Navigating rice culm resilience: High-throughput quantitative trait locus mapping in indica and tropical japonica derived population

Lodging resistance (LR) in rice is a complex trait determined by a plant's culm strength to withstand bending or breaking force, especially under high input and direct seeded rice (DSR) conditions. Although, the sd1 gene provided early gains in LR, it has now become insufficient in modern cultivars with increased biomass and plant height. Deeper understanding of the intricate morphological and anatomical attributes, mathematical relationships and physical principles governing culm structural strength offer promise for enhancing LR. To unravel the genetic and structural basis of LR, we comprehensively phenotyped 353 recombinant inbred lines (RILs) derived from an inter-subspecific cross between Swarna (indica) and IRGC 39111 (tropical japonica), over multiple seasons for 12 culm strength (CS) and seven grain yield (GY) traits. Breaking resistance (BR) as a measure of internode breaking weight (IBW) and section modulus (SM) emerged as primary contributors to LR. Extensive phenotypic evaluations revealed wide variation and high heritability for most CS traits, as reflected in best linear unbiased prediction (BLUP) estimates. Conversely, traits like tiller number exhibited low heritability as evidenced by the marked difference between their genotypic and phenotypic coefficients of variation indicating a strong environmental influence traits. Significant phenotypic correlations between CS and GY traits were observed. Histological analysis of the culm revealed that strong culm RILs possessed compact, thickened sclerenchymatous tissue and larger secondary vascular bundles compared to Swarna. NGS based GBS generated 63,367 SNP markers, and a high-density genetic map comprising 11,098 binned SNPs revealed 36 QTLs, including 15 major effect loci. Two consistent and major-effect QTLs-qCT7 (R²-14.49 %; 109 kb) and qIBW7 (R²-16.57 %; 33.83 kb) -on chromosome 7 were identified as key regions for LR. In-silico analysis of qCT7 revealed putative candidate genes including BRITTLE CULM1 like (OsBC1L 6, 7, 8), Cellulose synthase genes (OsCesA 3, 6, 8) and OsCSLF 1, 2, 9 involved in key processes underpinning cell wall thickening. The identification of qCT7 and its future cloning hold potential to enhance lodging resistance in rice, particularly under DSR conditions, contributing to the development of climate-resilient, high-yielding cultivars beyond the Green Revolution paradigm.