Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies
Objective The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain...
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Asian-Australasian Association of Animal Production Societies
2017-04-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-30-4-462.pdf |
| _version_ | 1818187877180243968 |
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| author | Qingli Meng Kejun Wang Xiaolei Liu Haishen Zhou Li Xu Zhaojun Wang Meiying Fang |
| author_facet | Qingli Meng Kejun Wang Xiaolei Liu Haishen Zhou Li Xu Zhaojun Wang Meiying Fang |
| author_sort | Qingli Meng |
| collection | DOAJ |
| description | Objective The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs. |
| first_indexed | 2024-12-11T23:18:00Z |
| format | Article |
| id | doaj.art-b8e599518346490a814daf149b417cf9 |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-11T23:18:00Z |
| publishDate | 2017-04-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-b8e599518346490a814daf149b417cf92022-12-22T00:46:26ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172017-04-0130446246910.5713/ajas.16.054823655Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studiesQingli Meng0Kejun Wang1Xiaolei Liu2Haishen Zhou3Li Xu4Zhaojun Wang5Meiying Fang6 Beijing Breeding Swine Center, Beijing 100194, China Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China Beijing Breeding Swine Center, Beijing 100194, China Beijing Breeding Swine Center, Beijing 100194, China Beijing Breeding Swine Center, Beijing 100194, China Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaObjective The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.http://www.ajas.info/upload/pdf/ajas-30-4-462.pdfYorkshire PigGenome-wide Association Studies (GWAS)Growth TraitSingle Nucleotide Polymorphisms (SNPs) |
| spellingShingle | Qingli Meng Kejun Wang Xiaolei Liu Haishen Zhou Li Xu Zhaojun Wang Meiying Fang Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies Asian-Australasian Journal of Animal Sciences Yorkshire Pig Genome-wide Association Studies (GWAS) Growth Trait Single Nucleotide Polymorphisms (SNPs) |
| title | Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies |
| title_full | Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies |
| title_fullStr | Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies |
| title_full_unstemmed | Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies |
| title_short | Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies |
| title_sort | identification of growth trait related genes in a yorkshire purebred pig population by genome wide association studies |
| topic | Yorkshire Pig Genome-wide Association Studies (GWAS) Growth Trait Single Nucleotide Polymorphisms (SNPs) |
| url | http://www.ajas.info/upload/pdf/ajas-30-4-462.pdf |
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