Trichomes are universally present in plants and their development is delicately regulated.Trichomes are responsible for pubescence,whose density is associated with some agronomic traits such as insect resis-tance,evapotranspiration,and yield.Almost a century ago,three dominant alleles related to pubescence density in soybean,namely Pd1(dense pubescence),Ps(sparse pubescence),and P1(glabrous),were iden-tified.However,their molecular identity and genetic relationships remain unclear.In this study,through a genome-wide association study and map-based cloning,we determined the genetic basis of these three traits.The sparse-pubescence phenotype of Ps was attributed to a copy-number variation of a 25.6-kb sequence that includes a gene encoding a protein with WD40 and RING domains.The dense-pubescence phenotype of Pd1 was attributed to a T-C transition in the last exon of an HD-Zip transcription factor gene,and the glabrous phenotype of P1 was caused by a G-A transition in the first exon of a lipid transfer protein gene.Genetic and biochemical analyses revealed that Pd1 functions as a transcriptional activator that can bind the promoters of the P1 and Ps genes to induce their expression;Interestingly,Pd1 can also bind its own promoter and inhibit its gene transcription.In addition,Ps can interact with Pd1 and weaken the tran-scriptional activity of Pd1.Taken together,our results demonstrate that Pd1,Ps,and P1 form a complex feedback loop to regulate pubescence formation in soybean.