Genetic linkage analysis of stable QTLs in Gossypium hirsutum RIL population revealed function of GhCesA4 in fiber development

•Genome-wide mining of QTLs of fiber yield and fiber quality traits were beneficial to better understanding their genome level distributions.•A total of 64 stable QTLs of fiber yield and 75 stable QTLs of fiber quality were identified, which formed 33 clusters, indicating that the correlations between fiber yield and quality traits have complex genetic components.•These QTLs formed expression network, via their candidate genes, to orchestrate fiber development and the formation fiber yield and quality.•The candidate gene, GH_D07G2262, an upland cotton cellulose synthase 4 (GhCesA 4) gene had pleiotropic functions during cotton fiber development, which positively regulates fiber length and strength, and negatively lint percentage.