1
|
Sahu BP, Das SP, Swain SK, Gadnayak A, Sahoo N, Nayak D. Complete mitogenome sequence analysis of an Indian Black Bengal goat, Capra hircus, and its phylogenetic consequences. 3 Biotech 2024; 14:143. [PMID: 38706930 PMCID: PMC11063009 DOI: 10.1007/s13205-024-03993-w] [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: 04/07/2022] [Accepted: 02/22/2024] [Indexed: 05/07/2024] Open
Abstract
Capra hircus (Black Bengal goat) is a prized goat breed reared across the Southeast Asian region. Known for its excellent chevon quality and adaptability to hot and humid climates, it supports the livelihood of millions of farmers. The present study reveals the complete mitogenome of a Black Bengal goat of Indian origin utilizing a next-generation sequencing approach (GenBank acc. no.-MZ073671). This newly assembled whole mitochondrial genome (16,637 bp) is composed of a non-coding control region (D-loop region), two ribosomal RNA (rRNA genes), 13 protein-coding genes, and 22 transfer RNA (tRNA). Overall, the current mitogenome shares 99.77% sequence homology with previously reported mitogenomes of Capra hircus. The phylogenetic analysis inferred that the current mitogenome shares a close relationship with the Teressa goat breed of the Andaman and Nicobar Islands.
Collapse
Affiliation(s)
- Basanta Pravas Sahu
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol 453552 India
| | - Sofia Priyadarsani Das
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Noida, India
| | - Subrat Kumar Swain
- IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, 751003 India
| | - Ayushman Gadnayak
- IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Kalinga Nagar, Bhubaneswar, 751003 India
| | - Niranjana Sahoo
- Department of Epidemiology and Preventive Medicine, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Debasis Nayak
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066 India
| |
Collapse
|
2
|
Li S, Jian Y, Zhang K, Li X, Wang R, Zhang L, Jian F. Host specific Eimeria genus diagnosis and qPCR development in Ovis aries and Capra hircus. J Microbiol Methods 2024; 220:106910. [PMID: 38452905 DOI: 10.1016/j.mimet.2024.106910] [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] [Received: 11/06/2022] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
The objective of the present study was to develop a real-time PCR (qPCR) technique for the diagnosis of Eimeria spp. in Ovis aries and Capra hircus. The qPCR technique was developed using SYBR Green, resulting in a PCR with high sensitivity, specificity, and reproducibility.
Collapse
Affiliation(s)
- Shijie Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yichen Jian
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Kaihui Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Rongjun Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fuchun Jian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| |
Collapse
|
3
|
Kirgiafini D, Kyrgiafini MA, Gournaris T, Mamuris Z. Understanding Circular RNAs in Health, Welfare, and Productive Traits of Cattle, Goats, and Sheep. Animals (Basel) 2024; 14:733. [PMID: 38473119 DOI: 10.3390/ani14050733] [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: 01/10/2024] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Circular RNAs (circRNAs) are unique noncoding RNA molecules, notable for their covalent closed-loop structures, which play a crucial role in regulating gene expression across a variety of biological processes. This review comprehensively synthesizes the existing knowledge of circRNAs in three key livestock species: Bos taurus (cattle), Ovis aries (sheep), and Capra hircus (goats). It focuses on their functional importance and emerging potential as biomarkers for disease detection, stress response, and overall physiological health. Specifically, it delves into the expression and functionality of circRNAs in these species, paying special attention to traits critical to livestock productivity such as milk production, meat quality, muscle development, wool production, immune responses, etc. We also address the current challenges faced in circRNA research, including the need for standardized methodologies and broader studies. By providing insights into the molecular mechanisms regulated by circRNAs, this review underscores their scientific and economic relevance in the livestock industry. The potential of circRNAs to improve animal health management and the quality of animal-derived products aligns with growing consumer concerns for animal welfare and sustainability. Thus, this paper aims to guide future research directions while supporting the development of innovative strategies in livestock management and breeding.
Collapse
Affiliation(s)
- Dimitra Kirgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
- Institute of Animal Genetic Improvement, University Center for Research and Innovation PA.K.E.K. "IASON", University of Thessaly, 38221 Volos, Greece
| | - Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
- Institute of Animal Genetic Improvement, University Center for Research and Innovation PA.K.E.K. "IASON", University of Thessaly, 38221 Volos, Greece
- Averofeio Agri-Food Technological Park of Thessaly, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Theocharis Gournaris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
- Institute of Animal Genetic Improvement, University Center for Research and Innovation PA.K.E.K. "IASON", University of Thessaly, 38221 Volos, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
- Institute of Animal Genetic Improvement, University Center for Research and Innovation PA.K.E.K. "IASON", University of Thessaly, 38221 Volos, Greece
- Averofeio Agri-Food Technological Park of Thessaly, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| |
Collapse
|
4
|
Cooke DM, Clarke C, Kerr TJ, Warren RM, Witte C, Miller MA, Goosen WJ. Detection of Mycobacterium bovis in nasal swabs from communal goats ( Capra hircus) in rural KwaZulu-Natal, South Africa. Front Microbiol 2024; 15:1349163. [PMID: 38419629 PMCID: PMC10899470 DOI: 10.3389/fmicb.2024.1349163] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Animal tuberculosis, caused by Mycobacterium bovis, presents a significant threat to both livestock industries and public health. Mycobacterium bovis tests rely on detecting antigen specific immune responses, which can be influenced by exposure to non-tuberculous mycobacteria, test technique, and duration and severity of infection. Despite advancements in direct M. bovis detection, mycobacterial culture remains the primary diagnostic standard. Recent efforts have explored culture-independent PCR-based methods for identifying mycobacterial DNA in respiratory samples. This study aimed to detect M. bovis in nasal swabs from goats (Capra hircus) cohabiting with M. bovis-infected cattle in KwaZulu-Natal, South Africa. Nasal swabs were collected from 137 communal goats exposed to M. bovis-positive cattle and 20 goats from a commercial dairy herd without M. bovis history. Swabs were divided into three aliquots for analysis. The first underwent GeneXpert® MTB/RIF Ultra assay (Ultra) screening. DNA from the second underwent mycobacterial genus-specific PCR and Sanger sequencing, while the third underwent mycobacterial culture followed by PCR and sequencing. Deep sequencing identified M. bovis DNA in selected Ultra-positive swabs, confirmed by region-of-difference (RD) PCR. Despite no other evidence of M. bovis infection, viable M. bovis was cultured from three communal goat swabs, confirmed by PCR and sequencing. Deep sequencing of DNA directly from swabs identified M. bovis in the same culture-positive swabs and eight additional communal goats. No M. bovis was found in commercial dairy goats, but various NTM species were detected. This highlights the risk of M. bovis exposure or infection in goats sharing pastures with infected cattle. Rapid Ultra screening shows promise for selecting goats for further M. bovis testing. These techniques may enhance M. bovis detection in paucibacillary samples and serve as valuable research tools.
Collapse
Affiliation(s)
- Deborah M. Cooke
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Charlene Clarke
- Faculty of Natural and Agricultural Sciences, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Tanya J. Kerr
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Carmel Witte
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
- The Center for Wildlife Studies, South Freeport, ME, United States
| | - Michele A. Miller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Wynand J. Goosen
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
5
|
Vlaic BA, Vlaic A, Russo IR, Colli L, Bruford MW, Odagiu A, Orozco-terWengel P. Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data. Animals (Basel) 2024; 14:560. [PMID: 38396528 PMCID: PMC10886219 DOI: 10.3390/ani14040560] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.
Collapse
Affiliation(s)
- Bogdan Alin Vlaic
- Department of Animal Breeding, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania;
| | - Augustin Vlaic
- Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania;
| | - Isa-Rita Russo
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti (DIANA), BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense n. 84, 29122 Piacenza, PC, Italy;
| | - Michael William Bruford
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | - Antonia Odagiu
- Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | | |
Collapse
|
6
|
Badjibassa A, Ouédraogo D, Burger PA, Rosen BD, Van Tassell CP, Sölkner J, Soudré A. Participatory investigation of goat farmers' breeding practices, trait preference, and selection criteria in Burkina Faso. Trop Anim Health Prod 2024; 56:35. [PMID: 38189997 DOI: 10.1007/s11250-023-03869-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024]
Abstract
The community-based breeding program (CBBP) is an innovative approach recommended for genetic improvement and sustainable use of animal genetic resources in extensive farming systems. Successful implementation of this approach requires an understanding of the characteristics of production systems, breeding objectives, and farmers' trait preference. This study aimed to identify the selection criteria of goat farmers in rural areas of Burkina Faso and their potential implications in establishing CBBP. Following focus group discussions, a well-structured questionnaire was designed and administered to 372 randomly selected goat farmers in two different agro-ecological zones. A list of traits obtained during focus group discussions was provided to farmers individually, and they were asked to rank the ones they preferentially use to select breeding animals. Statistical tests were conducted to compare data between the two agro-ecological zones. The results showed that the average goat flock per household was higher (P < 0.05) in the Sudanian (15.68 ± 13.76), compared to the Sudano-Sahelian area (12.93 ± 13.3). Adult females were the dominant age-sex group in both areas. Reasons for culling, keeping breeding bucks, and castration practice were significantly different (P < 0.05) among agro-ecological zones. The most important common criterion for selection in the two zones was body size, coat color, and growth rate for the bucks and does, while fertility (0.06) parameters including twining ability (0.18), kidding frequency (0.11), and mothering ability (0.15) were furthermore considered for breeding does selection. These findings provide valuable insights for developing CBBPs tailored to goat production in the study areas.
