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He C, Chen Y, Yang K, Zhai Z, Zhao W, Liu S, Ding J, Dai R, Yang L, Xu K, Zhou Z, Gu C, Huang Q, Meng H. Genetic pattern and gene localization of polydactyly in Beijing fatty chicken. PLoS One 2017; 12:e0176113. [PMID: 28489934 PMCID: PMC5425009 DOI: 10.1371/journal.pone.0176113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 04/05/2017] [Indexed: 11/29/2022] Open
Abstract
Polydactyly, a common heritable limb malformation in vertebrates, is characterized by supernumerary digits. In chickens, basic characteristics and rough dominant genes have been explored in past decades; however, the elaborate pattern of inheritance and the determinant gene remain obscure. In this study, different types of polydactylism were classified by the numbers and the shapes of toes, including the newly defined subtypes of B’ and G, for the Beijing fatty chicken, a native breed of chicken from China. Through experiments on hybridization, we demonstrated a complete dominant inheritance of polydactyly instead of an incomplete penetrance or genetic modification of the previous conjecture. In particular, by using the F2 population of the five-digit purebred line of Beijing fatty chicken backcrossed to Shiqiza chicken and by using restriction-site associated DNA based markers, we performed a genome-wide association study on the trait of polydactyly. Furthermore, whole genome resequencing strategy was applied to sweep SNPs across the whole genome. An outlier-based Fst approach was employed to search for signatures of selection, and results indicated that the determinant mutation was found in the region ranging from 8.3 Mb to 8.7 Mb, where the polydactyly candidate gene LMBR1 was located. The G/T mutation of rs80659072 was identified to be highly associated with polydactyly in our resequencing and was validated in random samples from an expanded population. Thus, we confirmed that LMBR1 was the causative gene of polydactyly in the Beijing fatty chicken by using GWAS with restriction-site associated DNA based markers and resequencing.
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Affiliation(s)
- Chuan He
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Yongcan Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Kaixuan Yang
- Animal Husbandry and Veterinary Research Institute, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Zhengxiao Zhai
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Wenjing Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Shuyun Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Jinmei Ding
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Ronghua Dai
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Lingyu Yang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Ke Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
| | - Zhenxiang Zhou
- Animal Husbandry and Veterinary Research Institute, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Caiju Gu
- Animal Husbandry and Veterinary Research Institute, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Qizhong Huang
- Animal Husbandry and Veterinary Research Institute, Shanghai Academy of Agricultural Science, Shanghai, China
- * E-mail: (HM); (QH)
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
- * E-mail: (HM); (QH)
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Zhang Z, Nie C, Jia Y, Jiang R, Xia H, Lv X, Chen Y, Li J, Li X, Ning Z, Xu G, Chen J, Yang N, Qu L. Parallel Evolution of Polydactyly Traits in Chinese and European Chickens. PLoS One 2016; 11:e0149010. [PMID: 26859147 PMCID: PMC4747547 DOI: 10.1371/journal.pone.0149010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/26/2016] [Indexed: 12/26/2022] Open
Abstract
Polydactyly is one of the most common hereditary congenital limb malformations in chickens and other vertebrates. The zone of polarizing activity regulatory sequence (ZRS) is critical for the development of polydactyly. The causative mutation of polydactyly in the Silkie chicken has been mapped to the ZRS; however, the causative mutations of other chicken breeds are yet to be established. To understand whether the same mutation decides the polydactyly phenotype in other chicken breeds, we detected the single-nucleotide polymorphism in 26 different chicken breeds, specifically, 24 Chinese indigenous breeds and 2 European breeds. The mutation was found to have fully penetrated chickens with polydactyly in China, indicating that it is causative for polydactyly in Chinese indigenous chickens. In comparison, the mutation showed no association with polydactyly in Houdan chickens, which originate from France, Europe. Based on the different morphology of polydactyly in Chinese and European breeds, we assumed that the trait might be attributable to different genetic foundations. Therefore, we subsequently performed genome-wide association analysis (GWAS) to locate the region associated with polydactyly. As a result, a ~0.39 Mb genomic region on GGA2p was identified. The region contains six candidate genes, with the causative mutation found in Chinese indigenous breeds also being located in this region. Our results demonstrate that polydactyly in chickens from China and Europe is caused by two independent mutation events that are closely located in the chicken genome.
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Affiliation(s)
- Zebin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Changsheng Nie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yaxiong Jia
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Haijian Xia
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Junying Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xianyao Li
- College of Animal Science, Shandong Agricultural University, Taian, 271018, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guiyun Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jilan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- * E-mail:
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