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. HIGHLIGHTThis study on the SM93 rice line identifies a major QTL for early heading and describes genes and SNP markers that are closely linked to this trait, which can be used in trait advancement. By fine-tuning heading date, we can help rice varieties better withstand temperature extremes, drought, and other climate-related stresses, making it a key target for genetic improvement and breeding strategies.