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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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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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Sheng X, Chen Y, Jia Y, Qi X, Feng Y, Huang Z, Guo Y. The identification of loci for polydactyly in chickens using a genome-wide association study. Gene 2015; 568:176-80. [PMID: 26003297 DOI: 10.1016/j.gene.2015.05.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
Polydactyly is a commonly observed limb malformation in humans and other vertebrates. The Beijing-You chicken expressing the polydactyly phenotype provides an opportunity to investigate the potential cause for polydactyly. Here we extensively exploited genetic determinants of the chicken polydactyly in a genome wide association study using over 580,000 SNPs characterized in a Beijing-You × Lohmann F1 cross, consisting of 79 animals. A total of 10 loci clustered on the short arm of chromosome 2 were identified to be significantly associated with the trait. Among the 10 significant SNPs, 7 were located in a linkage disequilibrium block of 1737kb. The strongest association signal (rs317674023, P=5.48×10(-8)) residing nearby Bone Morphogenetic Protein Receptor-Associated Molecule 1 (BRAM1) was identified in the genomic region. Our results provide insights to the genetic basis underlying chicken polydactyly and may facilitate studies of the limb malformation in humans and other species.
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Affiliation(s)
- Xihui Sheng
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 100026, China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing 100001, China
| | - Yaxiong Jia
- Beijing Municipal General Station of Animal Science, Beijing 100001, China
| | - Xiaolong Qi
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 100026, China
| | - Yun Feng
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 100026, China
| | - Zhen Huang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 100026, China
| | - Yong Guo
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 100026, China.
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Genome-wide linkage analysis and association study identifies loci for polydactyly in chickens. G3-GENES GENOMES GENETICS 2014; 4:1167-72. [PMID: 24752238 PMCID: PMC4065260 DOI: 10.1534/g3.114.011338] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Polydactyly occurs in some chicken breeds, but the molecular mechanism remains incompletely understood. Combined genome-wide linkage analysis and association study (GWAS) for chicken polydactyly helps identify loci or candidate genes for the trait and potentially provides further mechanistic understanding of this phenotype in chickens and perhaps other species. The linkage analysis and GWAS for polydactyly was conducted using an F2 population derived from Beijing-You chickens and commercial broilers. The results identified two QTLs through linkage analysis and seven single-nucleotide polymorphisms (SNPs) through GWAS, associated with the polydactyly trait. One QTL located at 35 cM on the GGA2 was significant at the 1% genome-wise level and another QTL at the 1% chromosome-wide significance level was detected at 39 cM on GGA19. A total of seven SNPs, four of 5% genome-wide significance (P < 2.98 × 10(-6)) and three of suggestive significance (5.96 × 10(-5)) were identified, including two SNPs (GGaluGA132178 and Gga_rs14135036) in the QTL on GGA2. Of the identified SNPs, the eight nearest genes were sonic hedgehog (SHH), limb region 1 homolog (mouse) (LMBR1), dipeptidyl-peptidase 6, transcript variant 3 (DPP6), thyroid-stimulating hormone, beta (TSHB), sal-like 4 (Drosophila) (SALL4), par-6 partitioning defective 6 homolog beta (Caenorhabditis elegans) (PARD6B), coenzyme Q5 (COQ5), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, etapolypeptide (YWHAH). The GWAS supports earlier reports of the importance of SHH and LMBR1 as regulating genes for polydactyly in chickens and other species, and identified others, most of which have not previously been associated with limb development. The genes and associated SNPs revealed here provide detailed information for further exploring the molecular and developmental mechanisms underlying polydactyly.
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