yield-related traits, while having relatively limited effects on nutritional traits. Multiple QTL mapping identified 11 QTLs distributed across eight chromosomes, collectively explaining 35.8% of phenotypic variation with individual effects ranging from 1.6% to 4.7%. Notably, 10 of 11 QTLs carried teosinte alleles that increased ESL values, indicating strong directional selection during the prolonged domestication and improvement process. The target QTL qESL1-1 was validated using near-isogenic lines, confirming its significant effect on ESL and pleiotropic effects. RNA-sequencing (RNA-seq) transcriptome analysis using near-isogenic lines identified 773 differentially expressed genes, with three promising candidate genes within the qESL1-1 locus: Zm00001d028720 (phosphatidylinositol transfer protein), Zm00001d028761 (chloroplast unusual positioning protein), and Zm00001d028766 (asparagine synthetase). Gene ontology enrichment analysis revealed significant enrichment in terms related to floral organ development, while pathway analysis highlighted roles in amino acid metabolism and mitogen-activated protein kinase (MAPK) signaling. This study provides insights into the polygenic architecture of ESL and identifies genetic resources from teosinte for optimizing maize plant architecture in modern breeding programs.