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<p>Salinity is one of the major abiotic constraints limiting rice productivity in irrigated and coastal ecosystems worldwide, thereby posing a serious threat to global food security. Rice (<i>Oryza sativa</i> L.) is particularly sensitive to salinity at the seedling stage, where excessive Na⁺ accumulation and reduced K⁺ uptake adversely affect plant growth and development. The present study carried out to detect quantitative trait loci (QTLs) for salinity tolerance at seedling-stage using 175 recombinant inbred lines (RILs) developed from the cross MTU 1001 × Kalarata, a salt-tolerant indica landrace. The RIL population was evaluated under hydroponic saline stress conditions (EC ~ 10 dS m⁻¹) for seven morpho-physiological traits, including salt injury score, root length, shoot length, shoot Na⁺, root Na⁺, shoot K⁺, and root K⁺ concentrations. Significant phenotypic variation was observed among the RILs. Genotyping-by-Sequencing (GBS)-based SNP genotyping generated 6,020 high-quality polymorphic markers for QTL analysis using Inclusive Composite Interval Mapping (ICIM). A total of seven QTLs associated with five traits were identified across chromosomes 2, 3, 4, 8, 9, and 12. Among these, qSL12.1, qSN2.1, and qRL8.1 were identified as major QTLs explaining 15.07%, 13.49%, and 10.87% of the phenotypic variance, respectively. These QTLs represent valuable genomic resources for marker-assisted breeding, QTL pyramiding, and genomic selection aimed at developing high-yielding salt-tolerant rice cultivars for salt-affected ecosystems.</p>

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Deciphering Genomic Regions Governing Salinity Tolerance at the Seedling Stage in Rice

  • 期刊论文

  • 发表日期：

    2026年7月21日

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  • BM Dushyanthakumar,
  • Himaja Reddy,
  • Suman Rathor,
  • Lokeshkumar BM,
  • Ashish Nain,
  • Vinaykumar NM,
  • AY Hugar,
  • SK Shashikala,
  • GN Housagouda,
  • PC Sharma,
  • Pradeep Sharma,
  • SL Krishnamurthy

摘要

Salinity is one of the major abiotic constraints limiting rice productivity in irrigated and coastal ecosystems worldwide, thereby posing a serious threat to global food security. Rice (Oryza sativa L.) is particularly sensitive to salinity at the seedling stage, where excessive Na⁺ accumulation and reduced K⁺ uptake adversely affect plant growth and development. The present study carried out to detect quantitative trait loci (QTLs) for salinity tolerance at seedling-stage using 175 recombinant inbred lines (RILs) developed from the cross MTU 1001 × Kalarata, a salt-tolerant indica landrace. The RIL population was evaluated under hydroponic saline stress conditions (EC ~ 10 dS m⁻¹) for seven morpho-physiological traits, including salt injury score, root length, shoot length, shoot Na⁺, root Na⁺, shoot K⁺, and root K⁺ concentrations. Significant phenotypic variation was observed among the RILs. Genotyping-by-Sequencing (GBS)-based SNP genotyping generated 6,020 high-quality polymorphic markers for QTL analysis using Inclusive Composite Interval Mapping (ICIM). A total of seven QTLs associated with five traits were identified across chromosomes 2, 3, 4, 8, 9, and 12. Among these, qSL12.1, qSN2.1, and qRL8.1 were identified as major QTLs explaining 15.07%, 13.49%, and 10.87% of the phenotypic variance, respectively. These QTLs represent valuable genomic resources for marker-assisted breeding, QTL pyramiding, and genomic selection aimed at developing high-yielding salt-tolerant rice cultivars for salt-affected ecosystems.