Multi-model genome-wide association studies identify stable QTLs and candidate genes for lodging resistance in indica rice

Lodging significantly limits rice yield and grain quality. Despite the identification of numerous QTLs and genes associated with lodging-related traits, the genetic framework for lodging resistance remains largely unclear. In this study, we evaluated 17 lodging-related traits over three consecutive years using a global collection of 370 indica rice accessions. From correlation analysis, eight representative traits, including plant height (PH), breaking resistance (BR), fresh weight (FW), stem length (SL), section modulus (SM), bending stress (BS), lodging index (LI), and the optimized parameter △BM, were selected for a genome-wide association study (GWAS). This study utilized 2,315,020 high-quality SNPs analyzed through the MLM, FarmCPU, and BLINK models. These models identified 10, 24, and 16 significant QTLs, respectively, with two stable QTLs, qBS3 and q△BM9 , consistently detected across all models. Haplotype analysis and expression profiling narrowed the candidate genes within the qBS3 and q△BM9 intervals down to seven, highlighting LOC_Os03g49610 (encoding beta-glucosidase 8) and LOC_Os09g28110 (encoding a hydroxyproline-rich glycoprotein) as promising candidate genes that warrant further functional validation for their roles in culm mechanical properties. Collectively, our results provide a valuable set of QTLs and candidate genes for marker-assisted breeding and offer mechanistic insights into the genetic basis of lodging resistance in indica rice, with the caveat that the two stable QTLs lie in close proximity to previously characterized loci and require fine-mapping to establish their independence.