Collapse
Affiliation(s)
- Akounda Badjibassa
- Unité de Formation et de Recherches Sciences et Technologie, Université Norbert ZONGO, BP 376, Koudougou, Burkina Faso
| | - Dominique Ouédraogo
- Centre Universitaire de Ziniaré, Université Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Benjamin D Rosen
- United States Department of Agriculture, Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - Curtis P Van Tassell
- United States Department of Agriculture, Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor-Mendel Strasse, 1180, Vienna, Austria
| | - Albert Soudré
- Unité de Formation et de Recherches Sciences et Technologie, Université Norbert ZONGO, BP 376, Koudougou, Burkina Faso.
| |
Collapse
|
7
|
Vijh RK, Sharma U, Kapoor P, Raheja M, Arora R, Ahlawat S, Dureja V. Design and validation of high-density SNP array of goats and population stratification of Indian goat breeds. Gene 2023; 885:147691. [PMID: 37544337 DOI: 10.1016/j.gene.2023.147691] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/06/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Goats are the supporting pillars of rural economy contributing significantly to meat and milk production in India. It is a species targeted for fulfilling the interdependent goals of poverty reduction and creation of employment for supporting the rural income. The increased demand for goat products necessitates their genetic characterization and improvement to augment the production of native breeds. Bi-allelic, genome wide, densely placed single nucleotide polymorphism (SNP) markers are most suitable for this purpose. This paper describes the design and validation of an Affymetrix Axiom-based high-density (HD) SNP chip for goats. The array was designed using a panel of 225 samples from 15 diverse goat breeds of India. In total, more than 38 million high quality SNPs were subjected to stringent filtering and 626,975 SNPs were finally tiled on the array. The average coverage of SNPs in our chip is one SNP per four kilobase (kb), providing a denser coverage of the goat genome than previously available arrays. The HD chip (Axiom_Cahi) was validated by genotyping 443 samples from 26 indigenous goat breeds/populations. The results revealed 95.83% markers to be highly informative and polymorphic in Indian goats. Multivariate analysis indicated population structuring, as 15 breeds could be segregated using the designed array. Phylogenetic analysis suggested stratification of breeds by geographic proximity. This HD SNP chip for goats is a valuable resource for genomic selection, genome wide association as well as population genetic studies in goats.
Collapse
Affiliation(s)
- Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Prerna Kapoor
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Meenal Raheja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Vandana Dureja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| |
Collapse
|
8
|
Chen Z, Cao J, Zhao F, He Z, Sun H, Wang J, Liu X, Li S. Identification of the Keratin-Associated Protein 22-2 Gene in the Capra hircus and Association of Its Variation with Cashmere Traits. Animals (Basel) 2023; 13:2806. [PMID: 37685070 PMCID: PMC10487131 DOI: 10.3390/ani13172806] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The Cashmere goat is an excellent local goat breed in Gansu Province of China, and it is expected to improve cashmere production and cashmere quality through selection and breeding to enhance its commercial value. Keratin-associated proteins (KAPs) play an important role in maintaining wool structure. The gene encoding the keratin-associated protein 22-2 (KAP22-2) gene has been identified in selected species other than goats, such as humans, mice, and sheep. In this study, the sequence of the sheep KAP22-2 gene (KRTAP22-2) was aligned into the goat genome, and the sequence with the highest homology was assumed to be the goat KRTAP22-2 sequence and used to design primers to amplify the goat gene sequence. A total of 356 Longdong Cashmere goats (Gansu Province, China) were used for screening of genetic variants. Four specific bands were detected by polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) analysis, and they formed a total of six band types individually or in combination. Four alleles were identified by DNA sequencing of PCR amplification products. A total of four single nucleotide polymorphic sites (SNPs) were detected in the four sequenced KRTAP22-2 alleles. Two of them are in the 5'UTR region and the other two are in the coding region, and the variants in the coding region are all non-synonymous mutations. In addition, there was a 6 bp length variation in allele C. The gene was expressed in the cortical layer of primary and secondary hair follicles, the inner root sheath, as well as hair papillae and hair maternal cells in goats. The results of the correlation analysis between genotypes and cashmere traits showed that after excluding genotypes with a gene frequency of less than 5%, the mean fiber diameter (MFD) of cashmere was significantly higher in the AB genotype than in the AA and AC genotypes. That is, the KRTAP22-2 gene variants are associated with mean fiber diameter in cashmere. The above results suggest that the goat KRTAP22-2 variant can be utilized as a molecular marker candidate gene for cashmere traits.
Collapse
Affiliation(s)
- Zhanzhao Chen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Jian Cao
- Faculty of Bioengineering, Jiuquan Vocational Technical College, Jiuquan 735000, China;
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Zhaohua He
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Hongxian Sun
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (J.W.); (X.L.)
| |
Collapse
|
9
|
Jeanjean M, McGrath K, Valenzuela-Lamas S, Nieto-Espinet A, Schafberg R, Parés-Casanova PM, Jiménez-Manchón S, Guintard C, Tekkouk F, Ridouh R, Mureau C, Evin A. ZooMS confirms geometric morphometrics species identification of ancient sheep and goat. R Soc Open Sci 2023; 10:230672. [PMID: 37771960 PMCID: PMC10523075 DOI: 10.1098/rsos.230672] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
Geometric morphometrics can effectively distinguish isolated third lower molars of present-day sheep and goat, but its applicability to archaeological specimens has yet to be established. Using a modern reference collection of 743 sheep and goats and a two-dimensional landmark-based geometric morphometric (GMM) protocol, this study aimed to morphometrically identify 109 archaeological specimens, used as case studies, dating from the Late Neolithic to the modern period/era. These morphometric identifications were then compared to molecular identifications via collagen peptide mass fingerprinting, known as Zooarcheology by Mass Spectrometry (ZooMS). ZooMS confirmed the morphometric identifications for 104 specimens, with the five misidentified specimens all morphometrically identified as goat. Modern sheep and goats have larger teeth and distinct shapes compared to their archaeological counterparts, suggesting strong differences between archaeological and modern specimens potentially linked with recent breed improvement or geographical origin of the specimens. In addition, for both species, some of the archaeological dental morphologies do not match with any of our modern references. This study validates the applicability of geometric morphometrics for identifying isolated archaeological sheep and goat teeth. It represents a stepping stone for future, non-destructive, bioarchaeological studies of the two species.
Collapse
Affiliation(s)
- Marine Jeanjean
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Krista McGrath
- Department of Prehistory & Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals de Recerca en Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), C/ Egipcíaques 15, 08001 Barcelona, Spain
| | - Ariadna Nieto-Espinet
- Grup d'Investigació Prehistòrica (GIP), Departament d'Història, Universidad de Lleida, 25005 Lleida, Spain
| | - Renate Schafberg
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | | | - Sergio Jiménez-Manchón
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals de Recerca en Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), C/ Egipcíaques 15, 08001 Barcelona, Spain
| | - Claude Guintard
- Laboratoire d'Anatomie comparée, Ecole Nationale Vétérinaire, de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique – ONIRIS, Nantes Cedex 03, France
- GEROM, UPRES EA 4658, LABCOM ANR NEXTBONE, Faculté de santé de l'Université d'Angers, Angers, France
| | - Faiza Tekkouk
- Institut des Sciences Vétérinaires, Laboratoire « Gestion de la santé et productions animales », Université des frères Mentouri, El Khroub, Algérie
| | - Rania Ridouh
- Institut des Sciences Vétérinaires, Laboratoire « Gestion de la santé et productions animales », Université des frères Mentouri, El Khroub, Algérie
| | - Cyprien Mureau
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Allowen Evin
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| |
Collapse
|
10
|
Shair MA, Hassan-Kadle AA, Osman AM, Ahmed KMY, Yusuf AA, Barros-Filho IR, Vieira RFC. Indigestible foreign bodies in the forestomach of slaughtered goats in Mogadishu, Somalia. Vet World 2023; 16:1829-1832. [PMID: 37859955 PMCID: PMC10583886 DOI: 10.14202/vetworld.2023.1829-1832] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 10/21/2023] Open
Abstract
Background and Aim The primary domestic animal in Somali communities is the goat. Their main economic importance is as a food source and a main form of agriculture in the country. There has been a recent decline in the goat population in Somalia, which may be due to the shortage of feed and an increasingly contaminated environment that is affecting the population's food supply and nutritional status. This study aimed to estimate the prevalence and the factors associated with indigestible foreign bodies (IFBs) ingestion in goats in Mogadishu, Somalia. Materials and Methods A cross-sectional study was conducted at the Somalia Meat Company in Mogadishu, Somalia, in February 2022. A total of 250 goats were included in this study, and records were kept on age, sex, body condition, and location. Following the slaughter, goats were inspected for IFBs, and their stomach compartments were incised and examined. Indigestible foreign body classifications was noted and subjected to analysis using the Statistical Package for the Social Sciences version 26.0. Results A total of 90/250 (36%; 95% confidence interval [CI]: 30.1-42.3) goats presented IFBs, being 71/90 (79%; 95% CI: 69-87) in the rumen, 12/90 (13%; 95% CI: 7-22) in the reticulum, and seven/90 (8%; 95% CI: 3-15) on both. The most observed IFBs were plastic in 71/90 (79%; 95% CI: 69-87), followed by ropes in eight/90 (10%; 95% CI: 5-18). A high IFB prevalence was observed in goats aged >2-≤3 years (44%), followed by >3 years (36%). The lowest frequency was observed in goats aged <2 years (30%). Overall, there was an association between IFBs in goats and poor body conditions (χ2 = 47%, p < 0.04). Conclusion The absence of a plastic waste disposal system in the area, and communal free-grazing of livestock in highly contaminated sites, appeared to be significant contributors to the high occurrence of IFBs in goats. Therefore, appropriate policies for solid waste management should be implemented.
