High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin
ABSTRACT: Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Ban...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579122005983 |
| _version_ | 1798016252531179520 |
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| author | Shijie Lyu Danny Arends Mostafa K. Nassar Annett Weigend Steffen Weigend Eryao Wang Gudrun A. Brockmann |
| author_facet | Shijie Lyu Danny Arends Mostafa K. Nassar Annett Weigend Steffen Weigend Eryao Wang Gudrun A. Brockmann |
| author_sort | Shijie Lyu |
| collection | DOAJ |
| description | ABSTRACT: Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens. In this study, 94 and 107 chickens from 4 Asian Game and 5 Asian Bantam type breeds, respectively, were genotyped using the chicken 580K single nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) and principal component analyses (PCA) were performed to identify genomic regions associated with body size related-traits such as wing length, shank length, shank thickness, keel length, and body weight. Hierarchical clustering of genotype data showed a clear genetic difference between the investigated Asian Game and Asian Bantam chicken types. GWAS identified 16 genomic regions associated with wing length (2, FDR ≤ 0.018), shank thickness (6, FDR ≤ 0.008), keel length (5, FDR ≤ 0.023), and body weight (3, FDR ≤ 0.041). PCA showed that the first principal component (PC1) separated the 2 chicken types and significantly correlated with the measured body size related-traits (P ≤ 2.24e-40). SNPs contributing significantly to PC1 were subjected to a more detailed investigation. This analysis identified 11 regions potentially associated with differences in body size related-traits. A region on chromosome 4 (GGA4) (17.3–21.3 Mb) was detected in both analyses GWAS and PCA. This region harbors 60 genes. Among them are myotubularin 1 (MTM1) and secreted frizzled-related protein 2 (SFPR2) which can be considered as potential candidate genes for body size related-traits. Our results clearly show that the investigated Asian Game type chicken breeds are genetically different from the Asian Bantam breeds. A region on GGA4 between 17.3 and 21.3 Mb was identified which contributes to the phenotypic difference, though further validation of candidate genes is necessary. |
| first_indexed | 2024-04-11T15:46:42Z |
| format | Article |
| id | doaj.art-31261c39dbb54b2e9c9694beaaa74961 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-04-11T15:46:42Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-31261c39dbb54b2e9c9694beaaa749612022-12-22T04:15:30ZengElsevierPoultry Science0032-57912023-01-011021102303High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian originShijie Lyu0Danny Arends1Mostafa K. Nassar2Annett Weigend3Steffen Weigend4Eryao Wang5Gudrun A. Brockmann6Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universitt zu Berlin, Berlin 10115, Germany; Institute of Animal Science and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaAlbrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universitt zu Berlin, Berlin 10115, Germany; Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UKAnimal Production Department, Faculty of Agriculture, Cairo University, Giza 12613, EgyptInstitute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee 31535, GermanyInstitute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee 31535, GermanyInstitute of Animal Science and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaAlbrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universitt zu Berlin, Berlin 10115, Germany; Corresponding author:ABSTRACT: Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens. In this study, 94 and 107 chickens from 4 Asian Game and 5 Asian Bantam type breeds, respectively, were genotyped using the chicken 580K single nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) and principal component analyses (PCA) were performed to identify genomic regions associated with body size related-traits such as wing length, shank length, shank thickness, keel length, and body weight. Hierarchical clustering of genotype data showed a clear genetic difference between the investigated Asian Game and Asian Bantam chicken types. GWAS identified 16 genomic regions associated with wing length (2, FDR ≤ 0.018), shank thickness (6, FDR ≤ 0.008), keel length (5, FDR ≤ 0.023), and body weight (3, FDR ≤ 0.041). PCA showed that the first principal component (PC1) separated the 2 chicken types and significantly correlated with the measured body size related-traits (P ≤ 2.24e-40). SNPs contributing significantly to PC1 were subjected to a more detailed investigation. This analysis identified 11 regions potentially associated with differences in body size related-traits. A region on chromosome 4 (GGA4) (17.3–21.3 Mb) was detected in both analyses GWAS and PCA. This region harbors 60 genes. Among them are myotubularin 1 (MTM1) and secreted frizzled-related protein 2 (SFPR2) which can be considered as potential candidate genes for body size related-traits. Our results clearly show that the investigated Asian Game type chicken breeds are genetically different from the Asian Bantam breeds. A region on GGA4 between 17.3 and 21.3 Mb was identified which contributes to the phenotypic difference, though further validation of candidate genes is necessary.http://www.sciencedirect.com/science/article/pii/S0032579122005983Asian Game type chickenAsian Bantam type chickengrowthGWASPCA |
| spellingShingle | Shijie Lyu Danny Arends Mostafa K. Nassar Annett Weigend Steffen Weigend Eryao Wang Gudrun A. Brockmann High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin Poultry Science Asian Game type chicken Asian Bantam type chicken growth GWAS PCA |
| title | High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin |
| title_full | High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin |
| title_fullStr | High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin |
| title_full_unstemmed | High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin |
| title_short | High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin |
| title_sort | high density genotyping reveals candidate genomic regions for chicken body size in breeds of asian origin |
| topic | Asian Game type chicken Asian Bantam type chicken growth GWAS PCA |
| url | http://www.sciencedirect.com/science/article/pii/S0032579122005983 |
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