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Wang T, Ma X, Ma C, Wu X, ZhaXi T, Yin L, Li W, Li Y, Liang C, Yan P. Whole genome resequencing-based analysis of plateau adaptation in Meiren yak ( Bos grunniens). Anim Biotechnol 2024; 35:2298406. [PMID: 38193808 DOI: 10.1080/10495398.2023.2298406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.
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Affiliation(s)
- Tong Wang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - XiaoMing Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - ChaoFan Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - XiaoYun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ta ZhaXi
- Qilian County Veterinary Animal Husbandry Station, Qinghai, China
| | - LiXin Yin
- Huazhi Biotech Co. Ltd, Changsha, China
| | - WeiGuo Li
- Huazhi Biotech Co. Ltd, Changsha, China
| | - YuFei Li
- Huazhi Biotech Co. Ltd, Changsha, China
| | - ChunNian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
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Morel E, Malineau L, Venet C, Gaillard V, Péron F. Prioritization of Appearance over Health and Temperament Is Detrimental to the Welfare of Purebred Dogs and Cats. Animals (Basel) 2024; 14:1003. [PMID: 38612242 PMCID: PMC11011023 DOI: 10.3390/ani14071003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Fashions in the appearance of purebred dogs and cats are encouraged by celebrity culture, social media, and online impulse buying. The popularity of characteristics perceived as cute, quirky, and anthropomorphic has driven increasingly exaggerated breed features appealing to aesthetics rather than health. 'Hypertypes' of some breeds have emerged that take a breed's distinctive appearance to extremes beyond the intended interpretation of breed standards. This has severe, direct and indirect health and welfare consequences. Extreme conformations are associated with chronic health conditions including brachycephalic obstructive airway disorder, ocular, dental, skin, and musculoskeletal disorders. Puppy and kitten farms and illegal traders that meet the demand for hypertypes are associated with poor husbandry that neglects the physical, behavioral, and mental health of parents and offspring. A multidimensional approach involving collaboration between breeders, geneticists, owners, veterinarians, kennel clubs, cat fanciers' associations, animal charities, the academic and research communities, commercial enterprises, and governments is needed to safeguard breeds and tackle these challenges. There are many ongoing initiatives by national kennel clubs and global partnerships to educate pet owners and support responsible pet ownership and sustainable breeding. The resounding message is that health, temperament, and well-being must be prioritized over appearance.
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Affiliation(s)
| | | | | | - Virginie Gaillard
- Royal Canin, 30470 Aimargues, France; (E.M.); (L.M.); (C.V.); (F.P.)
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Shastak Y, Pelletier W. Pet Wellness and Vitamin A: A Narrative Overview. Animals (Basel) 2024; 14:1000. [PMID: 38612239 PMCID: PMC11010875 DOI: 10.3390/ani14071000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The health of companion animals, particularly dogs and cats, is significantly influenced by nutrition, with vitamins playing a crucial role. Vitamin A, in particular, is indispensable, with diverse roles ranging from vision to immune modulation and reproduction. Despite its importance, the metabolism and dietary requirements of vitamin A in companion animals remain complex and not fully understood. This review provides a comprehensive overview of the historical perspective, the digestion, the metabolism, the physiological roles, the deficiency, the excess, and the interactions with other micronutrients of vitamin A in companion animals. Additionally, it highlights future research directions and gaps in our understanding. Insights into the metabolism of vitamin A in companion animals, personalized nutrition strategies based on genetic variability, longitudinal studies tracking the status of vitamin A, and investigations into its immunomodulatory effects are crucial for optimizing pet health and wellness. Furthermore, understanding the stability and bioavailability of vitamin A in pet food formulations is essential for ensuring the provision of adequate micronutrients. Overall, this review underscores the importance of vitamin A in companion animal nutrition and the need for further research to enhance our understanding and to optimize dietary recommendations for pet health and well-being.