Collapse
Affiliation(s)
- Mohamed A. Shair
- Graduate Program on Veterinary Sciences, Department of Veterinary Medicine, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Abrar Research and Training Center, Abrar University, Mogadishu, Somalia
| | - Ahmed A. Hassan-Kadle
- Graduate Program on Veterinary Sciences, Department of Veterinary Medicine, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Abrar Research and Training Center, Abrar University, Mogadishu, Somalia
- Somali One Health Center, Abrar University, Mogadishu, Somalia
| | - Aamir M. Osman
- Graduate Program on Veterinary Sciences, Department of Veterinary Medicine, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Somali One Health Center, Abrar University, Mogadishu, Somalia
- Department of Animal Health and Veterinary Services, Ministry of Livestock, Forestry, and Range, Mogadishu, Somalia
| | - Kaltumo M. Y. Ahmed
- Graduate Program on Veterinary Sciences, Department of Veterinary Medicine, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Abdulkarim A. Yusuf
- Abrar Research and Training Center, Abrar University, Mogadishu, Somalia
- Department of Slaughterhouses, Somali Meat Company, Mogadishu, Somalia
| | - Ivan R. Barros-Filho
- Graduate Program on Veterinary Sciences, Department of Veterinary Medicine, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rafael F. C. Vieira
- Department of Public Health Sciences, University of North Carolina at Charlotte, Charlotte, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, USA
| |
Collapse
|
11
|
Kawamoto Y, Honda G, Ome Y, Matsunaga Y, Uemura S, Yoshida N, Kotera Y, Ariizumi S. Laparoscopic left hepatectomy in a goat as a training model for laparoscopic anatomic liver resection: results of training courses with a total of 70 goats. Surg Endosc 2023; 37:3634-3641. [PMID: 36627539 DOI: 10.1007/s00464-023-09864-4] [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: 10/10/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
BACKGROUND To create a suitable animal model for the training of laparoscopic anatomic liver resection, we performed left hepatectomy using a goat and found its suitability. We have since started using goats for wet-lab training and have gradually standardized the relevant procedures. Herein, we report our standardized training procedures using a goat and discuss its feasibility as a novel training model. METHODS The standardized wet-lab training courses of laparoscopic liver resection conducted on 62 tables with a total of 70 goats were reviewed. The training course began by encircling the hepatoduodenal ligament for the Pringle maneuver, which was repeated during the parenchymal dissection. Following partial liver resection of the left lateral section, left hepatectomy was performed by a standardized procedure for humans in which the liver was split, exposing the entire length of the middle hepatic vein trunk from the dorsal side after extrahepatic transection of the left Glissonean pedicle. If a goat deceased before initiating left hepatectomy, the training was restarted with a new goat. The surgical procedures were performed by surgeons of varying skill levels. RESULTS A total of 184 surgeons including 10 surgical residents participated in the training. Partial liver resection was initiated in 62 tables, with 8 (13%) dying during or after the procedure of partial liver resection. Subsequently, left hepatectomy was initiated in 61 and completed in 59 tables (98%), regardless of whether the goat survived or deceased, and was not completed in 2 tables (3%) due to time limitation. In 14 tables (23%), the goats deceased during the procedure, however, the procedure was completed. The causes of death were multifactorial, including massive bleeding, reperfusion injury after the Pringle maneuver, and carbon dioxide gas embolism. CONCLUSIONS Left hepatectomy in a goat is useful as a training model for laparoscopic anatomic liver resection.
Collapse
Affiliation(s)
- Yusuke Kawamoto
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| | - Goro Honda
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan.
| | - Yusuke Ome
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| | - Yutaro Matsunaga
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| | - Shuichiro Uemura
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| | - Naoki Yoshida
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| | - Yoshihito Kotera
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| | - Shunichi Ariizumi
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo, 162-8666, Japan
| |
Collapse
|
12
|
Costa TC, Dutra LL, Mendes TAO, Dos Santos MM, Veroneze R, Gionbelli MP, Duarte MS. Impact of Maternal Feed Restriction at Different Stages of Gestation on the Proteomic Profile of the Newborn Skeletal Muscle. Animals (Basel) 2022; 12. [PMID: 35454257 DOI: 10.3390/ani12081011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
We aimed to investigate the effects of the maternal plane of nutrition during gestation on the proteome profile of the skeletal muscle of the newborn. Pregnant goats were assigned to the following experimental treatments: restriction maintenance (RM) where pregnant dams were fed at 50% of their maintenance requirements from 8−84 days of gestation, and then feed of 100% of the maintenance requirements was supplied from 85—parturition (n = 6); maintenance restriction (MR) where pregnant dams were fed at 100% of their maintenance requirements from 8−84 days of gestation, and then experienced feed restriction of 50% of the maintenance requirements from 85—parturition (n = 8). At birth, newborns were euthanized and samples of the Longissimus dorsi muscle were collected and used to perform HPLC-MS/MS analysis. The network analyses were performed to identify the biological processes and KEGG pathways of the proteins identified as differentially abundant protein and were deemed significant when the adjusted p-value (FDR) < 0.05. Our results suggest that treatment RM affects the energy metabolism of newborns’ skeletal muscle by changing the energy-investment phase of glycolysis, in addition to utilizing glycogen as a carbon source. Moreover, the RM plane of nutrition may contribute to fatty acid oxidation and increases in the cytosolic α-KG and mitochondrial NADH levels in the skeletal muscle of the newborn. On the other hand, treatment MR likely affects the energy-generation phase of glycolysis, contributing to the accumulation of mitochondrial α-KG and the biosynthesis of glutamine.
Collapse
|
13
|
Jiang A, Ankersmit-Udy A, Turner SA, Scholtens M, Littlejohn MD, Lopez-Villalobos N, Proser CG, Snell RG, Lehnert K. A Capra hircus chromosome 19 locus linked to milk production influences mammary conformation. J Anim Sci Biotechnol 2022; 13:4. [PMID: 35144696 PMCID: PMC8832686 DOI: 10.1186/s40104-021-00667-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background Economically important milk production traits including milk volume, milk fat and protein yield vary considerably across dairy goats in New Zealand. A significant portion of the variation is attributable to genetic variation. Discovery of genetic markers linked to milk production traits can be utilised to drive selection of high-performance animals. A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait locus (QTL) located on chromosome 19. The most significantly associated single nucleotide polymorphism (SNP) marker for this locus is located at position 26,610,610 (SNP marker rs268292132). This locus is associated with multiple milk production traits including fat, protein and volume. The predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2 kg fat, 1.9 kg protein and 73.6 kg milk yield. An outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic effects. An adverse relationship between milk production and udder health traits has been reported at this locus. Therefore, a genome wide association study was undertaken looking for loci associated with udder traits. Results The QTL and production associated marker rs268292132 was identified in this study to also be associated with several goat udder traits including udder depth (UD), fore udder attachment (FUA) and rear udder attachment (RUA). Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610 (SNP marker rs268292132) associated with an adverse change in UD, FUA and RUA. Conclusions Our study has confirmed the negative relationship between udder traits and production traits in the NZ goat population. We have found that the frequency of the high production allele is relatively high in the NZ goat population, indicating that its effect on udder conformation is not significantly detrimental on animal health. It will however be important to monitor udder conformation as the chromosome 19 locus is progressively implemented for marker assisted selection. It will also be of interest to determine if the gene underlying the production QTL has a direct effect on mammary gland morphology or whether the changes observed are a consequence of the increased milk volume. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00667-y.
Collapse
Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alex Ankersmit-Udy
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - Mathew D Littlejohn
- AL Rae Centre of Genetics and Breeding, Massey University, Hamilton, New Zealand
| | - Nicolas Lopez-Villalobos
- Dairy Cattle Breeding and Genetics, School of Agriculture & Environment, Massey University, Hamilton, New Zealand
| | | | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
14
|
Battini M, Renna M, Giammarino M, Battaglini L, Mattiello S. Feasibility and Reliability of the AWIN Welfare Assessment Protocol for Dairy Goats in Semi-extensive Farming Conditions. Front Vet Sci 2021; 8:731927. [PMID: 34746279 PMCID: PMC8566805 DOI: 10.3389/fvets.2021.731927] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to test the feasibility and reliability of the Animal Welfare Indicators (AWIN) protocol for welfare assessment of dairy goats when applied to semi-extensive farming conditions. We recruited 13 farms located in the NW Italian Alps where three assessors individually and independently applied a modified version of the AWIN welfare assessment protocol for goats integrated with some indicators derived from the AWIN welfare assessment protocol for sheep. The applied protocol consisted of nine individual-level (body condition score, hair coat condition, abscesses, overgrown claws, udder asymmetry, fecal soiling, nasal discharge, ocular discharge, and improper disbudding) and seven group-level (severe lameness, Qualitative Behavior Assessment-QBA, thermal stress, oblivion, Familiar Human Approach Test-FHAT, synchrony at grazing, synchrony at resting) animal-based indicators. On most farms, the level of welfare was good. Many of the considered welfare problems (overgrown claws, fecal soiling, discharges, and thermal stress) were never recorded. However, oblivion, severe lameness, hair coat condition and abscesses were detected on some farms, with percentages ranging from 5 to 35%. The mean percentage of animals with normal body condition was 67.9 ± 5.7. The level of synchronization during resting was on average low (14.3 ± 7.2%). The application of the whole protocol required more than 4 h/farm and 3 min/goat. The inter-observer reliability varied from excellent (udder asymmetry, overgrown claws, discharges, synchrony at resting, use of shelter) to acceptable (abscesses, fecal soiling, and oblivion), but insufficient for hair coat condition, improper disbudding, synchrony at grazing, QBA. Differences in background of the assessors and feasibility constraints (i.e., use of binoculars in unfenced pastures, individual-level assessment conducted during the morning milking in narrow and dark pens, difficulties when using the scan and instantaneous sampling method due to the high number of animals that moved at the same time) can affect the reliability of data collection. Extensive training seems necessary for properly scoring animals when applying the QBA, whereas the FHAT to evaluate the Human-Animal Relationship of goats at pasture seems promising but needs to be validated. Indicators that evaluate the synchrony of activities require to be validated to identify the best moment to perform the observations during the day.
