Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle
Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits mig...
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MDPI AG
2021-07-01
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| author | Ismail Mohamed Abdalla Xubin Lu Mudasir Nazar Abdelaziz Adam Idriss Arbab Tianle Xu Mohammed Husien Yousif Yongjiang Mao Zhangping Yang |
| author_facet | Ismail Mohamed Abdalla Xubin Lu Mudasir Nazar Abdelaziz Adam Idriss Arbab Tianle Xu Mohammed Husien Yousif Yongjiang Mao Zhangping Yang |
| author_sort | Ismail Mohamed Abdalla |
| collection | DOAJ |
| description | Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including <i>ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4</i> and <i>CADPS.</i> Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (<i>p</i> ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle. |
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| id | doaj.art-0056c70aba684fd3b8acf52137cef0b3 |
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| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T09:03:54Z |
| publishDate | 2021-07-01 |
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| series | Animals |
| spelling | doaj.art-0056c70aba684fd3b8acf52137cef0b32023-11-22T06:29:30ZengMDPI AGAnimals2076-26152021-07-01118225910.3390/ani11082259Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein CattleIsmail Mohamed Abdalla0Xubin Lu1Mudasir Nazar2Abdelaziz Adam Idriss Arbab3Tianle Xu4Mohammed Husien Yousif5Yongjiang Mao6Zhangping Yang7College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaJoint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, ChinaFaculty of Animal Production, West Kordufan University, Alnuhud City 12942, SudanCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaFeet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including <i>ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4</i> and <i>CADPS.</i> Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (<i>p</i> ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle.https://www.mdpi.com/2076-2615/11/8/2259feet and legGWASFarmCPUSNPfunctional analysisChinese Holstein cow |
| spellingShingle | Ismail Mohamed Abdalla Xubin Lu Mudasir Nazar Abdelaziz Adam Idriss Arbab Tianle Xu Mohammed Husien Yousif Yongjiang Mao Zhangping Yang Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle Animals feet and leg GWAS FarmCPU SNP functional analysis Chinese Holstein cow |
| title | Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle |
| title_full | Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle |
| title_fullStr | Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle |
| title_full_unstemmed | Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle |
| title_short | Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle |
| title_sort | genome wide association study identifies candidate genes associated with feet and leg conformation traits in chinese holstein cattle |
| topic | feet and leg GWAS FarmCPU SNP functional analysis Chinese Holstein cow |
| url | https://www.mdpi.com/2076-2615/11/8/2259 |
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