1
|
Wang S, Raza SHA, Zhang K, Mei C, Alamoudi MO, Aloufi BH, Alshammari AM, Zan L. Selection signatures of Qinchuan cattle based on whole-genome sequences. Anim Biotechnol 2023; 34:1483-1491. [PMID: 35152846 DOI: 10.1080/10495398.2022.2033252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on Fst, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that KMT2E, LTBP1 and NIPBL were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. ARIH2, DACT1 and DNM2, et al. are related to meat quality. Meanwhile, TBXA2R can be used as a gene associated with reproductive function, and USH2A affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.
Collapse
Affiliation(s)
- Sihu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Muna O Alamoudi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | - Bandar H Aloufi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | | | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
| |
Collapse
|
2
|
Chen X, Bai X, Liu H, Zhao B, Yan Z, Hou Y, Chu Q. Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken. Front Genet 2022; 13:830393. [PMID: 35391799 PMCID: PMC8980806 DOI: 10.3389/fgene.2022.830393] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3, NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, including HOXB7 for beard trait in Beijing You chicken; EDN3, SLMO2, TUBB1, and GFPT1 for melanin deposition in Silkie chicken; and SORCS2 for aggressiveness in Luxi Game fowl. Moreover, CSMD1 and NTRK3 with high duplications found exclusively in White Leghorn chicken, and POLR3H, MCM9, DOCK3, and AKR1B1L found in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.
Collapse
Affiliation(s)
- Xia Chen
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xue Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Binbin Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yali Hou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| |
Collapse
|