Collapse
Affiliation(s)
- Monica Battini
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Manuela Renna
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Mauro Giammarino
- Department of Prevention, ASL TO3, Veterinary Service, Turin, Italy
| | - Luca Battaglini
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Silvana Mattiello
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| |
Collapse
|
15
|
Henkel J, Dubacher A, Bangerter E, Herren U, Ammann P, Drögemüller C, Flury C, Leeb T. Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats. J Hered 2021; 112:452-457. [PMID: 34050662 DOI: 10.1093/jhered/esab024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/18/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The Valais Blackneck goat is a Swiss goat breed with a characteristic coat color phenotype. Before the revision of the breed standard in 1938, 4 different color varieties of Valais goats were known. Besides Blackneck animals resembling the modern breed standard, the brown and white Copperneck goat, the white Capra Sempione, and the greyish Grüenochte comprised the historic Valais goats. The brown pigmentation of Copperneck goats had previously been traced back to an introgression of a mutant TYRP1 allele from Toggenburg goats. In the present study, we identified additional introgression events of distinct ASIP alleles causing the remaining 2 rare coat color patterns within the Valais Blackneck goat breed. We identified the introgression of the AWt allele from Appenzell or Saanen goats in white Capra Sempione goats. Similarly, introgression of the Apc allele from Peacock goats resulted in the greyish Grüenochte phenotype. These results demonstrate past hybridization events between breeds that are separated today. A perfect genotype-phenotype association in 393 Valais goats supported the causality of the genotyped variants for the different coat color phenotypes. Our study gives insights into the introgression of functionally relevant copy number variant (CNV) alleles controlling pigmentation between goat breeds with strikingly different coat color patterns.
Collapse
Affiliation(s)
- Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Alexandra Dubacher
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | - Ursula Herren
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| |
Collapse
|
16
|
He C, Wang Y, Xu Q, Xiong Y, Zhu J, Lin Y. Overexpression of Krueppel like factor 3 promotes subcutaneous adipocytes differentiation in goat Capra hircus. Anim Sci J 2021; 92:e13514. [PMID: 33522088 DOI: 10.1111/asj.13514] [Citation(s) in RCA: 3] [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: 06/21/2020] [Revised: 11/28/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022]
Abstract
Previous research reported that KLF3 plays different roles in the regulation of adipose deposition across species. However, the exact function of KLF3 in goat subcutaneous adipocyte remains unknown. Here, the goat KLF3 gene was firstly cloned and showed that the mRNA sequence of the goat KLF3 gene was 1,264 bp (GenBank accession number: KU041753.1) and its coding sequence was 1,037 bp, encoding 345 amino acids with three classic zinc finger domains of KLFs family at its C-terminus. The alignment of the amino acid sequence of KLF3 among various species demonstrated that goat had the highest homology to that of sheep, presenting 99.4% similarity, while the homology similarity to that of mice presented only 93.62% in contrast. Furthermore, KLF3 had highest mRNA level in fat tissue and lowest level in the heart in comparison. Additionally, the mRNA level of KLF3 gradually tended to increase during adipogenesis. Interestingly, overexpression of KLF3 increased lipid accumulation. In line with this, the gain-of-function of KLF3 dramatically elevated the mRNA levels of TG synthetic genes and adipogenic maker genes (p < .01) . Moreover, overexpression of KLF3 upregulated all the potential target genes, except for C/EBPα. These results suggested that KLF3 is a positive regulator for subcutaneous adipocyte differentiation in goats.
Collapse
Affiliation(s)
- Changsheng He
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province, Chengdu, China.,College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province, Chengdu, China.,College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Qing Xu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province, Chengdu, China.,College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province, Chengdu, China.,College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province, Chengdu, China
| | - Yaqiu Lin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province, Chengdu, China.,College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, China
| |
Collapse
|
17
|
Ferreira-Silva JC, Oliveira Silva RL, Travassos Vieira JI, Silva JB, Tavares LS, Cavalcante Silva FA, Nunes Pena EP, Chaves MS, Moura MT, Junior TC, Benko-Iseppon AM, Figueirêdo Freitas VJ, Lemos Oliveira MA. Evaluation of quality and gene expression of goat embryos produced in vivo and in vitro after cryopreservation. Cryobiology 2021; 101:115-124. [PMID: 33964298 DOI: 10.1016/j.cryobiol.2021.04.008] [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: 10/06/2020] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/26/2022]
Abstract
In the present study, we aimed to identify morphological and molecular changes of in vivo and in vitro-produced goat embryos submitted to cryopreservation. In vivo embryos were recovered by transcervical technique from superovulated goats, whereas in vitro produced embryos were produced from ovaries collected at a slaughterhouse. Embryos were frozen by two-steps slow freezing method, which is defined as freezing to -32 °C followed by transfer to liquid nitrogen. Morphological evaluation of embryos was carried out by assessing blastocoel re-expansion rate and the total number of blastomeres. The expression profile of candidate genes related to thermal and oxidative stress, apoptosis, epigenetic, and implantation control was measured using RT-qPCR based SYBR Green system. In silico analyses were performed to identify conserved genes in goat species and protein-protein interaction networks were created. In vivo-produced embryos showed greater blastocoel re-expansion and more blastomere cells (P < 0.05). The expression level of CTP2 and HSP90 genes from in vitro cryopreserved embryos was higher than their in vivo counterparts. Unlikely, no significant difference was observed in the transcription level of SOD gene between groups. The high similarity of CPT2 and HSP90 proteins to their orthologs among mammals indicates that they share conserved functions. In summary, cryopreservation negatively affects the morphology and viability of goat embryos produced in vitro and changes the CPT2 and HSP90 gene expression likely in response to the in vitro production process.
Collapse
Affiliation(s)
- José Carlos Ferreira-Silva
- Laboratory of Reproductive Biotechniques, Department of Veterinary Medicine, Federal Rural University of Pernambuco, Brazil.
| | - Roberta Lane Oliveira Silva
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Brazil.
| | - Joane Isis Travassos Vieira
- Laboratory of Reproductive Biotechniques, Department of Veterinary Medicine, Federal Rural University of Pernambuco, Brazil.
| | - Jéssica Barboza Silva
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Brazil.
| | - Lethicia Souza Tavares
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Brazil.
| | | | - Elton Pedro Nunes Pena
- Laboratory of Plant Genomics and Proteomics, Department of Genetics, Federal University of Pernambuco, Brazil.
| | - Maiana Silva Chaves
- Laboratory of Reproductive Biotechniques, Department of Veterinary Medicine, Federal Rural University of Pernambuco, Brazil. maiana-@hotmail.com
| | - Marcelo Tigre Moura
- Laboratory of Reproductive Biotechniques, Department of Veterinary Medicine, Federal Rural University of Pernambuco, Brazil.
| | - Tercilio Calsa Junior
- Laboratory of Plant Genomics and Proteomics, Department of Genetics, Federal University of Pernambuco, Brazil.
| | - Ana Maria Benko-Iseppon
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Brazil.
| | | | - Marcos Antonio Lemos Oliveira
- Laboratory of Reproductive Biotechniques, Department of Veterinary Medicine, Federal Rural University of Pernambuco, Brazil.
| |
Collapse
|
18
|
Pareja J, Espunya C, Baraza E, Bartolomé J. Complementarity between microhistological analysis and PCR-capillary electrophoresis in diet analysis of goats and cattle using faecal samples. Animal 2020; 15:100145. [PMID: 33573931 DOI: 10.1016/j.animal.2020.100145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 07/08/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
An evaluation is made of the complementarity between two non-invasive techniques, cuticle microhistological analysis (CMA) and PCR-capillary electrophoresis (PCR-CE) DNA-based analysis, for the determination of herbivore diet composition from faecal samples. Cuticle microhistological analysis is based on the different microanatomical characteristics of the epidermal fragments remaining in the faeces. The PCR-CE technique combines PCR amplification of a trnL(UAA) genomic DNA region with amplicon length determination by CE, with this length being characteristic for each species or taxon. A total of 37 fresh stool samples were analyzed, including 16 from feral goats (Capra hircus) from the Tramuntana mountain range (Mallorca, Baleares) and 11 from Bruna dels Pirineus cattle breed (Bos taurus) from the surrounding Montserrat mountain range (Barcelona, Spain). All the animals were in a free grazing Mediterranean pine habitat, dominated by Aleppo pine (Pinus halepensis). The results showed that both techniques detected a similar number of plant components in the faeces of goats and cows. In the case of goats, a positive correlation was obtained between the percentage of samples in which a particular taxon is detected by CMA and the percentage of samples in which that taxon is detected by PCR-CE. This correlation was not observed in the case of cows. It is concluded that PCR-CE is a fast and reliable method to detect the different plant components in the faeces of herbivores. However, it cannot be considered as an alternative to CMA, but as a complementary method, since both techniques can detect some taxa that are not detected by the other technique. In addition, CMA detected the presence of the different taxa in a greater number of samples, and at the same time, it enables quantitative data to be obtained for plant diet composition. The species of herbivore also seems to influence the results obtained by PCR-CE, so more studies are required to address this aspect.
