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<p>Silicon (Si) is widely recognized for its role in mitigating the uptake and translocation of toxic heavy metals such as Pb, Cd, and Hg from soil to grain, partly through its effects on metal transporters and apoplastic barriers. However, its impact on the transport and accumulation of essential mineral nutrients remains poorly understood. Given the importance of Si in rice growth and stress tolerance, this study aims to investigate how Si supplementation influences the accumulation of key nutrients, including calcium (Ca), magnesium (Mg), iron (Fe), and manganese (Mn), in the Vietnamese rice panel. Each rice genotype was cultivated under two conditions, with and without Si supplementation, followed by biochemical phenotyping. The results revealed substantial genotypic variation in mineral accumulation responses, with 54% to 65% of the germplasm exhibiting reduced mineral content in grains under Si supplementation. Genome-wide association study analysis (GWAS) identified 52 significant single polymorphisms (SNPs), from which 11 quantitative trait loci (QTLs) were defined. These QTLs were primarily associated with Mg and Mn content and harbored several candidate genes involved in metal transport and homeostasis. Notable gene families included aquaporins, ATP-binding cassette transporters, boron efflux transporters, amino acid, and polyamine transporters, heavy metal-associated isoprenylated plant proteins (HIPPs), F-box proteins, cytochrome P450s, heat shock proteins, and zinc finger transcription factors. Among these candidates, the aquaporin gene <i>OsPIP1;1</i>, located within <i>QTL2.4</i>, emerged as the most promising candidate. As a member of the plasma membrane intrinsic protein (PIP) family, <i>OsPIP1;1</i> plays a crucial role in facilitating transmembrane water and solute transport and may mediate mineral uptake and stress responses under Si supplementation. These findings provide new insights into the genetic architecture underlying mineral accumulation in rice and underscore the potential of Si in modulating transporter-mediated nutrient use efficiency and heavy metal resilience.</p>

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Genome-wide association study reveals new potential quantitative trait loci (QTLs) and genes associated with mineral accumulation under silicon supplementation in Vietnamese rice landraces

  • 期刊论文

  • 发表日期：

    2026年7月2日

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  • Quynh Hoa Nguyen,
  • Giang Son Tran,
  • Huong Mai,
  • Thi Mai Huong To

摘要

Silicon (Si) is widely recognized for its role in mitigating the uptake and translocation of toxic heavy metals such as Pb, Cd, and Hg from soil to grain, partly through its effects on metal transporters and apoplastic barriers. However, its impact on the transport and accumulation of essential mineral nutrients remains poorly understood. Given the importance of Si in rice growth and stress tolerance, this study aims to investigate how Si supplementation influences the accumulation of key nutrients, including calcium (Ca), magnesium (Mg), iron (Fe), and manganese (Mn), in the Vietnamese rice panel. Each rice genotype was cultivated under two conditions, with and without Si supplementation, followed by biochemical phenotyping. The results revealed substantial genotypic variation in mineral accumulation responses, with 54% to 65% of the germplasm exhibiting reduced mineral content in grains under Si supplementation. Genome-wide association study analysis (GWAS) identified 52 significant single polymorphisms (SNPs), from which 11 quantitative trait loci (QTLs) were defined. These QTLs were primarily associated with Mg and Mn content and harbored several candidate genes involved in metal transport and homeostasis. Notable gene families included aquaporins, ATP-binding cassette transporters, boron efflux transporters, amino acid, and polyamine transporters, heavy metal-associated isoprenylated plant proteins (HIPPs), F-box proteins, cytochrome P450s, heat shock proteins, and zinc finger transcription factors. Among these candidates, the aquaporin gene OsPIP1;1, located within QTL2.4, emerged as the most promising candidate. As a member of the plasma membrane intrinsic protein (PIP) family, OsPIP1;1 plays a crucial role in facilitating transmembrane water and solute transport and may mediate mineral uptake and stress responses under Si supplementation. These findings provide new insights into the genetic architecture underlying mineral accumulation in rice and underscore the potential of Si in modulating transporter-mediated nutrient use efficiency and heavy metal resilience.