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<p>The genetic basis of mesocotyl length and its associated loci is critical for improving seedling emergence and establishment in direct-seeded rice systems. This study investigated the phenotypic variation and genetic architecture of mesocotyl length in a diverse panel of 192 rice genotypes using a genome-wide association study (GWAS) approach. The panel, comprising germplasm accessions, advanced breeding lines, and released varieties, was genotyped using a 44&#xa0;K SNP array, resulting in 19,613 high-quality polymorphic SNPs after stringent filtering. Phenotypic evaluation revealed continuous variation in mesocotyl length, ranging from 2.48 to 18.98&#xa0;mm, with high broad-sense heritability (71.2%), indicating quantitative inheritance of the trait. GWAS using a mixed linear model (MLM) identified six quantitative trait loci (QTLs) significantly associated with mesocotyl length, primarily distributed on chromosomes 6 and 9. Multi-locus GWAS using the mrMLM model further detected one significant quantitative trait nucleotide (QTN) on chromosome 2 (Affx-122689992), explaining 5.96% of the variation. Candidate gene analysis within ± 100&#xa0;kb of significant SNPs revealed four key genes, <i>KAO</i> (<i>Os06g0110000</i>),<i> D3</i> (<i>Os06g0154200</i>),<i> AMY2A</i> (<i>Os06g0713800</i>), and <i>OsSAUR11</i> (<i>Os02g0643800</i>), functionally associated with phytohormone biosynthesis, signal transduction, and carbohydrate metabolism. The favourable allele ‘AA’ at Affx-122689992 was positively correlated with longer mesocotyl length, and ten donor genotypes carrying this allele were identified as potential sources for breeding programs. The identified loci and candidate genes offer valuable understanding into the molecular regulation of mesocotyl length and provide useful genomic markers that can be used to develop rice cultivars with improved emergence and adaptability under direct-seeded rice conditions.</p>

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Identification of Genetic Loci for Mesocotyl Length in Rice (Oryza sativa L.) using Genome-Wide Association Approach

  • 期刊论文

  • 发表日期：

    2026年5月18日

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  • Debobrata Dey,
  • Sasmita Behera,
  • Soumya Priyadarsinee Mohanty,
  • Debashis Moharana,
  • Lambodar Behera,
  • Anjani Kumar,
  • Rameswar Prasad Sah,
  • Abhishek Kumar Sahu,
  • Reshmi Raj K.R.,
  • Beena R.,
  • Madhav Pandit,
  • Priya Medha,
  • Tapash Dasgupta,
  • Bhubaneswar Pradhan,
  • Bishnu Charan Marndi

摘要

The genetic basis of mesocotyl length and its associated loci is critical for improving seedling emergence and establishment in direct-seeded rice systems. This study investigated the phenotypic variation and genetic architecture of mesocotyl length in a diverse panel of 192 rice genotypes using a genome-wide association study (GWAS) approach. The panel, comprising germplasm accessions, advanced breeding lines, and released varieties, was genotyped using a 44 K SNP array, resulting in 19,613 high-quality polymorphic SNPs after stringent filtering. Phenotypic evaluation revealed continuous variation in mesocotyl length, ranging from 2.48 to 18.98 mm, with high broad-sense heritability (71.2%), indicating quantitative inheritance of the trait. GWAS using a mixed linear model (MLM) identified six quantitative trait loci (QTLs) significantly associated with mesocotyl length, primarily distributed on chromosomes 6 and 9. Multi-locus GWAS using the mrMLM model further detected one significant quantitative trait nucleotide (QTN) on chromosome 2 (Affx-122689992), explaining 5.96% of the variation. Candidate gene analysis within ± 100 kb of significant SNPs revealed four key genes, KAO (Os06g0110000), D3 (Os06g0154200), AMY2A (Os06g0713800), and OsSAUR11 (Os02g0643800), functionally associated with phytohormone biosynthesis, signal transduction, and carbohydrate metabolism. The favourable allele ‘AA’ at Affx-122689992 was positively correlated with longer mesocotyl length, and ten donor genotypes carrying this allele were identified as potential sources for breeding programs. The identified loci and candidate genes offer valuable understanding into the molecular regulation of mesocotyl length and provide useful genomic markers that can be used to develop rice cultivars with improved emergence and adaptability under direct-seeded rice conditions.