Collapse
Affiliation(s)
- J Pareja
- Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - C Espunya
- Independent researcher, 08290 Cerdanyola del Vallès, Spain
| | - E Baraza
- Department of Biology, Universidad de las Islas Baleares, 07122 Palma de Mallorca, Mallorca, Spain
| | - J Bartolomé
- Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| |
Collapse
|
19
|
Martonos CO, Gudea A, Damian A, Lăcătuș R, Purdoiu R, Cocan D, Stan FG. Morphological and morphometrical aspects of the auditory ossicles in goat ( Capra hircus). Anat Histol Embryol 2020; 50:184-191. [PMID: 32946143 DOI: 10.1111/ahe.12617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/21/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 11/27/2022]
Abstract
The present paper deals with a detailed description of the auditory ossicles in Capra hircus. The paper focuses on the morphological and morphometrical description of the ossicular assembly, formed by malleus, incus and stapes. The malleus (overall length, as average- 8.16 mm) comprises the head of malleus (Caput mallei), a slightly strictured part-neck (Collum mallei) with 3 distinctive processes (lateral, rostral and muscular) (Processus lateralis, Processus rostralis and Processus muscularis) and a handle (Manubrium mallei). The head of malleus has an oval aspect with an obtuse articular surface on its medial surface (Facies articularis). The neck is evident with three bony processes described-the anterior, almost triangular, the muscular one quite reduced and the lateral one which is the most developed one. The manubrium is the longest sector-4.4 mm and appears as a slightly curved piece. The incus presents a body of 1.3 mm and two processes-the short and long crus (Crus breve and Crus longum). The overall shape of the ossicle resembles a biradicular molar. The lenticular process is a continuation of the distal part of the long crus. The stapes-the smallest in size of the three ossicles (2.7 mm), has a head (Caput stapedis), an anterior (Crus rostrale) and a caudal (Crus caudale) arm and a footplate (Basis stapedis). The two processes are slightly different in size and morphology, delimiting the intercrural space that shows the presence of a bony spicule. The footplate (1.6 mm2 area) is ellipsoidal, with an anterior narrower extremity.
Collapse
Affiliation(s)
- Cristian Olimpiu Martonos
- Department of Anatomy, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Alexandru Gudea
- Department of Anatomy, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Aurel Damian
- Department of Anatomy, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Radu Lăcătuș
- Department of Radiology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Robert Purdoiu
- Department of Radiology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Daniel Cocan
- Department of Physiology, Faculty of Zootechnics and Biotechnology, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Florin Gheorghe Stan
- Department of Anatomy, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| |
Collapse
|
20
|
Gao J, Lyu Y, Zhang D, Reddi KK, Sun F, Yi J, Liu C, Li H, Yao H, Dai J, Xu F. Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat ( Capra hircus). Front Genet 2020; 11:901. [PMID: 32973871 PMCID: PMC7472782 DOI: 10.3389/fgene.2020.00901] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/21/2020] [Indexed: 12/23/2022] Open
Abstract
The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide FST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.
Collapse
Affiliation(s)
- Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Yuhua Lyu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Defu Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Kiran Kumar Reddi
- Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Fengping Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianzhong Yi
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chengqian Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong Li
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huijuan Yao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Fuyi Xu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| |
Collapse
|
21
|
Aguirre-Riofrio L, Maza-Tandazo T, Quezada-Padilla M, Albito-Balcazar O, Flores-Gonzalez A, Camacho-Enriquez O, Martinez-Martinez A, Consortium B, Delgado-Bermejo JV. Genetic Characterization of the "Chusca Lojana", a Creole Goat Reared in Ecuador, and Its Relationship with Other Goat Breeds. Animals (Basel) 2020; 10:E1026. [PMID: 32545665 DOI: 10.3390/ani10061026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022] Open
Abstract
The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named "Chusca Lojana", has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species' genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an FIS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: FIS = 0.087, FIT = 0.176, and FST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (FST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected.
Collapse
|
22
|
Liu K, Jin Y, Zhang FY, Zhang YZ, Quan XQ, Han QD, Liu LX, Liu YG, Lv SJ, Qu XM. The complete mitochondrial DNA sequence of Yimeng black goat ( Capra hircus) and its potential application in mutton discrimination. Mitochondrial DNA B Resour 2020; 5:2303-2305. [PMID: 33457768 PMCID: PMC7782185 DOI: 10.1080/23802359.2020.1773337] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Yimeng black goat is one of the national breeds of geographical indication in China and is one of the key protected local livestock and poultry breeds of Shandong province. The complete mitochondrial genome sequence of Yimeng black goat was investigated in this study (GenBank accession no. MT134111). The mitogenome (16,640 bp) consisted of a non-coding control region (D-loop region), two ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and 22 transfer RNA (tRNA) genes. The complete mitochondrial genome sequence and the neighbour-joining tree of the Yimeng black goat would contribute to further study in genetic mechanism and phylogenomic research of goats.
Collapse
Affiliation(s)
- Ke Liu
- College of Life Sciences and Technology, Xinjiang University, Urumqi, China.,College of Life Sciences, Linyi University, Linyi, China
| | - Ying Jin
- Qingdao Customs District P.R. China, Qingdao, China
| | - Feng-Yan Zhang
- Qingdao Institute for Food and Drug Control, Qingdao, China
| | - Yan-Zhen Zhang
- College of Life Sciences and Technology, Xinjiang University, Urumqi, China.,College of Life Sciences, Linyi University, Linyi, China
| | - Xian-Qing Quan
- College of Life Sciences, Linyi University, Linyi, China
| | - Qing-Dian Han
- College of Life Sciences, Linyi University, Linyi, China
| | - Ling-Xiao Liu
- Linyi Academy of Agricultural Sciences, Linyi, China
| | - Yun-Guo Liu
- College of Life Sciences, Linyi University, Linyi, China
| | - Shen-Jin Lv
- College of Life Sciences, Linyi University, Linyi, China
| | - Xiao-Ming Qu
- Liaoning Center for Disease Control and Prevention, Shenyang, China
| |
Collapse
|
23
|
Ceccobelli S, Lasagna E, Demir E, Rovelli G, Albertini E, Veronesi F, Sarti FM, Rosellini D. Molecular Identification of the "Facciuta Della Valnerina" Local Goat Population Reared in the Umbria Region, Italy. Animals (Basel) 2020; 10:E601. [PMID: 32244771 PMCID: PMC7222817 DOI: 10.3390/ani10040601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 11/17/2022] Open
Abstract
Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local goat population of Italy, compared with the cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. A total of 116 microsatellite alleles ranging from 4 to 13 were detected at 16 loci in the three goat populations/breeds. A total of 23 private alleles with frequencies lower than 0.3 were detected in the Facciuta della Valnerina population. The mean numbers of alleles were 6.67, 4.58, and 4.92 in Facciuta della Valnerina, Camosciata delle Alpi, and Saanen, respectively. The expected heterozygosity ranged from 0.20 to 0.86. Most loci were highly polymorphic and informative (polymorphic information content ≥0.50). Factorial correspondence analysis and principal components analysis revealed very clear separation between Facciuta della Valnerina and the two reference goat breeds. Reducing the number of markers from 16 to 12 (on the basis of polymorphic information content and the number of alleles) still allowed us to distinguish the local population, indicating that microsatellite markers are capable of discriminating local livestock breeds at a low cost.
Collapse
Affiliation(s)
- Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| | - Eymen Demir
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, 07058, Turkey
| | - Giacomo Rovelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| | - Fabio Veronesi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| | - Daniele Rosellini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX giugno 74, 06121, Italy; (S.C.); (E.D.); (G.R.); (E.A.); (F.V.); (D.R.)
| |
Collapse
|
24
|
Simon R, Lischer HEL, Pieńkowska-Schelling A, Keller I, Häfliger IM, Letko A, Schelling C, Lühken G, Drögemüller C. New genomic features of the polled intersex syndrome variant in goats unraveled by long-read whole-genome sequencing. Anim Genet 2020; 51:439-448. [PMID: 32060960 DOI: 10.1111/age.12918] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/03/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 01/19/2023]
Abstract
In domestic goats, the polled intersex syndrome (PIS) refers to XX female-to-male sex reversal associated with the absence of horn growth (polled). The causal variant was previously reported as a 11.7 kb deletion at approximately 129 Mb on chromosome 1 that affects the transcription of both FOXL2 and several long non-coding RNAs. In the meantime the presence of different versions of the PIS deletion was postulated and trials to establish genetic testing with the existing molecular genetic information failed. Therefore, we revisited this variant by long-read whole-genome sequencing of two genetically female (XX) goats, a PIS-affected and a horned control. This revealed the presence of a more complex structural variant consisting of a deletion with a total length of 10 159 bp and an inversely inserted approximately 480 kb-sized duplicated segment of a region located approximately 21 Mb further downstream on chromosome 1 containing two genes, KCNJ15 and ERG. Publicly available short-read whole-genome sequencing data, Sanger sequencing of the breakpoints and FISH using BAC clones corresponding to both involved genome regions confirmed this structural variant. A diagnostic PCR was developed for simultaneous genotyping of carriers for this variant and determination of their genetic sex. We showed that the variant allele was present in all 334 genotyped polled goats of diverse breeds and that all analyzed 15 PIS-affected XX goats were homozygous. Our findings enable for the first time a precise genetic diagnosis for polledness and PIS in goats and add a further genomic feature to the complexity of the PIS phenomenon.
Collapse
Affiliation(s)
- R Simon
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - H E L Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, 3001, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - A Pieńkowska-Schelling
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland.,Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - I Keller
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.,Department for BioMedical Research, University of Bern, Bern, 3001, Switzerland
| | - I M Häfliger
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - A Letko
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - G Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - C Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| |
Collapse
|
25
|
Saif R, Henkel J, Jagannathan V, Drögemüller C, Flury C, Leeb T. The LCORL Locus is under Selection in Large-Sized Pakistani Goat Breeds. Genes (Basel) 2020; 11:genes11020168. [PMID: 32033434 PMCID: PMC7074466 DOI: 10.3390/genes11020168] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Goat domestication and human selection for valued traits have formed diverse breeds with characteristic phenotypes. This process led to the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity-so-called "selection signatures". We previously reported an analysis of selection signatures based on pooled whole-genome sequencing data of 20 goat breeds and bezoar goats. In the present study, we reanalyzed the data and focused on a subset of eight Pakistani goat breeds (Angora, Barbari, Beetal, Dera Din Panah, Kamori, Nachi, Pahari, Teddy). We identified 749 selection signatures based on reduced heterozygosity in these breeds. A search for signatures that are shared across large-sized goat breeds revealed that five medium-to-large-sized Pakistani goat breeds had a common selection signature on chromosome 6 in a region harboring the LCORL gene, which has been shown to modulate height or body size in several mammalian species. Fine-mapping of the region confirmed that all five goat breeds with the selection signature were nearly fixed for the same haplotype in a ~191 kb region spanning positions 37,747,447-37,938,449. From the pool sequencing data, we identified a frame-shifting single base insertion into an isoform-specific exon of LCORL as a potential candidate causal variant mediating the size-increasing effect. If this preliminary result can be confirmed in independent replication studies, genotyping of this variant might be used to improve breeding programs and the selection for stature in goats.