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Affiliation(s)
- Yauheni Shastak
- Nutrition & Health Division, BASF SE, 67063 Ludwigshafen am Rhein, Germany
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Morrill K, Chen F, Karlsson E. Comparative neurogenetics of dog behavior complements efforts towards human neuropsychiatric genetics. Hum Genet 2023; 142:1231-1246. [PMID: 37578529 DOI: 10.1007/s00439-023-02580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023]
Abstract
Domestic dogs display a wide array of heritable behaviors that have intermediate genetic complexity thanks to a long history of human-influenced selection. Comparative genetics in dogs could address the scarcity of non-human neurogenetic systems relevant to human neuropsychiatric disorders, which are characterized by mental, emotional, and behavioral symptoms and involve vastly complex genetic and non-genetic risk factors. Our review describes the diverse behavioral "phenome" of domestic dogs, past and ongoing sources of behavioral selection, and the state of canine behavioral genetics. We highlight two naturally disordered behavioral domains that illustrate how dogs may prove useful as a comparative, forward neurogenetic system: canine age-related cognitive dysfunction, which can be examined more rapidly given the attenuated lifespan of dogs, and compulsive disorders, which may have genetic roots in purpose-bred behaviors. Growing community science initiatives aimed at the companion dog population will be well suited to investigating such complex behavioral phenotypes and offer a comparative resource that parallels human genomic initiatives in scale and dimensionality.
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Affiliation(s)
- Kathleen Morrill
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Morningside Graduate School of Biomedical Sciences UMass Chan Medical School, Worcester, MA, USA.
| | - Frances Chen
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Li Z, Wang Z, Chen Z, Voegeli H, Lichtman JH, Smith P, Liu J, DeWan AT, Hoh J. Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds. BMC Genomics 2023; 24:302. [PMID: 37277710 DOI: 10.1186/s12864-023-09390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND In light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated. RESULTS Using the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs. Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions. CONCLUSION Given the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease.
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Affiliation(s)
- Zicheng Li
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA.
| | - Zuoheng Wang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Zhiyuan Chen
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Heidi Voegeli
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Judith H Lichtman
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Peter Smith
- Department of Comparative Medicine, School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Ju Liu
- Medical Research Center, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, 16766 Jingshi Road, Jinan, Shandong, 250014, China
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
- Center for Perinatal Pediatric and Environmental Epidemiology, Yale University, New Haven, CT, 06510, USA
| | - Josephine Hoh
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA.
- Department of Ophthalmology and Visual Science, School of Medicine, Yale University, New Haven, CT, 06510, USA.
- Department of Applied Mathematics, Yale University, New Haven, CT, 06510, USA.
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Hsu WT, Williamson P, Khatkar MS. Identification of Genomic Signatures in Bullmastiff Dogs Using Composite Selection Signals Analysis of 23 Purebred Clades. Animals (Basel) 2023; 13:ani13071149. [PMID: 37048405 PMCID: PMC10093657 DOI: 10.3390/ani13071149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Dog breeds represent canine sub-populations with distinctive phenotypic features and limited genetic diversity. We have established a resource to study breed-specific genetic diversity. Utilising genetic resources within our laboratory biobank, public domain genotype data and the phylogenetic framework of 23 breed clades, the primary objective for this study was to identify genomic regions that differentiate the Bullmastiff breed. Through application of a composite index analysis (CSS), genomic signatures were identified in Bullmastiffs when compared to the formative breeds, Mastiffs and Bulldogs, and to 22 other breed groups. Significant regions were identified on 15 chromosomes, with the most differentiated regions found on CFA1, CFA9, and CFA18. These regions may reflect genetic drift following establishment of the breed or the effects of selective breeding during development of the modern Bullmastiff. This was supported by analysis of genes from the identified genomic regions, including 458 genes from the multi-clade analysis, which revealed enriched pathways that may be related to characteristic traits and distinct morphology of the breed. The study demonstrates the utility of the CSS method in breed-specific genome analysis and advances our understanding of genetic diversity in Bullmastiff dogs.
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Affiliation(s)
- Wei-Tse Hsu
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Peter Williamson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mehar Singh Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Roseworthy, SA 5371, Australia
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