Population genomics identifies patterns of genetic diversity and selection in chicken
Abstract Background There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. Resul...
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5622-4 |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Diyan Li Yan Li Miao Li Tiandong Che Shilin Tian Binlong Chen Xuming Zhou Guolong Zhang Uma Gaur Majing Luo Kai Tian Mengnan He Shen He Zhongxian Xu Long Jin Qianzi Tang Yifei Dai Huailiang Xu Yaodong Hu Xiaoling Zhao Huadong Yin Yan Wang Rongjia Zhou Chaowu Yang Huarui Du Xiaosong Jiang Qing Zhu Mingzhou Li |
| spellingShingle |
Diyan Li Yan Li Miao Li Tiandong Che Shilin Tian Binlong Chen Xuming Zhou Guolong Zhang Uma Gaur Majing Luo Kai Tian Mengnan He Shen He Zhongxian Xu Long Jin Qianzi Tang Yifei Dai Huailiang Xu Yaodong Hu Xiaoling Zhao Huadong Yin Yan Wang Rongjia Zhou Chaowu Yang Huarui Du Xiaosong Jiang Qing Zhu Mingzhou Li Population genomics identifies patterns of genetic diversity and selection in chicken BMC Genomics Population genomics Genetic diversity Selection Chicken |
| author_facet |
Diyan Li Yan Li Miao Li Tiandong Che Shilin Tian Binlong Chen Xuming Zhou Guolong Zhang Uma Gaur Majing Luo Kai Tian Mengnan He Shen He Zhongxian Xu Long Jin Qianzi Tang Yifei Dai Huailiang Xu Yaodong Hu Xiaoling Zhao Huadong Yin Yan Wang Rongjia Zhou Chaowu Yang Huarui Du Xiaosong Jiang Qing Zhu Mingzhou Li |
| author_sort |
Diyan Li |
| title |
Population genomics identifies patterns of genetic diversity and selection in chicken |
| title_short |
Population genomics identifies patterns of genetic diversity and selection in chicken |
| title_full |
Population genomics identifies patterns of genetic diversity and selection in chicken |
| title_fullStr |
Population genomics identifies patterns of genetic diversity and selection in chicken |
| title_full_unstemmed |
Population genomics identifies patterns of genetic diversity and selection in chicken |
| title_sort |
population genomics identifies patterns of genetic diversity and selection in chicken |
| publisher |
BMC |
| series |
BMC Genomics |
| issn |
1471-2164 |
| publishDate |
2019-04-01 |
| description |
Abstract Background There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. Results Here, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources. Conclusions The work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic traits. |
| topic |
Population genomics Genetic diversity Selection Chicken |
| url |
http://link.springer.com/article/10.1186/s12864-019-5622-4 |
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doaj-1b28a4d67eb14699931ce61747e795aa2020-11-25T02:59:33ZengBMCBMC Genomics1471-21642019-04-0120111210.1186/s12864-019-5622-4Population genomics identifies patterns of genetic diversity and selection in chickenDiyan Li0Yan Li1Miao Li2Tiandong Che3Shilin Tian4Binlong Chen5Xuming Zhou6Guolong Zhang7Uma Gaur8Majing Luo9Kai Tian10Mengnan He11Shen He12Zhongxian Xu13Long Jin14Qianzi Tang15Yifei Dai16Huailiang Xu17Yaodong Hu18Xiaoling Zhao19Huadong Yin20Yan Wang21Rongjia Zhou22Chaowu Yang23Huarui Du24Xiaosong Jiang25Qing Zhu26Mingzhou Li27Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolDepartment of Animal Science, Oklahoma State UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityHubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityNovogene Bioinformatics InstituteInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityHubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan UniversitySichuan Animal Science AcademySichuan Animal Science AcademySichuan Animal Science AcademyInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityAbstract Background There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. Results Here, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources. Conclusions The work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic traits.http://link.springer.com/article/10.1186/s12864-019-5622-4Population genomicsGenetic diversitySelectionChicken |