Collapse
Affiliation(s)
- Rashid Saif
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (R.S.); (J.H.); (V.J.); (C.D.)
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore 54000, Pakistan
| | - Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (R.S.); (J.H.); (V.J.); (C.D.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (R.S.); (J.H.); (V.J.); (C.D.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (R.S.); (J.H.); (V.J.); (C.D.)
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland;
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (R.S.); (J.H.); (V.J.); (C.D.)
- Correspondence: ; Tel.: +41-31-631-23-26
| |
Collapse
|
26
|
Berihulay H, Li Y, Gebrekidan B, Gebreselassie G, Liu X, Jiang L, Ma Y. Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations. Front Genet 2019; 10:1190. [PMID: 31850061 PMCID: PMC6892828 DOI: 10.3389/fgene.2019.01190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
Ethiopia is considered as the main gateway for the introduction of livestock species, including goat, to the African continent. Ethiopian goats are characterized by their unique adaptive ability, and different physical characteristics in terms of morphology, body size, coat colors, and other important traits. The comparative population genomic analysis provides useful genomic information associated with important traits. Whole-genome resequencing of 44 Ethiopian indigenous goats produced 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. Specifically, 11,137,576, 10,760,581, 10,833,847, 12,229,657 and 10,749,996 putative SNPs were detected in Abergelle, Afar, Begait, Central Highland and Meafure goat populations, respectively. In this study, we used population differentiation (FST) and pooled heterozygosity (HP) Cbased approaches. From the FST analysis, we identified 480 outlier windows. The HP approach detected 108 and 205 outlier windows for Abergelle, and Begait, respectively. About 11 and 5 genes under selective signals were common for both approaches that were associated with important traits. After genome annotation, we found 41 Gene ontology (GO) terms (12 in biological processes, 8 in cellular components and 11 in the molecular function) and 10 Kyoto Encyclopedia of Genes and Genomes pathways. Several of the candidate genes are involved in the reproduction, body weight, fatty acids, and disease related traits. Our investigation contributes to deliver valuable genetic information and paves the way to design conservation strategy, breed management, genetic improvement, and utilization programs. The genomic resources generated in the study will offer an opportunity for further investigations.
Collapse
Affiliation(s)
- Haile Berihulay
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Veterinary Science, Mekelle University, Mekelle, Ethiopia
| | - Yefang Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Berihu Gebrekidan
- College of Veterinary Science, Mekelle University, Mekelle, Ethiopia
| | | | - Xuexue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
27
|
Barik S, Saini M, Chandra Mohan S, Ramesh D, Gupta PK. Functional characterization of partial recombinant goat conglutinin: Its role as innate immunity marker and use as antigen in sandwich ELISA. Vet Immunol Immunopathol 2019; 220:109987. [PMID: 31790920 DOI: 10.1016/j.vetimm.2019.109987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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] [Received: 04/30/2019] [Revised: 10/25/2019] [Accepted: 11/22/2019] [Indexed: 11/15/2022]
Abstract
Conglutinin, a liver synthesized versatile innate immune marker consisting C-type lectin domain belongs to collectin superfamily of proteins. The protein, first detected in bovine serum as soluble pattern recognition receptor (PRR) has wide range of antimicrobial activities. In the present study, open reading frame (ORF) encoding neck and carbohydrate recognition domain (NCRD) of goat conglutinin gene ligated to the vector pRSET-A was expressed in E. coli BL-21(pLys) cells. The 27 kDa recombinant protein (rGCGN) purified by single step Ni+2 -NTA affinity chromatography was found to cross-react with recombinant anti-buffalo conglutinin antibody raised in poultry. Further, it displayed calcium-dependant sugar binding activity towards yeast mannan and calcium-independent binding activity towards LPS. The mannan binding activity of rGCGN was inhibited in the presence of N-acetyl-glucosamine because of higher affinity towards this sugar. The recombinant protein was found to stimulate production of superoxide ions and hydrogen peroxide in goat neutrophils, which are instrumental in stimulating phagocytic activity of cells. When used as antigen in Sandwich ELISA, straight line (Y = 0.299x + 0.067, R2 = 0.997) was observed within the concentration range of 200-1000 ng/100 μl of rGCGN. Using this equation, the native conglutinin concentration in goat sera was estimated to be 0.5-7.5 μg/ml. The results indicated that prokaryotically expressed functionally active rGCGN can be used as antigen to assess native serum conglutinin levels in Sandwich ELISA and as immunomodulator in therapeutic applications to sequester unwanted immune complexes from the circulation.
Collapse
Affiliation(s)
- Sasmita Barik
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India.
| | - Mohini Saini
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India
| | - S Chandra Mohan
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India
| | - D Ramesh
- Department of Physiology and Biochemistry, Hassan Veterinary College, KVAFSU-Bidar, India
| | - Praveen K Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, India
| |
Collapse
|
28
|
Piccione G, Giannetto C, Giudice E, Refinetti R. Persistent homeothermy in large domestic mammals maintained under standard farming conditions. J Basic Clin Physiol Pharmacol 2019; 31:/j/jbcpp.ahead-of-print/jbcpp-2018-0121/jbcpp-2018-0121.xml. [PMID: 31730521 DOI: 10.1515/jbcpp-2018-0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 07/07/2018] [Accepted: 09/15/2019] [Indexed: 11/15/2022]
Abstract
Background Mammals, particularly large domestic ones, are considered to be year-round homeotherms. Surprisingly, however, very few long-term studies of the stability of core temperature of large domestic mammals have been conducted. Methods We monitored the auricular temperature and rectal temperature of goats, sheep, cows, and donkeys monthly for 2 years and compared their annual variation with their daily and day-to-day variations. Results Although ambient temperature varied from 8 °C in the winter to 30 °C in the summer, auricular temperature varied less than 0.5 °C, and rectal temperature varied less than 0.3 °C. We found that the daily oscillation in body temperature was up to three times as large as the day-to-day and month-to-month variations and that month-to-month variation was negligibly larger than day-to-day variation. Conclusion Our results confirm persistent homeothermy in large domestic mammals with unrestricted access to food and water and provide a quantitative measure of the relationship between long-term homeothermy and the wider range of daily/circadian oscillation.
Collapse
Affiliation(s)
- Giuseppe Piccione
- Veterinary Chronophysiology Laboratory, Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Claudia Giannetto
- Veterinary Chronophysiology Laboratory, Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Elisabetta Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Roberto Refinetti
- Circadian Rhythm Laboratory, Department of Psychological Science, Boise State University, Boise, ID83725,USA, Phone: +1-208-426-4117
| |
Collapse
|
29
|
Risalde MA, Roy Á, Bezos J, Pineda C, Casal C, Díez-Guerrier A, Lopez-Villalba I, Fernández-Manzano Á, Moreno I, De Juan L, Domínguez L, Gortazar C. Hypervitaminosis D has no positive effects on goat tuberculosis and may cause chronic renal lesions. Vet Rec 2019; 185:759. [PMID: 31690642 DOI: 10.1136/vr.105411] [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: 02/11/2019] [Revised: 08/12/2019] [Accepted: 10/18/2019] [Indexed: 11/03/2022]
Abstract
BACKGROUND There is evidence for a link between vitamin D deficiency and active tuberculosis (TB). In human beings, several trials have evaluated the role of vitamin D supplementation in TB treatment with conflicting results. However, the role of vitamin D supplementation in animal TB control has received less attention. The authors evaluated the benefit of vitamin D supplementation for preventing mycobacterial infection or reducing TB lesions (TBL) in a controlled trial with goats naturally exposed to Mycobacterium caprae. METHODS Two groups of goats, a vitamin D-supplemented group and a non-supplemented control group, were housed for 10 months in direct contact with M caprae-infected adult goats. Upon contact with the infected adult goats, all animals were TB-tested every two months. RESULTS No experimental evidence of a protective effect of vitamin D supplementation based on M caprae culture prevalence, TBL prevalence, median TBL score or the proportion of single versus multiple organs presenting TBL was observed. CONCLUSION The results indicate that, in the conditions used in this study, vitamin D supplementation in goats does not reduce TB infection risk nor the diffusion and severity of TBL. In addition, vitamin D-supplemented goats presented hyperphosphataemia and renal injury with calcifications suggestive of vitamin D intoxication.
