Dynamic QTL mapping reveals the genetic architecture of stem diameter across developmental stages in foxtail millet

Dynamic QTL analysis identified the key QTL qSD-9-1 and candidate genes SiGPI8, SiCesA5 and SiNPC1 associated with the developmental stages of foxtail millet stem diameter. Abstact. Stem diameter (SD) is a critical agronomic trait influencing lodging and yield in foxtail millet, yet its potential in selective breeding remains under-explored. Additionally, limited research has examined the dynamics of SD across various developmental stages. To address this gap, this study utilized two RIL populations (F₈), RYRIL and JYRIL, comprising 215 and 224 lines, respectively. Dynamic QTL analysis of SD traits was conducted in two distinct environments, encompassing five developmental stages, to comprehensively investigate the genetic architecture of SD. Results revealed that the h_B² values for SD ranged from 60.19% to 82.51%, peaking during the maturity stage in both populations. A total of 26 unconditional and 16 conditional QTLs were identified, explaining 1.09-17.99% and 3.10-16.55% of the phenotypic variations, respectively. Notably, qSD-9-1 was consistently detected in both unconditional and conditional QTL mappings across the two populations, accounting for 1.66-17.99% of phenotypic variation. Phenotype-genotype association analysis within the bin marker interval of qSD-9-1 revealed significant differences in SD among RIL lines carrying parental genotypes. Furthermore, by predicting candidate genes within the physical interval of qSD-9-1 and integrating phenotype-haplotype association analysis, SiGPI8, SiCesA5 and SiNPC1 were identified as key candidate genes potentially regulating SD. This study advances our understanding of the genetic basis of SD in foxtail millet and provides a theoretical foundation for marker-assisted selection (MAS) in breeding lodging-resistant varieties.