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

## TL;DR

A SNP chip was developed to study genetic diversity and relationships among 10 pigeon breeds, revealing three main genetic groups and aiding in breed identification.

## Contribution

A 5 K SNP chip was developed and applied to classify pigeon breeds into genetic clusters, offering a new tool for breed differentiation and resource evaluation.

## Key findings

- Pigeon breeds clustered into three genetic groups: homing/Tarim, Dianzi/Xinjiang Roller, and commercial meat breeds.
- Yellow and Red Carneau pigeons showed similar genetic backgrounds despite differing feather colors.
- Danish King and Silver King pigeons were genetically distinct despite similar plumage.

## Abstract

This study developed a single-nucleotide polymorphism chip to analyze genomic relationships and genetic diversity among 10 pigeon breeds (meat, racing, fancy). Principal component analysis clustered them into three groups: homing and Tarim pigeons; Dianzi and Xinjiang Roller varieties; and commercial meat breeds (Euro-pigeon, Danish King, Silver King, etc.). Phylogenetic trees showed close ties between homing/Tarim and Dianzi/Xinjiang Roller, while Yellow and Red Carneau had similar genetic backgrounds despite feather color differences. Danish King and Silver King, though similar in plumage, were genetically distinct. The chip effectively differentiates pigeon populations, aiding germplasm resource identification, especially pure breed verification and new resource exploration.

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.