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<p>Grain phytic acid is a key anti-nutrient in rice that limits mineral bio-availability and exhibits considerable natural variation in aromatic germplasm. In this study, we evaluated phytic acid content in 138 aromatic rice accessions of indigenous and exotic origin and characterized the genetic diversity and population structure using 14 candidate gene–based simple sequence repeat&#xa0;(cgSSR) markers. The experiment was conducted at ICAR-Central Rice Reserch Institute, Cuttack, India during wet season of 2022 and 2023. The natural grain phytic acid content ranged from 0.54 to 2.13%, detected 24 alleles (mean gene diversity = 0.41; mean PIC = 0.36) and obtained two principal genetic clusters accounting for 45.1% of variation via principal component. The marker trait association identified M7 (<i>LOC_Os04g55800</i>) marker derived from gene <i>LPA</i> gene (<i>OsSULTR3;3</i>) is signifianly associated with grain phytic acid content, explaining 4.87% of phytic acid variance and differentiating two alleles (215&#xa0;bp, 224&#xa0;bp) with mean phytic acid contents of 1.12 and 1.31% (p ≤ 0.05). Sequencing of low-phytic acid (APA111; 0.84%) and high-phytic acid (APA44; 1.72%) lines revealed a frameshift-inducing insertion and multiple InDel mutations in APA111 versus two non-synonymous substitutions in APA44, confirming functional variation at the <i>LPA</i> locus. Correlation analysis indicate novel positive associations of phytic acid content with grain area (r = 0.18), grain length (r = 0.23), and length/breadth ratio (r = 0.23), while grain breadth correlated exclusively with length/breadth ratio (r = 0.55). Thus, the diverse allelic variation and clear population structure identified among 138 aromatic rice accessions provide a rich reservoir for breeding low-phytic acid cultivars without sacrificing grain quality. Indigenous lines APA111 (Karigilas) carrying the low-phytic acid allele serve as ideal donor parents, minimizing linkage drag compared to mutant-derived sources. Additionally, the positive correlations between phytic acid content and grain morphology traits suggest that simultaneous selection for desirable grain shape (e.g., slender, long grains) may indirectly favor lower phytic acid levels. By combining functional markers, natural donor germplasm, and phenotypic indices for grain shape, breeders can efficiently develop aromatic rice cultivars with enhanced mineral bioavailability and premium grain characteristics.</p>

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Candidate gene–based characterization of loci underlying grain quality and phytic acid in aromatic rice

  • 期刊论文

  • 发表日期：

    2026年1月14日

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  • Sasmita Behera,
  • Rameswar Prasad Sah,
  • Awadhesh Kumar,
  • Khirod Kumar Sahoo,
  • Muhammed Azharudheen TP,
  • Soumya Priyadarshinee Mohanty,
  • Abhishek Kumar Sahu,
  • Anilkumar C,
  • Bishnu Charan Marndi,
  • Debashis Moharana,
  • Sunil Kumar Nair,
  • Namita Singh,
  • Lambodar Behera,
  • Sanghamitra Samantaray

摘要

Grain phytic acid is a key anti-nutrient in rice that limits mineral bio-availability and exhibits considerable natural variation in aromatic germplasm. In this study, we evaluated phytic acid content in 138 aromatic rice accessions of indigenous and exotic origin and characterized the genetic diversity and population structure using 14 candidate gene–based simple sequence repeat (cgSSR) markers. The experiment was conducted at ICAR-Central Rice Reserch Institute, Cuttack, India during wet season of 2022 and 2023. The natural grain phytic acid content ranged from 0.54 to 2.13%, detected 24 alleles (mean gene diversity = 0.41; mean PIC = 0.36) and obtained two principal genetic clusters accounting for 45.1% of variation via principal component. The marker trait association identified M7 (LOC_Os04g55800) marker derived from gene LPA gene (OsSULTR3;3) is signifianly associated with grain phytic acid content, explaining 4.87% of phytic acid variance and differentiating two alleles (215 bp, 224 bp) with mean phytic acid contents of 1.12 and 1.31% (p ≤ 0.05). Sequencing of low-phytic acid (APA111; 0.84%) and high-phytic acid (APA44; 1.72%) lines revealed a frameshift-inducing insertion and multiple InDel mutations in APA111 versus two non-synonymous substitutions in APA44, confirming functional variation at the LPA locus. Correlation analysis indicate novel positive associations of phytic acid content with grain area (r = 0.18), grain length (r = 0.23), and length/breadth ratio (r = 0.23), while grain breadth correlated exclusively with length/breadth ratio (r = 0.55). Thus, the diverse allelic variation and clear population structure identified among 138 aromatic rice accessions provide a rich reservoir for breeding low-phytic acid cultivars without sacrificing grain quality. Indigenous lines APA111 (Karigilas) carrying the low-phytic acid allele serve as ideal donor parents, minimizing linkage drag compared to mutant-derived sources. Additionally, the positive correlations between phytic acid content and grain morphology traits suggest that simultaneous selection for desirable grain shape (e.g., slender, long grains) may indirectly favor lower phytic acid levels. By combining functional markers, natural donor germplasm, and phenotypic indices for grain shape, breeders can efficiently develop aromatic rice cultivars with enhanced mineral bioavailability and premium grain characteristics.