The Genetic Structure and Diversity of Different Pigeon Breeds Based on a 5 K Single Nucleotide Polymorphism Chip

China has the largest population of pigeons globally, particularly for commercial meat production. Due to insufficient emphasis on bloodline preservation, there is a significant occurrence of breed hybridization, which presents challenges to the differentiation and identification of various pigeon breeds. In this study, a single-nucleotide polymorphism chip was developed to elucidate genomic relationships and genetic diversity among 10 pigeon breeds, encompassing meat, racing, and ornamental varieties. Principal component analysis revealed that this resource population could be classified into three major clusters: homing and Tarim pigeons; the Dianzi (DZ) and Xinjiang Roller (XR) varieties; and commercial meat pigeon breeds, including the Euro-pigeon (EP), Danish King (DK), Silver King (SK), Yellow Carneau (YC), Red Carneau (RC), and Taishen (TS) varieties. Phylogenetic tree analysis indicated that the HP, TR, DZ, and XR varieties clustered into a large group. Of these, the HP and TR groups and the DZ and XR group were closely genetically related. Other meat pigeon varieties clustered into a large group. The genetic relationship between the YC and RC pigeons was intertwined, suggesting that although there were differences in feather color, the genetic backgrounds are similar. The phylogenetic tree results also demonstrated that the DK and SK pigeons had a considerable genetic distance, indicating that although the feather color was similar, the birds belong to two distinct genetic groups. The Pigeon 5 K liquid chip can effectively discriminate among different pigeon populations and provides a method for the identification and evaluation of pigeon germplasm resources, especially for pure breed identification and exploration of new resources.