Omics-driven Identification of Candidate Genes and SNP markers in a Major QTL Controlling Early Heading in Rice

Precise control of heading date is essential for optimizing regional adaptability, enhancing climate resilience, and maximizing grain yield in rice, making it a key breeding target. The SM93 rice line exhibits a 7-10-day earlier heading than the elite Indian variety, Samba Mahsuri (SM). F2 populations derived from a cross of SM with SM93 were phenotyped for heading date across three successive kharif (rainy) seasons (2019-2021), revealing consistent early heading and notable transgressive segregation. Initial QTL-seq analysis identified a high-confidence QTL on Chr3, qDTH3 , strongly associated with days to heading (DTH). KASP assays and association mapping were subsequently performed to refine the QTL, narrowing it down to a 2.53 Mb region, explaining ∼25% of the trait. SNP markers closely linked to heading were identified. Transcriptomic analysis revealed significant differential regulation of genes within qDTH3 and upregulation of the MADS- box network in SM93 during panicle initiation, suggesting their role in promoting early heading. Our integrative strategy led to the identification of candidate genes within qDTH3 , associated with heading date, phytohormone regulation, and protein turnover, include the transcription factors, OsMADS34/PAP2 ( Os03g0753100 ), OsZHD11 ( Os03g0718500 ), HSFA2A ( Os03g0745000 ), OsH3 ( Os03g0727200 ), OSH1/Oskn1 ( Os03g0727000 ), a histidine kinase, HK4 ( Os03g0717700 ), and a Serine carboxypeptidase, OsSCP19 ( Os03g0730400 ). Our findings provide SNP markers in and around these genes, as potentially valuable tools for breeding early-maturing rice varieties with improved adaptability.