A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken
Lueyang black-bone chicken is a domestic breed in China. The genetic mechanism of the formation of important economic traits of this breed has not been studied systematically. Therefore, in this study, whole genome resequencing was used to systematically analyze and evaluate the genetic diversity of...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-07-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579123002432 |
| _version_ | 1797802246114639872 |
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| author | Zhen Xue Ling Wang Yingmin Tian Yufei Yang Pan Li Ge Yang Hongzhao Lu Shanshan Wang Wenxian Zeng Tao Zhang |
| author_facet | Zhen Xue Ling Wang Yingmin Tian Yufei Yang Pan Li Ge Yang Hongzhao Lu Shanshan Wang Wenxian Zeng Tao Zhang |
| author_sort | Zhen Xue |
| collection | DOAJ |
| description | Lueyang black-bone chicken is a domestic breed in China. The genetic mechanism of the formation of important economic traits of this breed has not been studied systematically. Therefore, in this study, whole genome resequencing was used to systematically analyze and evaluate the genetic diversity of the black-feather and white-feather populations, and to screen and identify key genes related to phenotypes. The results of principal component analysis and population structure analysis showed that Lueyang black-feathered chickens and white-feathered chickens could be divided into 2 subgroups, and the genetic diversity of black-feathered chicken was richer than that of white-feathered chickens. Linkage disequilibrium analysis also showed that the selection intensity of black-feathered chickens was lower than for white-feathered chickens, which was mainly due to the small population size of white-feathered chickens and a certain degree of inbreeding. Fixation index (FST) analysis revealed that the candidate genes related to feather color traits were G-gamma, FA, FERM, Kelch, TGFb, Arf, FERM, and melanin synthesis-related gene tyrosinase (TYR). Based on Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Jak-STAT, mTOR, and TGF-β signaling pathways were mainly related to melanogenesis and plume color. The findings of this study supported important information for the evaluation and protection of chicken genetic resources and help to analyze the unique genetic phenotypes such as melanin deposition and feather color of Lueyang black-bone chicken. Additionally, it could provide basic research data for the improvement and breeding of Lueyang black-bone chicken with characteristic traits. |
| first_indexed | 2024-03-13T05:03:52Z |
| format | Article |
| id | doaj.art-7fba1a5c93174b3f9c63b2cd9f01f142 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-03-13T05:03:52Z |
| publishDate | 2023-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-7fba1a5c93174b3f9c63b2cd9f01f1422023-06-17T05:17:21ZengElsevierPoultry Science0032-57912023-07-011027102721A genome-wide scan to identify signatures of selection in Lueyang black -bone chickenZhen Xue0Ling Wang1Yingmin Tian2Yufei Yang3Pan Li4Ge Yang5Hongzhao Lu6Shanshan Wang7Wenxian Zeng8Tao Zhang9School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, ChinaSchool of Mathematics and Computer Science, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, Shaanxi, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, Shaanxi, China; Corresponding author:Lueyang black-bone chicken is a domestic breed in China. The genetic mechanism of the formation of important economic traits of this breed has not been studied systematically. Therefore, in this study, whole genome resequencing was used to systematically analyze and evaluate the genetic diversity of the black-feather and white-feather populations, and to screen and identify key genes related to phenotypes. The results of principal component analysis and population structure analysis showed that Lueyang black-feathered chickens and white-feathered chickens could be divided into 2 subgroups, and the genetic diversity of black-feathered chicken was richer than that of white-feathered chickens. Linkage disequilibrium analysis also showed that the selection intensity of black-feathered chickens was lower than for white-feathered chickens, which was mainly due to the small population size of white-feathered chickens and a certain degree of inbreeding. Fixation index (FST) analysis revealed that the candidate genes related to feather color traits were G-gamma, FA, FERM, Kelch, TGFb, Arf, FERM, and melanin synthesis-related gene tyrosinase (TYR). Based on Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Jak-STAT, mTOR, and TGF-β signaling pathways were mainly related to melanogenesis and plume color. The findings of this study supported important information for the evaluation and protection of chicken genetic resources and help to analyze the unique genetic phenotypes such as melanin deposition and feather color of Lueyang black-bone chicken. Additionally, it could provide basic research data for the improvement and breeding of Lueyang black-bone chicken with characteristic traits.http://www.sciencedirect.com/science/article/pii/S0032579123002432lueyang black-bone chickenwhole genome resequencingplumageSNP |
| spellingShingle | Zhen Xue Ling Wang Yingmin Tian Yufei Yang Pan Li Ge Yang Hongzhao Lu Shanshan Wang Wenxian Zeng Tao Zhang A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken Poultry Science lueyang black-bone chicken whole genome resequencing plumage SNP |
| title | A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken |
| title_full | A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken |
| title_fullStr | A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken |
| title_full_unstemmed | A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken |
| title_short | A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken |
| title_sort | genome wide scan to identify signatures of selection in lueyang black bone chicken |
| topic | lueyang black-bone chicken whole genome resequencing plumage SNP |
| url | http://www.sciencedirect.com/science/article/pii/S0032579123002432 |
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