Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks
ABSTRACT: Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome reseq...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-07-01
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| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579123002675 |
| _version_ | 1797802254517927936 |
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| author | Lanlan Li Jinqiang Quan Caixia Gao Hongyi Liu Haibo Yu Hongyan Chen Changyou Xia Shengguo Zhao |
| author_facet | Lanlan Li Jinqiang Quan Caixia Gao Hongyi Liu Haibo Yu Hongyan Chen Changyou Xia Shengguo Zhao |
| author_sort | Lanlan Li |
| collection | DOAJ |
| description | ABSTRACT: Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources. |
| first_indexed | 2024-03-13T05:03:58Z |
| format | Article |
| id | doaj.art-9da7e8b6b6f0494ba67ad53dcf91515b |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-03-13T05:03:58Z |
| publishDate | 2023-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-9da7e8b6b6f0494ba67ad53dcf91515b2023-06-17T05:17:25ZengElsevierPoultry Science0032-57912023-07-011027102748Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducksLanlan Li0Jinqiang Quan1Caixia Gao2Hongyi Liu3Haibo Yu4Hongyan Chen5Changyou Xia6Shengguo Zhao7State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China; College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR ChinaCollege of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR ChinaState Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China; Corresponding author:State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR ChinaState Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR ChinaState Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR ChinaState Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR ChinaCollege of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR ChinaABSTRACT: Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources.http://www.sciencedirect.com/science/article/pii/S0032579123002675laboratory duckswhole-genome resequencinggenetic characteristicsselection signaturesingle nucleotide polymorphisms |
| spellingShingle | Lanlan Li Jinqiang Quan Caixia Gao Hongyi Liu Haibo Yu Hongyan Chen Changyou Xia Shengguo Zhao Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks Poultry Science laboratory ducks whole-genome resequencing genetic characteristics selection signature single nucleotide polymorphisms |
| title | Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks |
| title_full | Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks |
| title_fullStr | Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks |
| title_full_unstemmed | Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks |
| title_short | Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks |
| title_sort | whole genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen free ducks |
| topic | laboratory ducks whole-genome resequencing genetic characteristics selection signature single nucleotide polymorphisms |
| url | http://www.sciencedirect.com/science/article/pii/S0032579123002675 |
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