A Pd1–Ps–P1 Feedback Loop Controls Pubescence Density in Soybean

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 resistance, 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 identified. 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 transcriptional activity of Pd1. Taken together, our results demonstrate that Pd1, Ps, and P1 form a complex feedback loop to regulate pubescence formation in soybean.