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Zhang R, Mu C, Chang L, Shen X, Bu Z, Yang M, Fu S, Tang Q, Liu P, Yang X. Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon. Animals (Basel) 2024; 14:1047. [PMID: 38612286 PMCID: PMC11011069 DOI: 10.3390/ani14071047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.
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Affiliation(s)
- Rui Zhang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Chunyu Mu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Lingling Chang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Xinyue Shen
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Zhu Bu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Mingjun Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Shengyong Fu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Qingping Tang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Peiyao Liu
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Xiaoming Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
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Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023; 12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
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Affiliation(s)
- Kai Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Yonggang Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
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Zhang M, Han W, Tang H, Li G, Zhang M, Xu R, Liu Y, Yang T, Li W, Zou J, Wu K. Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs. BMC Genomics 2018; 19:598. [PMID: 30092770 PMCID: PMC6085637 DOI: 10.1186/s12864-018-4973-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/31/2018] [Indexed: 11/25/2022] Open
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.
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Affiliation(s)
- Mengmeng Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wei Han
- National Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125 People’s Republic of China
| | - Hui Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, 271018 People’s Republic of China
| | - Guohui Li
- National Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125 People’s Republic of China
| | - Minjie Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- Beijing Key Laboratory for Animal Genetic Improvement, Beijing, 100193 People’s Republic of China
| | - Ran Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Yijun Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- College of Animal Science, Southwest University, Chongqing, 402460 People’s Republic of China
| | - Tao Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenting Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 People’s Republic of China
| | - Jianmin Zou
- National Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125 People’s Republic of China
| | - Keliang Wu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
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Chu Q, Yan Z, Zhang J, Usman T, Zhang Y, Liu H, Wang H, Geng A, Liu H. Association of SNP rs80659072 in the ZRS with polydactyly in Beijing You chickens. PLoS One 2017; 12:e0185953. [PMID: 29016641 PMCID: PMC5633194 DOI: 10.1371/journal.pone.0185953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/24/2017] [Indexed: 12/16/2022] Open
Abstract
The Beijing You chicken is a Chinese native breed with superior meat quality and a unique appearance. The G/T mutation of SNP rs80659072 in the Shh long-range regulator of GGA2 is highly associated with the polydactyly phenotype in some chicken breeds. In the present study, this SNP was genotyped using the TaqMan detection method, and its association with the number of toes was analyzed in a flock of 158 birds of the Beijing You population maintained at the Beijing Academy of Agriculture and Forestry Sciences. Furthermore, the skeletal structure of the digits was dissected and assembled in 113 birds. The findings revealed that the toes of Beijing You chickens were rich and more complex than expected. The plausible mutation rs80659072 in the zone of polarizing activity regulatory sequence (ZRS) in chickens was an essential but not sufficient condition for polydactyly and polyphalangy in Beijing You chickens. Several individuals shared the T allele but showed normal four-digit conformations. However, breeding trials demonstrated that the T allele could serve as a strong genetic marker for five-toe selection in Beijing You chickens.
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Affiliation(s)
- Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Tahir Usman
- College of Veterinary Science and Animal Husbandry, Garden Campus, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yao Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Hui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Haihong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Ailian Geng
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China
- * E-mail:
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