Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing
Abstract Background Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide associ...
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| Format: | Article |
| Language: | English |
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BMC
2022-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-08236-3 |
| _version_ | 1819228988249210880 |
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| author | Yaping Guo Hetian Huang Zhenzhen Zhang Yanchao Ma Jianzeng Li Hehe Tang Haoxiang Ma Zhuanjian Li Wenting Li Xiaojun Liu Xiangtao Kang Ruili Han |
| author_facet | Yaping Guo Hetian Huang Zhenzhen Zhang Yanchao Ma Jianzeng Li Hehe Tang Haoxiang Ma Zhuanjian Li Wenting Li Xiaojun Liu Xiangtao Kang Ruili Han |
| author_sort | Yaping Guo |
| collection | DOAJ |
| description | Abstract Background Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers. Results In total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene. Conclusions The results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness. |
| first_indexed | 2024-12-23T11:06:01Z |
| format | Article |
| id | doaj.art-9d75b7b3e9c84f3a8d76cc206f4e9baa |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-23T11:06:01Z |
| publishDate | 2022-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9d75b7b3e9c84f3a8d76cc206f4e9baa2022-12-21T17:49:29ZengBMCBMC Genomics1471-21642022-01-0123111110.1186/s12864-021-08236-3Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencingYaping Guo0Hetian Huang1Zhenzhen Zhang2Yanchao Ma3Jianzeng Li4Hehe Tang5Haoxiang Ma6Zhuanjian Li7Wenting Li8Xiaojun Liu9Xiangtao Kang10Ruili Han11College of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityCollege of animal science and technology, Henan Agricultural UniversityAbstract Background Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers. Results In total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene. Conclusions The results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness.https://doi.org/10.1186/s12864-021-08236-3BroilerValgus-varus deformityGenome-wide association studyGrowth performanceSerum indicators |
| spellingShingle | Yaping Guo Hetian Huang Zhenzhen Zhang Yanchao Ma Jianzeng Li Hehe Tang Haoxiang Ma Zhuanjian Li Wenting Li Xiaojun Liu Xiangtao Kang Ruili Han Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing BMC Genomics Broiler Valgus-varus deformity Genome-wide association study Growth performance Serum indicators |
| title | Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing |
| title_full | Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing |
| title_fullStr | Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing |
| title_full_unstemmed | Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing |
| title_short | Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing |
| title_sort | genome wide association study identifies snps for growth performance and serum indicators in valgus varus deformity broilers gallus gallus using ddgbs sequencing |
| topic | Broiler Valgus-varus deformity Genome-wide association study Growth performance Serum indicators |
| url | https://doi.org/10.1186/s12864-021-08236-3 |
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