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High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin

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 c...

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Autores principales: Lyu, Shijie, Arends, Danny, Nassar, Mostafa K., Weigend, Annett, Weigend, Steffen, Wang, Eryao, Brockmann, Gudrun A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9706647/
https://www.ncbi.nlm.nih.gov/pubmed/36436378
http://dx.doi.org/10.1016/j.psj.2022.102303
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author Lyu, Shijie
Arends, Danny
Nassar, Mostafa K.
Weigend, Annett
Weigend, Steffen
Wang, Eryao
Brockmann, Gudrun A.
author_facet Lyu, Shijie
Arends, Danny
Nassar, Mostafa K.
Weigend, Annett
Weigend, Steffen
Wang, Eryao
Brockmann, Gudrun A.
author_sort Lyu, Shijie
collection PubMed
description 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.
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spelling pubmed-97066472022-11-30 High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin Lyu, Shijie Arends, Danny Nassar, Mostafa K. Weigend, Annett Weigend, Steffen Wang, Eryao Brockmann, Gudrun A. Poult Sci GENETICS AND MOLECULAR BIOLOGY 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. Elsevier 2022-10-29 /pmc/articles/PMC9706647/ /pubmed/36436378 http://dx.doi.org/10.1016/j.psj.2022.102303 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle GENETICS AND MOLECULAR BIOLOGY
Lyu, Shijie
Arends, Danny
Nassar, Mostafa K.
Weigend, Annett
Weigend, Steffen
Wang, Eryao
Brockmann, Gudrun A.
High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin
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 GENETICS AND MOLECULAR BIOLOGY
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9706647/
https://www.ncbi.nlm.nih.gov/pubmed/36436378
http://dx.doi.org/10.1016/j.psj.2022.102303
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