Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

Abstract

BackgroundMaintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs.ResultsNinety DNA samples were collected from three generations for each breed. In the most recent generation, the highest genetic diversity was observed in LSC, followed by BEC and BYC. Inbreeding coefficients based on ROH for the three breeds declined slightly between the first and middle generations, and then rapidly increased. No inbreeding coefficients exceeded 0.1. Population structure assessments using neighbor-joining tree analysis, principal components analysis, and STRUCTURE analysis indicated that no genetic differentiation existed within breeds. LD decay and ROH at different cut-off lengths were used to identify traces left by recent or ancient inbreeding. Few long ROH were identified, indicating that inbreeding has been largely avoided with the current conservation strategy. The observed losses in genetic diversity and occurrences of inbreeding might be consequences of sub-optimal effective population sizes.ConclusionsThe conserved Chinese chicken populations have high genomic diversity under the current conservation program (R: F). Furthermore, this study highlights the need to monitor dynamic changes in genetic diversity in conserved breeds over successive generations. Our research provides new insights into genetic diversity dynamics in conserved populations, and lays a solid foundation for improving conservation schemes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4973-6) contains supplementary material, which is available to authorized users.

Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

“…Our results indicated that those breeds have higher genetic diversity (heterozygosity and nucleotide diversity) than exotic commercial breeds, which is in agreement with previous studies ( Chen et al, 2018 ; Nie et al, 2019 ). For local breeds, observed heterozygosity (Ho) was either equal to or higher than expected heterozygosity (He), indicating that diversity protection has improved in recent years, as previously reported ( Zhang M. et al, 2018 ). Game chickens are mostly used in competitive games, and crossbreeding is quite extensive among them, which has resulted in heterosis and greater genetic diversity ( Liu and Zhao, 2010 ).…”

“…Molecular tools provide geneticists an opportunity to estimate the genetic structure of different populations, using strategies such as genome-wide analyses, which have already been applied in many domestic animals ( Johnsson et al, 2016 ; Zhang M. et al, 2018 ; Zhang Z. et al, 2018 ; Malomane et al, 2019 ). The popularity of single nucleotide polymorphism (SNP) analysis, such as microarrays and genomic sequencing, allows comprehensive evaluation of the population genetics of chickens ( Khanyile et al, 2015 ; Nie et al, 2019 ).…”

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

“…However, the Chinese indigenous breeds also presented unequal polymorphisms among themselves. Three Chinese indigenous breeds, namely, SG, SK, and BY, exhibited relatively lower P N and higher r 2 than those of HS and TB, which might be related to the low-priority conservation status of the HS breed (Zhang et al. 2018).…”

“…2018), random-amplified polymorphic DNA (Lynch and Milligan 1994), amplified fragment length polymorphisms (Christian 2004), and genome-wide single-nucleotide polymorphisms (SNPs) (Chen et al. 2018; Zhang et al. 2018).…”

“…Simultaneously, Chinese Government has made considerable efforts for conserving several indigenous chicken breeds (Chen et al. 2008; Zhang et al. 2018).…”