Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study
Abstract Background Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand the molecular mechanism underlying egg yolk moisture content, this stud...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09221-8 |
| _version_ | 1797865492503855104 |
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| author | Ruiqi Zhang Fusheng Yao Xue Cheng Mengyuan Yang Zhonghua Ning |
| author_facet | Ruiqi Zhang Fusheng Yao Xue Cheng Mengyuan Yang Zhonghua Ning |
| author_sort | Ruiqi Zhang |
| collection | DOAJ |
| description | Abstract Background Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand the molecular mechanism underlying egg yolk moisture content, this study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) using a mixed linear model. Results We determined the phenotype and heritability of thermogelled egg yolk water content (TWC) and found that the average TWC was 47.73%. Moreover, significant variations occurred (41.06–57.12%), and the heritability was 0.11, which indicates medium-low heritability. Through the GWAS, 48 single nucleotide polymorphisms (SNPs) related to TWC (20 significantly, 28 suggestively) were obtained, and they were mainly located on chromosomes 10 and 13. We identified 36 candidate genes based on gene function and found that they were mainly involved in regulating fat, protein, and water content and embryonic development. FGF9, PIAS1, FEM1B, NOX5, GLCE, VDAC1, IGFBP7, and THOC5 were involved in lipid formation and regulation; AP3S2, GNPDA1, HSPA4, AP1B1, CABP7, EEF1D, SYTL3, PPP2CA, SKP1, and UBE2B were involved in protein folding and hydrolysis; and CSF2, SOWAHA, GDF9, FSTL4, RAPGEF6, PAQR5, and ZMAT5 were related to embryonic development and egg production. Moreover, MICU2, ITGA11, WDR76, BLM, ANPEP, TECRL, EWSR1, and P4HA2 were related to yolk quality, while ITGA11, WDR76, BLM, and ANPEP were potentially significantly involved in egg yolk water content and thus deserve further attention and research. In addition, this study identified a 19.31–19.92 Mb genome region on GGA10, and a linkage disequilibrium analysis identified strong correlations within this region. Thus, GGA10 may represent a candidate region for TWC traits. Conclusion The molecular genetic mechanism involved in TWC was revealed through heritability measurements and GWAS, which identified a series of SNPs, candidate genes, and candidate regions related to TWC. These results provide insights on the molecular mechanism of egg yolk moisture content and may aid in the development of new egg traits. |
| first_indexed | 2024-04-09T23:09:12Z |
| format | Article |
| id | doaj.art-b60ab2dea76c47a4aebaf8fb59868bd5 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:09:12Z |
| publishDate | 2023-03-01 |
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| series | BMC Genomics |
| spelling | doaj.art-b60ab2dea76c47a4aebaf8fb59868bd52023-03-22T10:30:45ZengBMCBMC Genomics1471-21642023-03-012411910.1186/s12864-023-09221-8Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association studyRuiqi Zhang0Fusheng Yao1Xue Cheng2Mengyuan Yang3Zhonghua Ning4Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityAbstract Background Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand the molecular mechanism underlying egg yolk moisture content, this study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) using a mixed linear model. Results We determined the phenotype and heritability of thermogelled egg yolk water content (TWC) and found that the average TWC was 47.73%. Moreover, significant variations occurred (41.06–57.12%), and the heritability was 0.11, which indicates medium-low heritability. Through the GWAS, 48 single nucleotide polymorphisms (SNPs) related to TWC (20 significantly, 28 suggestively) were obtained, and they were mainly located on chromosomes 10 and 13. We identified 36 candidate genes based on gene function and found that they were mainly involved in regulating fat, protein, and water content and embryonic development. FGF9, PIAS1, FEM1B, NOX5, GLCE, VDAC1, IGFBP7, and THOC5 were involved in lipid formation and regulation; AP3S2, GNPDA1, HSPA4, AP1B1, CABP7, EEF1D, SYTL3, PPP2CA, SKP1, and UBE2B were involved in protein folding and hydrolysis; and CSF2, SOWAHA, GDF9, FSTL4, RAPGEF6, PAQR5, and ZMAT5 were related to embryonic development and egg production. Moreover, MICU2, ITGA11, WDR76, BLM, ANPEP, TECRL, EWSR1, and P4HA2 were related to yolk quality, while ITGA11, WDR76, BLM, and ANPEP were potentially significantly involved in egg yolk water content and thus deserve further attention and research. In addition, this study identified a 19.31–19.92 Mb genome region on GGA10, and a linkage disequilibrium analysis identified strong correlations within this region. Thus, GGA10 may represent a candidate region for TWC traits. Conclusion The molecular genetic mechanism involved in TWC was revealed through heritability measurements and GWAS, which identified a series of SNPs, candidate genes, and candidate regions related to TWC. These results provide insights on the molecular mechanism of egg yolk moisture content and may aid in the development of new egg traits.https://doi.org/10.1186/s12864-023-09221-8Thermogelled egg yolksWater contentHeritabilityGenome-wide association study |
| spellingShingle | Ruiqi Zhang Fusheng Yao Xue Cheng Mengyuan Yang Zhonghua Ning Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study BMC Genomics Thermogelled egg yolks Water content Heritability Genome-wide association study |
| title | Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study |
| title_full | Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study |
| title_fullStr | Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study |
| title_full_unstemmed | Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study |
| title_short | Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study |
| title_sort | identification of candidate genomic regions for egg yolk moisture content based on a genome wide association study |
| topic | Thermogelled egg yolks Water content Heritability Genome-wide association study |
| url | https://doi.org/10.1186/s12864-023-09221-8 |
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