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<p>Aerobic rice presents a promising approach for cultivation in water-limited environments. This study identified 19 meta-QTLs (MQTLs) associated with five key traits for aerobic adaptation by integrating 474 QTLs onto a consensus map comprising 9,679 markers. These MQTLs had confidence intervals (CIs) ranging from 0.22 to 26.43&#xa0;cM, with an average of 8.95&#xa0;cM—2.81 times narrower than original QTLs (mean CI: 24.33&#xa0;cM), indicating improved mapping resolution. Cross-validation with genome-wide association studies (GWAS) confirmed 15 MQTLs, while synteny and collinearity analysis across rice, wheat, and maize revealed nine conserved ortho-MQTLs. Chromosome 6 emerged as a key linkage group for drought tolerance and aerobic adaptation. Candidate gene (CG) analysis within MQTL regions identified 1,555 genes, of which 22 were differentially expressed between tillering and heading stages under aerobic conditions. Among them, four genes—LOC_Os06g09390 (AP2/ERF transcription factor), LOC_Os06g06980 (Caffeoyl-CoA 3-O-methyltransferase), LOC_Os11g14220 (Alpha-tubulin), and LOC_Os04g26910 (IN2-2 protein)—showed significantly elevated expression. Thirteen high-confidence CGs including bZIP, Nodulin, WRKY, and glutathione S-transferase were also mapped to MQTLs. Meta-regions were enriched with genes encoding AP2/ERF, MYB, NAC, Zinc finger, LEA, ABC transporter, and glutathione S-transferase proteins, highlighting their functional relevance. Haplotype analysis of three candidate genes (LOC_Os06g06980, LOC_Os11g13890, and LOC_Os01g25386) revealed two to four haplotypes per gene. These findings enhance our molecular understanding of aerobic adaptation and provide a valuable resource for precise molecular breeding to develop rice cultivars better suited to water-deficient conditions.</p>

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Defining genomic landscape for identification of aerobic rice adaptation related candidate genes through meta-QTL analysis

  • 期刊论文

  • 发表日期：

    2026年7月29日

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  • Anil Namdev Kale,
  • Vinay Kumar Sharma,
  • Praful Mukund Damdar,
  • Sharanbasappa D. Madival,
  • Nitesh Kumar Sharma,
  • Karma Landup Bhutia,
  • Anurag Mishra

摘要

Aerobic rice presents a promising approach for cultivation in water-limited environments. This study identified 19 meta-QTLs (MQTLs) associated with five key traits for aerobic adaptation by integrating 474 QTLs onto a consensus map comprising 9,679 markers. These MQTLs had confidence intervals (CIs) ranging from 0.22 to 26.43 cM, with an average of 8.95 cM—2.81 times narrower than original QTLs (mean CI: 24.33 cM), indicating improved mapping resolution. Cross-validation with genome-wide association studies (GWAS) confirmed 15 MQTLs, while synteny and collinearity analysis across rice, wheat, and maize revealed nine conserved ortho-MQTLs. Chromosome 6 emerged as a key linkage group for drought tolerance and aerobic adaptation. Candidate gene (CG) analysis within MQTL regions identified 1,555 genes, of which 22 were differentially expressed between tillering and heading stages under aerobic conditions. Among them, four genes—LOC_Os06g09390 (AP2/ERF transcription factor), LOC_Os06g06980 (Caffeoyl-CoA 3-O-methyltransferase), LOC_Os11g14220 (Alpha-tubulin), and LOC_Os04g26910 (IN2-2 protein)—showed significantly elevated expression. Thirteen high-confidence CGs including bZIP, Nodulin, WRKY, and glutathione S-transferase were also mapped to MQTLs. Meta-regions were enriched with genes encoding AP2/ERF, MYB, NAC, Zinc finger, LEA, ABC transporter, and glutathione S-transferase proteins, highlighting their functional relevance. Haplotype analysis of three candidate genes (LOC_Os06g06980, LOC_Os11g13890, and LOC_Os01g25386) revealed two to four haplotypes per gene. These findings enhance our molecular understanding of aerobic adaptation and provide a valuable resource for precise molecular breeding to develop rice cultivars better suited to water-deficient conditions.