Collapse
Affiliation(s)
- Maria Angeles Risalde
- Department of Comparative Pathology, University of Córdoba-Agrifood Campus of International Excellence (ceiA3), Cordoba, Spain.,Infectious Diseases Unit. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC). Hospital Universitario Reina Sofía de Córdoba - Universidad de Córdoba, Córdoba, Spain
| | - Álvaro Roy
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain.,CZ Vaccines, Porriño, Pontevedra, Spain
| | - Javier Bezos
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain.,Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Pineda
- Departamento de Medicina y Cirugía Animal, Universidad de Córdoba, Córdoba, Spain
| | - Carmen Casal
- Laboratorios SYVA S.A.U. Technological Park, León, Spain
| | - Alberto Díez-Guerrier
- Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.,MAEVA SERVET S.L, Alameda del Valle, Madrid, Spain
| | | | | | - Inmaculada Moreno
- Servicio de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Investigación Carlos III, Majadahonda, Madrid
| | - Lucía De Juan
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain.,Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucas Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain.,Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Christian Gortazar
- SaBio (Health and Biotechnology), Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM), Ciudad Real, Spain
| |
Collapse
|
30
|
Chowdhury SMZH, Nazir KHMNH, Hasan S, Kabir A, Mahmud MM, Robbani M, Tabassum T, Afroze T, Rahman A, Islam MR, Hossain M. Whole genome analysis of Black Bengal goat from Savar Goat Farm, Bangladesh. BMC Res Notes 2019; 12:687. [PMID: 31651366 PMCID: PMC6813047 DOI: 10.1186/s13104-019-4700-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/03/2019] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Single nucleotide polymorphisms (SNPs) play critical roles in genetic diversity and disease. Many traits and diseases are linked with exonic SNPs that are significant for gene function, regulation or translation. This study focuses on SNPs that potentially act as the genetic basis for desirable traits in the Black Bengal Goat. This variety of goat is native to South Asia, and is identified as one of the most commercially important meat producing animals in the world. The aim of this study was to sequence the genome of Black Bengal Goats and identify SNPs that might play a significant role in determining meat quality in the organism. The study focuses on exonic SNPs for their greater likelihood of affecting the final translated protein product. RESULTS Approximately 76,000 exonic variants were identified in the study. After filtration using a Wilcoxon test based score, the number came down to 49, 965 which were found to be distributed in 11,568 genes. The functional pathways affected by these variations included fatty acid metabolism and degradation, which are important processes that influence meat quality.
Collapse
Affiliation(s)
| | - K H M Nazmul Hussain Nazir
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Saam Hasan
- Department of Biochemistry and Microbiology, NSU Genome Research Institute (NGRI), Baridhara, Bashundhara, North South University, Dhaka, 1229, Bangladesh
| | - Ajran Kabir
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Muket Mahmud
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mahdi Robbani
- Department of Biochemistry and Microbiology, NSU Genome Research Institute (NGRI), Baridhara, Bashundhara, North South University, Dhaka, 1229, Bangladesh
| | - Tahmina Tabassum
- Department of Biochemistry and Microbiology, NSU Genome Research Institute (NGRI), Baridhara, Bashundhara, North South University, Dhaka, 1229, Bangladesh
| | - Tamanna Afroze
- NSU Genome Research Institute (NGRI), Baridhara, Bashundhara, North South University, Dhaka, 1229, Bangladesh
| | - Aura Rahman
- Department of Biochemistry and Microbiology, NSU Genome Research Institute (NGRI), Baridhara, Bashundhara, North South University, Dhaka, 1229, Bangladesh
| | - Md Rafiqul Islam
- Livestock Division, Bangladesh Agricultural Research Council, Farmgate, Dhaka, Bangladesh
| | - Maqsud Hossain
- NSU Genome Research Institute (NGRI), Baridhara, Bashundhara, North South University, Dhaka, 1229, Bangladesh.
| |
Collapse
|
31
|
Wang Z, Zhang X, Jiang E, Yan H, Zhu H, Chen H, Liu J, Qu L, Pan C, Lan X. InDels within caprine IGF2BP1 intron 2 and the 3'-untranslated regions are associated with goat growth traits. Anim Genet 2019; 51:117-121. [PMID: 31625179 DOI: 10.1111/age.12871] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2019] [Indexed: 12/31/2022]
Abstract
Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) is involved in the Hedgehog pathway and has been shown to regulate the RNA stability of several growth-related target genes. It is located in a quantitative trait locus showing a strong association with traits related to body size in ducks. Fibroblast growth factor receptor 1 (FGFR1) also participates in Hedgehog signaling pathways and has been reported to be associated with organic growth and development. FGFR1-knockout mice have been shown to have severe postnatal growth defects, including an approximately 50% reduction in body weight and bone mass. Meanwhile, nonsense-mediated mRNA decay factor (SMG6) can maintain genomic stability, which is associated with organic growth and development. Therefore, we hypothesized that IGF2BP1, FGFR1 and SMG6 genes may play important roles in the growth traits of goats. In this study, the existence of two insertion/deletion (InDel) variants within IGF2BP1, one InDel within FGFR1 and two InDels within SMG6 was verified and their correlation with growth traits was analyzed in 2429 female Shaanbei white cashmere goats. Results showed both the 15 bp InDel in intron 2 and the 5 bp InDel in the 3' regulatory region within IGF2BP1 were significantly associated with growth traits (P < 0.05) and goats with the combinatorial homozygous insertion genotypes of these two loci had the highest body weight (P = 0.046). The other InDels within FGFR1 and SMG6 were not obviously associated with growth traits (P > 0.05). Therefore, the two InDels in IGF2BP1 were vital mutations affecting goat growth traits.
Collapse
Affiliation(s)
- Z Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - E Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - H Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.,College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - H Zhu
- College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - H Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - J Liu
- College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - L Qu
- College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - C Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
32
|
Costa RC, Mesquita LP, de Oliveira IM, Zannato DA, Emanuel Dos Santos Mesquita L, Biihrer DA, de Oliveira Massoco Salles Gomes C, Varaschin MS, Maiorka PC. The pathogenicity of two Neospora caninum goat strains in a BALB/c mouse model. Exp Parasitol 2019; 205:107736. [PMID: 31442455 DOI: 10.1016/j.exppara.2019.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/02/2019] [Revised: 06/25/2019] [Accepted: 08/02/2019] [Indexed: 01/14/2023]
Abstract
Goats are frequently described as an intermediate host for the protozoan Neospora caninum, manifesting the disease mainly by recurrent abortions with placentitis and encephalitis in fetuses. Several reports of natural and experimental infections in cattle and mice show differences in the immune response, and the outcome of the infection can be variable depending on the species affected and by the behavior of the infective strain. This study describes for the first time two Neospora caninum strains isolated from naturally infected goats from the state of Minas Gerais, Brazil. One placenta and one brain from different goats were processed for a first bioassay in gerbils (Meriones unguiculatus). Subsequently, a second bioassay was performed by inoculating the processed brain samples from gerbils into Interferon gamma (IFN-γ) knockout mice (KO mice). Tachyzoites collected from the peritoneal fluid of the KO mice were inoculated into VERO cell monolayers, where they presented a very slow growth rate. The tachyzoites were also inoculated into BALB/c mice with a dose of 106 tachyzoites per animal. After a 5-week follow up, the animals infected with both of the strains developed a strong polarized Th1 response with increased serum and spleen gene expression levels of pro-inflammatory cytokines (mainly IFN-γ and TNF-α) in the first week. Tissue lesions were mild in the animals infected with both strains. Despite the strong immune response preventing an infection in the visceral organs, the parasite was able to reach the brain, causing progressive brain lesions from the second to fifth week post infection. The NC-goat1-infected mice presented with severe meningoencephalitis, but the NC-goat2-infected animals had considerable histological brain lesions only at week 5. Immunohistochemical analysis of the mouse brains revealed a different pattern of inflammatory cells compared to the naturally infected goats. A severe inflammatory infiltrate of CD3+ T lymphocytes was found in the NC-goat1-infected mice. A more discrete infiltrate of CD3+ T cells was found in the NC-goat2-infected animals. Additionally, IBA1 IHC revealed an intense microglial reaction and monocyte perivascular cuffs in the NC-goat1-infected animals and lower microglia/monocyte infiltrates in the NC-goat2-infected mice. This work contributes knowledge on the pathogenicity of new Neospora caninum strains in mice, comparable with other well-established mouse models of the disease, and demonstrates the importance of studying goats as an intermediate host of this parasite.
Collapse
Affiliation(s)
- Rafael Carneiro Costa
- Department of Pathology- School of Veterinary Medicine and and Animal Sciences, FMVZ-USP, São Paulo, SP, Brazil.
| | - Leonardo Pereira Mesquita
- Department of Pathology- School of Veterinary Medicine and and Animal Sciences, FMVZ-USP, São Paulo, SP, Brazil.
| | | | - Dennis Albert Zannato
- Department of Pathology- School of Veterinary Medicine and and Animal Sciences, FMVZ-USP, São Paulo, SP, Brazil.
| | | | - Daniel Arrais Biihrer
- Department of Pathology- School of Veterinary Medicine and and Animal Sciences, FMVZ-USP, São Paulo, SP, Brazil.
| | | | - Mary Suzan Varaschin
- Department of Veterinary Medicine- Federal University of Lavras- UFLA, Lavras, MG, Brazil.
| | - Paulo César Maiorka
- Department of Pathology- School of Veterinary Medicine and and Animal Sciences, FMVZ-USP, São Paulo, SP, Brazil.
| |
Collapse
|
33
|
Mahmoudi P, Rashidi A, Rostamzadeh J, Razmkabir M. Association between c.1189G>A single nucleotide polymorphism of GDF9 gene and litter size in goats: A meta-analysis. Anim Reprod Sci 2019; 209:106140. [PMID: 31514933 DOI: 10.1016/j.anireprosci.2019.106140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 04/01/2019] [Revised: 06/24/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
Abstract
Litter size is one of the most important traits in goat production and breeding. The most common and presumed single nucleotide polymorphism (SNP) detected in the Growth Differentiation Factor 9 gene is c.1189G>A (rs637044681, Ensembl) which results in an altered sequence of the encoded protein. In some studies, there was no effect of this SNP on litter size, while in other studies there was an effect. In the present study there was a meta-analysis conducted by pooling results from 11 eligible published studies to investigate effects of c.1189G>A polymorphism on litter size using four different genetic models including dominant (AA + AG compared with GG), recessive (AA compared with AG + GG), additive (AA compared with GG) and co-dominant (AA + GG compared with AG). Data were analyzed using fixed and random-effect models based on the I-squared value. Results indicate the c.1189G>A polymorphism is positively associated with litter size with use of the dominant model (SMD = 0.093, 95% CI = 0.028 to 0.158, P-Value = 0.005). There, however, was no effect of the c.1189G>A polymorphism using the recessive (SMD = 0.065, 95% CI = -0.164 to 0.295, P-Value = 0.577), additive (SMD = 0.172, 95% CI = -0.169 to 0.513, P-Value = 0.324) and co-dominant (SMD = -0.083, 95% CI = -0.200 to 0.034, P-Value = 0.164) genetic models. Results from use of the sensitivity analysis indicate the GG genotype affect litter size with use of the additive model (P < 0.01). The results from this meta-analysis indicate the GG genotype is associated with litter size in goats.
