Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study
ABSTRACT: Egg yolk texture is an important indicator for evaluating egg yolk quality. Genetic markers associated with economic traits predict genomes and facilitate mining for potential genes. Numerous genome-wide association studies have been conducted on egg traits. However, studies on the genetic...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579122006964 |
| _version_ | 1828001842056921088 |
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| author | Ruiqi Zhang Xinghua Li Ying Ma Yuchen Liu Yalan Zhang Xue Cheng Zhonghua Ning |
| author_facet | Ruiqi Zhang Xinghua Li Ying Ma Yuchen Liu Yalan Zhang Xue Cheng Zhonghua Ning |
| author_sort | Ruiqi Zhang |
| collection | DOAJ |
| description | ABSTRACT: Egg yolk texture is an important indicator for evaluating egg yolk quality. Genetic markers associated with economic traits predict genomes and facilitate mining for potential genes. Numerous genome-wide association studies have been conducted on egg traits. However, studies on the genetic basis of thermogelled yolk texture are still lacking. The aim of the present study was to find significant single nucleotide polymorphism (SNP) sites and candidate genes related to thermogelled yolk texture in Hetian Dahei chicken (HTHD) flocks that can be used as genetic markers. Five traits, including hardness, cohesiveness, gumminess, chewiness, and resilience, had low heritability (0.044–0.078). Ten genes, including U6, FSHR, PKDCC, SLC7A11, TIMM9, ARID4A, PSMA3, ACTR10, EML4, and SLC35F4 may control the hardness of the thermogelled egg yolks. In addition, 12 SNPs associated with cohesiveness were identified. RELCH located on GGA2 participates in cholesterol transport. The candidate gene LRRK2, which is associated with gumminess, influences the concentrations of very low-density lipoprotein in blood. Eight SNPs associated with resilience were identified, mainly on GGA3 and GCA28. In total, 208 SNPs associated with chewiness were identified, and 159 candidate genes, which were mainly involved in proteasome-mediated ubiquitin-dependent protein catabolic process, negative regulation of transport, lipid droplet organization, and vehicle docking involved in exocytosis, were found near these regions. Thermogel egg yolk texture is a complex phenotype controlled by multiple genes. Based on heritability assays and GWAS results, there is a genetic basis for the texture of thermogelled egg yolks. We identified a series of SNPs associated with yolk texture and candidate genes. Our result provides a theoretical basis for breeding high-quality egg yolk using molecular marker-assisted selection and could facilitate the development of novel traits. |
| first_indexed | 2024-04-10T06:35:01Z |
| format | Article |
| id | doaj.art-4c7760b4f2f84ce8815c16de0dd1c928 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-04-10T06:35:01Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-4c7760b4f2f84ce8815c16de0dd1c9282023-03-01T04:30:13ZengElsevierPoultry Science0032-57912023-03-011023102402Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association studyRuiqi Zhang0Xinghua Li1Ying Ma2Yuchen Liu3Yalan Zhang4Xue Cheng5Zhonghua Ning6National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaCorresponding author:; National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaABSTRACT: Egg yolk texture is an important indicator for evaluating egg yolk quality. Genetic markers associated with economic traits predict genomes and facilitate mining for potential genes. Numerous genome-wide association studies have been conducted on egg traits. However, studies on the genetic basis of thermogelled yolk texture are still lacking. The aim of the present study was to find significant single nucleotide polymorphism (SNP) sites and candidate genes related to thermogelled yolk texture in Hetian Dahei chicken (HTHD) flocks that can be used as genetic markers. Five traits, including hardness, cohesiveness, gumminess, chewiness, and resilience, had low heritability (0.044–0.078). Ten genes, including U6, FSHR, PKDCC, SLC7A11, TIMM9, ARID4A, PSMA3, ACTR10, EML4, and SLC35F4 may control the hardness of the thermogelled egg yolks. In addition, 12 SNPs associated with cohesiveness were identified. RELCH located on GGA2 participates in cholesterol transport. The candidate gene LRRK2, which is associated with gumminess, influences the concentrations of very low-density lipoprotein in blood. Eight SNPs associated with resilience were identified, mainly on GGA3 and GCA28. In total, 208 SNPs associated with chewiness were identified, and 159 candidate genes, which were mainly involved in proteasome-mediated ubiquitin-dependent protein catabolic process, negative regulation of transport, lipid droplet organization, and vehicle docking involved in exocytosis, were found near these regions. Thermogel egg yolk texture is a complex phenotype controlled by multiple genes. Based on heritability assays and GWAS results, there is a genetic basis for the texture of thermogelled egg yolks. We identified a series of SNPs associated with yolk texture and candidate genes. Our result provides a theoretical basis for breeding high-quality egg yolk using molecular marker-assisted selection and could facilitate the development of novel traits.http://www.sciencedirect.com/science/article/pii/S0032579122006964egg yolk texturegenetic markerssingle nucleotide polymorphismsgenome-wide association study |
| spellingShingle | Ruiqi Zhang Xinghua Li Ying Ma Yuchen Liu Yalan Zhang Xue Cheng Zhonghua Ning Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study Poultry Science egg yolk texture genetic markers single nucleotide polymorphisms genome-wide association study |
| title | Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study |
| title_full | Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study |
| title_fullStr | Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study |
| title_full_unstemmed | Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study |
| title_short | Identification of candidate genomic regions for thermogelled egg yolk traits based on a genome-wide association study |
| title_sort | identification of candidate genomic regions for thermogelled egg yolk traits based on a genome wide association study |
| topic | egg yolk texture genetic markers single nucleotide polymorphisms genome-wide association study |
| url | http://www.sciencedirect.com/science/article/pii/S0032579122006964 |
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