Meta‑analysis unravels genomic regions and candidate genes underlying fiber length and strength in upland cotton

Cotton fiber length (FL) and strength (FS) are critical determinants of yarn quality and overall textile performance. Although numerous quantitative trait loci (QTLs) associated with these traits have been reported, their practical application in breeding programs is often constrained by broad confidence intervals, limited mapping resolution, and poor reproducibility across studies. In this study, we performed a genome-wide meta-QTL (MQTL) analysis by integrating 677 previously reported QTLs into a high‑density consensus map. This approach pinpointed 49 stable MQTLs with confidence intervals reduced by an average of 2.9‑fold. Among the 49 MQTLs, 28 were supported by colocalization with independent GWAS signals (designated as high-confidence MQTLs), while the remaining 21 lacked GWAS support (putative MQTLs). The high-confidence MQTLs provide robust targets for further investigation. Transcriptomic analysis linked several candidate genes within MQTL regions to key biological processes, including cell wall composition. Notably, we identified a receptor-like kinase gene, LECRK3 , in which a missense mutation exerts pleiotropic effects on both FL and FS. Collectively, these findings refine the genetic architecture underlying cotton fiber quality. A functional KASP marker was developed and validated for the pleiotropic candidate gene LECRK3, providing an immediately applicable tool for marker-assisted breeding aimed at improving both fiber length and strength. • Conducted a genome-wide meta-QTL analysis for fiber length and strength in upland cotton by integrating 677 reported QTLs into a high-density consensus genetic map comprising 20,954 markers. • Identified 49 stable MQTLs, achieving an average 2.9‑fold reduction in confidence intervals, which substantially improves mapping precision. • Discovered and functionally validated LECRK3 as a key pleiotropic gene, in which a missense mutation exerts significant effects on both fiber length and strength, offering a precise target for molecular breeding.