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<p>With climate change intensifying global temperatures, developing heat-resilient rice varieties has become a critical challenge for future food security. In this study, we explored the allelic variation of a Glycolipid Transfer Protein (GLTP) gene in rice and its role in physiological adaptation to heat stress. A diverse panel of 96 rice genotypes was evaluated over two seasons under both control and heat-stress environments for five key traits: relative water content, membrane stability index, malondialdehyde content, antioxidant activity, and chlorophyll concentration. Sequence analysis of the GLTP gene and its promoter revealed 172 mutations, including 14 coding SNPs that defined 9 haplotypes and 6 protein isoforms. Association mapping identified several significant SNP-trait linkages, particularly in intronic and promoter regions, with strong effects on oxidative stress indicators. Notably, a rare haplotype, Hap4, comprising a single genotype (NERICA Line 44) exhibited superior physiological performance under heat stress. The poor haplotype, Hap9, was found to be structurally distinct at the C-terminal domain, as predicted by the AlphaFold3 modelling. These findings highlight the functional importance of natural non-coding variation and demonstrate how specific GLTP3 alleles can enhance thermo-tolerance. This work provides novel molecular insights and valuable allelic resources to accelerate the breeding of climate-smart rice cultivars.</p>

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Leveraging natural variations in a rice GLTP gene for building climate-smart rice varieties

  • 期刊论文

  • 发表日期：

    2025年10月22日

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  • Bipratip Dutta,
  • Amit Kumar Mazumder,
  • Ritapa Datta,
  • Deepesh Kumar,
  • Archana Singh,
  • Pranab Kumar Mandal,
  • Amolkumar U. Solanke,
  • Amitha Mithra Sevanthi

摘要

With climate change intensifying global temperatures, developing heat-resilient rice varieties has become a critical challenge for future food security. In this study, we explored the allelic variation of a Glycolipid Transfer Protein (GLTP) gene in rice and its role in physiological adaptation to heat stress. A diverse panel of 96 rice genotypes was evaluated over two seasons under both control and heat-stress environments for five key traits: relative water content, membrane stability index, malondialdehyde content, antioxidant activity, and chlorophyll concentration. Sequence analysis of the GLTP gene and its promoter revealed 172 mutations, including 14 coding SNPs that defined 9 haplotypes and 6 protein isoforms. Association mapping identified several significant SNP-trait linkages, particularly in intronic and promoter regions, with strong effects on oxidative stress indicators. Notably, a rare haplotype, Hap4, comprising a single genotype (NERICA Line 44) exhibited superior physiological performance under heat stress. The poor haplotype, Hap9, was found to be structurally distinct at the C-terminal domain, as predicted by the AlphaFold3 modelling. These findings highlight the functional importance of natural non-coding variation and demonstrate how specific GLTP3 alleles can enhance thermo-tolerance. This work provides novel molecular insights and valuable allelic resources to accelerate the breeding of climate-smart rice cultivars.