Evaluation of the genetic diversity and population structure of 5 pheasant breeds in Shanghai

Abstract

The genetics of pheasant breeds in Chinese farms has not been investigated yet. Understanding their genetic diversity and population structure is important for future advancements in pheasant breeding. In this study, the whole-genome resequencing was used to analyze a total of 352 samples from 5 pheasant species (American pheasant, White pheasant, Green pheasant, Shenhong pheasant, and Fengxian blue pheasant). The average effective population size (Ne) was 45.82. The average of expected heterozygosity (He) and observed heterozygosity (Ho) was 0.28514 and 0.27938, respectively. The Green pheasant had the lowest values of He (0.2730) and Ho (0.2692), whereas Fengxian blue pheasant had the highest values of He (0.2885) and Ho (0.2937), respectively. In addition, the 5 pheasant breeds could be divided into four different genetic populations. A similar genetic structure was also observed between American pheasant and Shenhong pheasant, whereas the other three pheasant breeds (White pheasant, Green pheasant, and Fengxian blue pheasant) exhibited obviously different genetic structures. Further analysis of population structure showed that some individuals among all 5 pheasant breeds had a high genetic distance and weak genetic relationships. A certain degree of inbreeding might exist in the population of White pheasant. Thus, effective breeding and conservation plans should be conducted to retain the genetic distinctiveness for White pheasant. Our data is of great significance for promoting the conservation and development of pheasant genetic resources.

Keywords: Genetic diversity; Pheasant; Population structure; Whole-genome re-sequencing.

Fig. 1

A: male American pheasant, B: female American pheasant, C: male White pheasant, D: female White pheasant, E: male Green pheasant, F: female Green pheasant, G: male Shenhong pheasant, H: female Shenhong pheasant, I: male Fengxian blue pheasant, J: female Fengxian blue pheasant.

Fig. 2

Linkage disequilibrium of 5 pheasant breeds. A, American pheasant; B, White pheasant; C, Green pheasant; D, Shenhong pheasant; E, Fengxian blue pheasant; LD, linkage disequilibrium.

Fig. 3

Phylogenetic relationships and population structure of 5 pheasant breeds. (A) Neighbor-joining (NJ) phylogenetic tree reconstructed from SNP data among 5 pheasant breeds. (B) Plot of principal component analysis (PCA). (C) The cross-validation (CV) error rate. (D) Plot of Admixture analysis with assumed ancestral number (K = 2–6). Each column indicates an individual, and the same color represents the same ancestral cluster. A, American pheasant; B, White pheasant; C, Green pheasant; D, Shenhong pheasant; E, Fengxian blue pheasant.

Fig. 4

Identity by state (IBS) distance matrix of 5 pheasant breeds. The color of each small square exhibits the genetic distance value between sampled individuals. A, American pheasant; B, White pheasant; C, Green pheasant; D, Shenhong pheasant; E, Fengxian blue pheasant.

Fig. 5

The G matrix of 5 pheasant breeds. The color of each small square exhibits the kinship value between sampled individuals. A, American pheasant; B, White pheasant; C, Green pheasant; D, Shenhong pheasant; E, Fengxian blue pheasant.