Simple SummaryAmong the most important factors in the production of livestock are morphological traits, such as body weight, body length, chest depth, chest width, cannon circumference, and the body index. Platelet-derived growth factor D (PDGFD) is a candidate gene that has the potential to affect fat deposition and body size in sheep. In this study, we discovered two intronic InDels (13 bp deletion, 14 bp insertion) with the potential to significantly affect the morphological traits of three different indigenous Chinese sheep breeds. These InDels can be used as DNA markers for sheep marker-assisted selection (MAS) breeding.AbstractPlatelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations inPDGFDand body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 ofPDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation ofPDGFDwas found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates thatPDGFDInDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.