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.
Highlights
Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes
In order to investigate the effectiveness of the schemes that are currently used to conserve chicken genetic resources in China, we evaluated the genetic diversity of three conserved indigenous chicken breeds
Sampling Three Chinese indigenous chicken breeds that have been enrolled in conservation programs were used in this study: Baier Yellow Chicken (BEC), Beijing You Chicken (BYC), and Langshan Chicken (LSC)
Summary
Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. 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. As one of the earliest centers of domestication for chickens, China has the most abundant chicken genetic resources in the world, with 107 indigenous chicken breeds. As one of the earliest centers of domestication for chickens, China has the most abundant chicken genetic resources in the world, with 107 indigenous chicken breeds These breeds play an essential role in the Chinese poultry. An efficient in situ conservation scheme relies on an effective population size, as well as an effective selection and mating strategy [1]. The mating systems that are in use are: (i) random mating and random selection (R: R), (ii) random mating within families, with one son kept per sire family and one daughter kept per dam family (R: F), and (iii) family rotational mating (F: R) [4]
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