Short variation of the sheep PDGFD gene is correlated with litter size

•A 18 bp deletion in PDGFD gene was detected in Australian white sheep and associated with litter size trait.•The PDGFD gene showed the highest expression level in reproductive system according to Ruminant Genome Database.•The PDGFD may not only affect fat deposition in the tail of sheep but also affect litter size.•This indel could be a potential DNA marker for MAS method to improve reproductive performance in Australian white sheep.