Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs
Abstract Background Maintaining 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 con...
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| Format: | Article |
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BMC
2018-08-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4973-6 |
| _version_ | 1818957264728358912 |
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| author | Mengmeng Zhang Wei Han Hui Tang Guohui Li Minjie Zhang Ran Xu Yijun Liu Tao Yang Wenting Li Jianmin Zou Keliang Wu |
| author_facet | Mengmeng Zhang Wei Han Hui Tang Guohui Li Minjie Zhang Ran Xu Yijun Liu Tao Yang Wenting Li Jianmin Zou Keliang Wu |
| author_sort | Mengmeng Zhang |
| collection | DOAJ |
| description | Abstract Background Maintaining 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. Results Ninety 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. Conclusions The 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. |
| first_indexed | 2024-12-20T11:07:05Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T11:07:05Z |
| publishDate | 2018-08-01 |
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| series | BMC Genomics |
| spelling | doaj.art-26f58acef8ba4ebfa832b1128423bdfe2022-12-21T19:42:51ZengBMCBMC Genomics1471-21642018-08-0119111210.1186/s12864-018-4973-6Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPsMengmeng Zhang0Wei Han1Hui Tang2Guohui Li3Minjie Zhang4Ran Xu5Yijun Liu6Tao Yang7Wenting Li8Jianmin Zou9Keliang Wu10Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityNational Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural ScienceCollege of Animal Science and Technology, Shandong Agricultural UniversityNational Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural ScienceDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityNational Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural ScienceDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityAbstract Background Maintaining 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. Results Ninety 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. Conclusions The 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.http://link.springer.com/article/10.1186/s12864-018-4973-6Chinese indigenous chickenGenomic diversityConservation schemeGenome-wide SNPs |
| spellingShingle | Mengmeng Zhang Wei Han Hui Tang Guohui Li Minjie Zhang Ran Xu Yijun Liu Tao Yang Wenting Li Jianmin Zou Keliang Wu Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs BMC Genomics Chinese indigenous chicken Genomic diversity Conservation scheme Genome-wide SNPs |
| title | Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs |
| title_full | Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs |
| title_fullStr | Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs |
| title_full_unstemmed | Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs |
| title_short | Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs |
| title_sort | genomic diversity dynamics in conserved chicken populations are revealed by genome wide snps |
| topic | Chinese indigenous chicken Genomic diversity Conservation scheme Genome-wide SNPs |
| url | http://link.springer.com/article/10.1186/s12864-018-4973-6 |
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