Integrated QTL, Candidate-Gene and Transcriptomic Analysis Reveals Molecular Networks Underlying Pre-Harvest Sprouting Resistance in Rice (Oryza sativa L.)

Pre-harvest sprouting (PHS) is a quantitative trait influenced by seed dormancy, hormone metabolism and germination-associated pathways. Ten rice genotypes contrasting for PHS response were evaluated during Kharif 2025, and resistant and susceptible groups were characterized using physiological, biochemical and molecular approaches. Five major QTLs were detected on chromosomes 1, 3, 6, 7 and 11, with qPHS7 showing the largest phenotypic effect (LOD 9.84; PVE 32.6%). SDR4, OsNCED5, ABI3 and ABI5 showed higher expression in resistant material, whereas GA20ox2, GA3ox and α-amylase were higher in susceptible material. Resistant alleles of SDR4, OsNCED5, ABI3 and ABI5 were significantly enriched in resistant genotypes. RNA-seq identified 943 differentially expressed genes, supporting enhanced ABA-associated dormancy and reduced GA- and carbohydrate-associated germination in resistant material. The integrated results identify candidate molecular components for further validation and breeding use. Keywords: rice; pre-harvest sprouting; seed dormancy; QTL; SDR4; ABA; gibberellin; RNA-seq; candidate genes. Title: Integrated QTL, Candidate-Gene and Transcriptomic Analysis Reveals Molecular Networks Underlying Pre-Harvest Sprouting Resistance in Rice (Oryza sativa L.) Author: Siddhartha Biswas, Dr. Nitin B. Mehetre International Journal of Life Sciences Research ISSN 2348-313X (Print), ISSN 2348-3148 (online) Vol. 14, Issue 4, October 2026 - December 2026 Page No: 34-42 Research Publish Journals Website: www.researchpublish.com Published Date: 13-October-2026 DOI: https://doi.org/10.5281/zenodo.23340112 Paper Download Link (Source) https://www.researchpublish.com/papers/integrated-qtl-candidate-gene-and-transcriptomic-analysis-reveals-molecular-networks-underlying-pre-harvest-sprouting-resistance-in-rice-oryza-sativa-l