Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs
Abstract Understanding the genetic factors related to meat drip loss is of great importance for animal breeding and production. In this study, we employed a combination of genome‐wide association study (GWAS) mapping and RNA sequencing (RNA‐seq) data to effectively identify potentially functional si...
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| Format: | Article |
| Language: | English |
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Wiley
2024-11-01
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| Series: | Animal Research and One Health |
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| Online Access: | https://doi.org/10.1002/aro2.32 |
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| author | Hongmei Gao Jingjing Tian Run Zhang Xiance Liu Hai Liu Fuping Zhao Zhenhua Xue Lixian Wang Xitao Jing Longchao Zhang |
| author_facet | Hongmei Gao Jingjing Tian Run Zhang Xiance Liu Hai Liu Fuping Zhao Zhenhua Xue Lixian Wang Xitao Jing Longchao Zhang |
| author_sort | Hongmei Gao |
| collection | DOAJ |
| description | Abstract Understanding the genetic factors related to meat drip loss is of great importance for animal breeding and production. In this study, we employed a combination of genome‐wide association study (GWAS) mapping and RNA sequencing (RNA‐seq) data to effectively identify potentially functional single nucleotide polymorphisms (SNPs) as well as candidate genes associated with drip loss (DL) in Beijing Black pigs. Initially, we conducted a single‐ and multi‐trait GWAS on drip loss traits in 441 Beijing Black pigs at 24 (DL24) and 48 (DL48) hours postmortem using the Illumina pig 50K SNP chip. Five SNPs with annotations for four genes (FGGY, LHFPL6, OSBPL1A, and NMNAT3) were consistently identified in single or multiple trait GWAS results, indicating their potential pleiotropic effects on drip loss. Next, a comprehensive comparative transcriptomic analysis was performed on samples of Beijing Black pigs exhibiting extremely high and low drip loss, resulting in the identification of 21 differentially expressed genes (DGEs) as potential candidates. Additionally, protein–protein interaction (PPI) network analysis revealed reciprocal regulatory relationships between FOXO1, OSBPL1A, DOCK1 (identified from GWAS) and the candidate DGEs obtained from RNA‐seq data. Therefore, we propose that these genes may impact drip loss traits through gene interactions. In conclusion, our integrative analysis screened candidate genes that may affect the drip loss traits in Beijing Black pigs, which provides crucial insights into the molecular mechanisms of drip loss and serves as a theoretical reference for improving meat quality in Beijing Black pigs. |
| format | Article |
| id | doaj-art-eee491aaeee64e6497fc22b7b7533ea7 |
| institution | Kabale University |
| issn | 2835-5075 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Animal Research and One Health |
| spelling | doaj-art-eee491aaeee64e6497fc22b7b7533ea72024-11-15T14:19:40ZengWileyAnimal Research and One Health2835-50752024-11-012444645710.1002/aro2.32Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigsHongmei Gao0Jingjing Tian1Run Zhang2Xiance Liu3Hai Liu4Fuping Zhao5Zhenhua Xue6Lixian Wang7Xitao Jing8Longchao Zhang9Institute of Animal Science Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Animal Science Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Animal Science Chinese Academy of Agricultural Sciences Beijing ChinaBeijing Heiliu Animal Husbandry Technology Co, Ltd Beijing ChinaBeijing Heiliu Animal Husbandry Technology Co, Ltd Beijing ChinaInstitute of Animal Science Chinese Academy of Agricultural Sciences Beijing ChinaThe Municipal Animal Husbandry General Station of Beijing Beijing ChinaInstitute of Animal Science Chinese Academy of Agricultural Sciences Beijing ChinaBeijing Heiliu Animal Husbandry Technology Co, Ltd Beijing ChinaInstitute of Animal Science Chinese Academy of Agricultural Sciences Beijing ChinaAbstract Understanding the genetic factors related to meat drip loss is of great importance for animal breeding and production. In this study, we employed a combination of genome‐wide association study (GWAS) mapping and RNA sequencing (RNA‐seq) data to effectively identify potentially functional single nucleotide polymorphisms (SNPs) as well as candidate genes associated with drip loss (DL) in Beijing Black pigs. Initially, we conducted a single‐ and multi‐trait GWAS on drip loss traits in 441 Beijing Black pigs at 24 (DL24) and 48 (DL48) hours postmortem using the Illumina pig 50K SNP chip. Five SNPs with annotations for four genes (FGGY, LHFPL6, OSBPL1A, and NMNAT3) were consistently identified in single or multiple trait GWAS results, indicating their potential pleiotropic effects on drip loss. Next, a comprehensive comparative transcriptomic analysis was performed on samples of Beijing Black pigs exhibiting extremely high and low drip loss, resulting in the identification of 21 differentially expressed genes (DGEs) as potential candidates. Additionally, protein–protein interaction (PPI) network analysis revealed reciprocal regulatory relationships between FOXO1, OSBPL1A, DOCK1 (identified from GWAS) and the candidate DGEs obtained from RNA‐seq data. Therefore, we propose that these genes may impact drip loss traits through gene interactions. In conclusion, our integrative analysis screened candidate genes that may affect the drip loss traits in Beijing Black pigs, which provides crucial insights into the molecular mechanisms of drip loss and serves as a theoretical reference for improving meat quality in Beijing Black pigs.https://doi.org/10.1002/aro2.32Beijing Black pigdrip lossgenome‐wide association studytranscriptomicswater holding capacity |
| spellingShingle | Hongmei Gao Jingjing Tian Run Zhang Xiance Liu Hai Liu Fuping Zhao Zhenhua Xue Lixian Wang Xitao Jing Longchao Zhang Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs Animal Research and One Health Beijing Black pig drip loss genome‐wide association study transcriptomics water holding capacity |
| title | Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs |
| title_full | Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs |
| title_fullStr | Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs |
| title_full_unstemmed | Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs |
| title_short | Integrative analysis of genome‐wide association study and transcriptomics to identify potential candidate genes influencing drip loss in Beijing Black pigs |
| title_sort | integrative analysis of genome wide association study and transcriptomics to identify potential candidate genes influencing drip loss in beijing black pigs |
| topic | Beijing Black pig drip loss genome‐wide association study transcriptomics water holding capacity |
| url | https://doi.org/10.1002/aro2.32 |
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