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<p>Rice blast, caused by <i>Magnaporthe oryzae</i>, severely threatens global rice production. Molecular markers like SSRs offer rapid method for indirect selection of blast-resistant genotypes, yet their robustness across genetic backgrounds requires validation. This study evaluated 30 SSR markers associated with meta-QTLs (MQTLs) from prior meta-analyses to identify reliable markers for blast resistance QTLs. Markers were prioritized based on phenotypic variation explained (R²), density of constituent QTLs, and gene content within MQTL regions. Primers proximal to MQTL peaks were tested on 24 recombinant inbred lines (F11, 12 resistant, 12 susceptible), selected from a 153-individual RIL population, derived from parents IR28 (resistant) and Shahpasand (susceptible). Analysis of the 30 primers revealed that 11 primers were polymorphic between IR28 and Shahpasand and were selected for further investigation. The validation results indicated that primers RM5432 and RM547 (linked to MQTL8.1 and MQTL8.4 respectively) had the highest accuracy (100% and 96%, respectively; <i>P</i> &lt; 0.001, <InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(\phi\)</EquationSource> </InlineEquation> ≥ 0.92), supporting their potential for population-specific marker-assisted selection (MAS). In silico analysis of MQTL8.1 and MQTL8.4 revealed 64 and 88 genes, respectively. Expression profiling identified 15 candidate genes, most upregulated post-<i>Magnaporthe oryzae</i> infection. Key candidates included <i>TPS46</i> and <i>OsTPS31</i> which are involved in biotic stress responses, while the <i>GLP</i> gene cluster within MQTL8.4 may contribute to stress responses. Gene ontology (GO) analysis highlighted significant enrichment in terpenoid biosynthesis, fatty acid metabolism, and brassinosteroid-mediated signaling pathways, indicating potential roles of these genes in biotic stress responses.</p>

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Validation of SSR markers linked to identified meta-QTLs associated with blast disease resistance in rice with bioinformatic candidate gene evaluation

  • 期刊论文

  • 发表日期：

    2026年4月11日

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  • Reza Jalalifar,
  • Atefeh Sabouri,
  • Sedigheh Mousanejad,
  • Ahmad Reza Dadras

摘要

Rice blast, caused by Magnaporthe oryzae, severely threatens global rice production. Molecular markers like SSRs offer rapid method for indirect selection of blast-resistant genotypes, yet their robustness across genetic backgrounds requires validation. This study evaluated 30 SSR markers associated with meta-QTLs (MQTLs) from prior meta-analyses to identify reliable markers for blast resistance QTLs. Markers were prioritized based on phenotypic variation explained (R²), density of constituent QTLs, and gene content within MQTL regions. Primers proximal to MQTL peaks were tested on 24 recombinant inbred lines (F11, 12 resistant, 12 susceptible), selected from a 153-individual RIL population, derived from parents IR28 (resistant) and Shahpasand (susceptible). Analysis of the 30 primers revealed that 11 primers were polymorphic between IR28 and Shahpasand and were selected for further investigation. The validation results indicated that primers RM5432 and RM547 (linked to MQTL8.1 and MQTL8.4 respectively) had the highest accuracy (100% and 96%, respectively; P < 0.001, \(\phi\) ≥ 0.92), supporting their potential for population-specific marker-assisted selection (MAS). In silico analysis of MQTL8.1 and MQTL8.4 revealed 64 and 88 genes, respectively. Expression profiling identified 15 candidate genes, most upregulated post-Magnaporthe oryzae infection. Key candidates included TPS46 and OsTPS31 which are involved in biotic stress responses, while the GLP gene cluster within MQTL8.4 may contribute to stress responses. Gene ontology (GO) analysis highlighted significant enrichment in terpenoid biosynthesis, fatty acid metabolism, and brassinosteroid-mediated signaling pathways, indicating potential roles of these genes in biotic stress responses.