Collapse
Affiliation(s)
- Peyman Mahmoudi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Kurdistan, Iran
| | - Amir Rashidi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Kurdistan, Iran.
| | - Jalal Rostamzadeh
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Kurdistan, Iran.
| | - Mohammad Razmkabir
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Kurdistan, Iran
| |
Collapse
|
34
|
Siddiki A, Billah M, Alam M, Shawrob KSM, Kumkum M, Saha S, Chowdhury M, Rahman AH, Stear M, Khan MKI, Miah G, M Mollah AK, Baten A. Complete mitochondrial genome sequence of Black Bengal goat ( Capra hircus). Mitochondrial DNA B Resour 2019; 4:2121-2122. [PMID: 33365435 PMCID: PMC7687613 DOI: 10.1080/23802359.2019.1623098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The Black Bengal goat (Capra hircus), is a native breed found in Bangladesh, popular due to its economic contribution. Here, we report the complete mitochondrial genome sequence of Black Bengal goat. The circular genome is 16,640 bp long, comprising of 60.89% AT content. The genome contains 37 genes, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region (D-loop).
Collapse
Affiliation(s)
- Amam Siddiki
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Masum Billah
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Mohammad Alam
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Kazi Shefaul Mulk Shawrob
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Mahadia Kumkum
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Sourav Saha
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Muntaha Chowdhury
- Genomics Research Group, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh.,Department of Biological Sciences, Asian University for Women (AUW), Chattogram, Bangladesh
| | - Atif H Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology (BUET), Dhaka, Bangladesh
| | - Michael Stear
- AgriBio, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Australia
| | - Mohammad K I Khan
- Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Gous Miah
- Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - A K M Mollah
- Department of Biological Sciences, Asian University for Women (AUW), Chattogram, Bangladesh
| | - Abdul Baten
- AgResearch, Palmerston North, New Zealand.,Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| |
Collapse
|
35
|
Siddiki AZ, Baten A, Billah M, Alam MAU, Shawrob KSM, Saha S, Chowdhury M, Rahman AH, Stear M, Miah G, Kumkum M, Islam MS, Hossain MA, Mollah AKMM, Khan MKI. The genome of the Black Bengal goat ( Capra hircus). BMC Res Notes 2019; 12:362. [PMID: 31248431 DOI: 10.1186/s13104-019-4400-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/22/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Black Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest. DATA DESCRIPTION The genomic DNA of a local (Chattogram, Bangladesh) healthy male Black Bengal goat (Capra hircus) was extracted and then sequenced. Sequencing was completed using the Illumina HiSeq 2500 sequencing platform and the draft assembly was generated using the "ARS1" genome as the reference. MAKER gene annotation pipeline was utilized to annotate 26,458 gene models. Genome completeness was assessed using BUSCO (Benchmarking Universal Single-Copy Orthologs) which showed 82.5% completeness of the assembled genome.
Collapse
|
36
|
Tabata R, Kawaguchi F, Sasazaki S, Yamamoto Y, Bakhtin M, Kazymbet P, Meldevekob A, Suleimenov MZ, Nishibori M, Mannen H. The Eurasian Steppe is an important goat propagation route: A phylogeographic analysis using mitochondrial DNA and Y-chromosome sequences of Kazakhstani goats. Anim Sci J 2018; 90:317-322. [PMID: 30586684 DOI: 10.1111/asj.13144] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 09/05/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022]
Abstract
Goats (Capra hircus) were domesticated in the Fertile Crescent and propagated all over the world. The Silk Road through the Eurasian Steppe belt is a possible propagation route for domestic goats to Central Asia. Kazakhstan is in close geographical proximity to domestication centers and covers the majority of the Eurasian Steppe belt. In this study, we examined the genetic diversity and phylogeographic structure of Kazakhstani goats. The mtDNA sequences of 141 Kazakhstani goats were categorized into haplogroups A, C, and D, of which haplogroup A was predominant (97%), whereas haplogroups C and D were detected at low frequencies (1.4% each). The Kazakhstani haplotypes C were thzen categorized into Asian mtDNA type. Sequence analysis of the SRY gene on the Y-chromosome in 67 male Kazakhstani goats revealed two haplotypes: Y1A (64%) and Y2A (36%). Analysis of the distribution of mtDNA haplogroups and SRY haplotypes from Eurasia and Africa demonstrated genetic similarity among animals from Kazakhstan, Mongolia, and Northwest China located on the Eurasian Steppe belt. These phylogeographic results suggested that the Eurasian Steppe belt was an important propagation route for goats to Central Asia.
Collapse
Affiliation(s)
- Risa Tabata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yoshio Yamamoto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Meirat Bakhtin
- Radiobiology Scientific Center, Astana Medical University, Astana, Kazakhstan
| | - Polat Kazymbet
- Radiobiology Scientific Center, Astana Medical University, Astana, Kazakhstan
| | | | | | - Masahide Nishibori
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| |
Collapse
|
37
|
Oget C, Servin B, Palhière I. Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation. Anim Genet 2018; 50:54-63. [PMID: 30549070 PMCID: PMC6590323 DOI: 10.1111/age.12752] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 12/31/2022]
Abstract
After domestication 11 000 years ago in Asia Minor, the goat followed human migration to Europe and Asia. It was then introduced in Africa and is now raised all over the world. In this study, we exploited a dataset composed of 54 000 SNPs (Illumina goat DNA chip) to analyze the genetic diversity of 223 individuals belonging to eight French breeds (Alpine, Angora, Corse, Fossés, Poitevine, Provençale, Pyrénées and Saanen). Analyses carried out included individual-based approaches (principal component analysis and population structure) and population-based approaches (phylogenetic tree constructions). The results of the genetic diversity analyses revealed that French breeds are clearly differentiated, in particular, the Angora breed that originates from south west Asia. The Provençale breed shows a very original genetic pattern that could be the result of ancient admixture. Then, selection signatures were detected by identifying regions of outlying genetic differentiation between populations. Five genomic regions were detected under selection on chromosomes 5, 6, 11, 13 and 20, revealing mainly soft selective sweeps and a few hard selective sweeps and highlighting candidate genes that had been selected for during the evolutionary history of these breeds. Among them, two coat coloration genes (ADAMTS20 and ASIP) and one gene related to milk composition (CSN1S1) were involved.
Collapse
Affiliation(s)
- C Oget
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | - B Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | - I Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| |
Collapse
|
38
|
Zhu X, Jiao J, Zhou C, Tang S, Wang M, Kang J, Han X, Tan Z. LPAR5, GNAT3 and partial amino acid transporters messenger RNA expression patterns in digestive tracts, metabolic organs and muscle tissues of growing goats. Animal 2019; 13:1394-402. [PMID: 30378518 DOI: 10.1017/S1751731118002823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sufficient amino acid (AA) transport is essential to ensure the normal physiological function and growth of growing animals. The processes of AA sensing and transport in humans and murine animals, but rarely in goats, have been arousing great interest recently. This study was conducted to investigate the messenger RNA expression patterns of lysophosphatidic acid receptor 5 (LPAR5), guanine nucleotide-binding protein α-transducing 3 (GNAT3) and important partial AA transporters in digestive tracts, metabolic organs and muscles of growing goats. The results showed that these genes were widely expressed in goats, and had different expression patterns. LPAR5, GNAT3, solute carrier (SLC38A2), SLC7A7, SLC7A1 and SLC3A1 were rarely expressed in the rumen, but were highly expressed in the abomasum and intestine which are the main sites of AA absorption. GNAT3, SLC38A1, SLC38A2, SLC6A19, SLC7A7 and SLC7A1 showed comparatively high expression in the pancreas and the vital digestive glands, and the relatively high expression of these nine genes were noted in the tibialis posterior, the active muscle in energy metabolism. The correlation analysis showed that there were certain positive correlation among most genes. The current results indicate that the AA sensing and transport occur extensively in the abomasum and small intestine, metabolic organs and muscle tissues of ruminants, and that related genes have tissue specificity.
Collapse
|
39
|
Xiong Y, Xu Q, Lin S, Wang Y, Lin Y, Zhu J. Knockdown of LXRα Inhibits Goat Intramuscular Preadipocyte Differentiation. Int J Mol Sci 2018; 19:E3037. [PMID: 30301149 DOI: 10.3390/ijms19103037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/21/2018] [Accepted: 09/28/2018] [Indexed: 01/11/2023] Open
Abstract
Goat intramuscular fat (IMF) content is mainly determined by the processes of intramuscular preadipocytes adipogenic differentiation and mature adipocyte lipid accumulation. However, the underlying regulators of these biological processes remain largely unknown. Here, we report that the expression of Liver X receptor alpha (LXRα) reaches a peak at early stage and then gradually decreases during goat intramuscular adipogenesis. Knockdown of LXRα mediated by two independent siRNAs significantly inhibits intramuscular adipocytes lipid accumulation and upregulates preadipocytes marker- preadipocyte factor 1 (pref1) expression. Consistently, siRNA treatments robustly decrease mRNA level of adipogenic related genes, including CCAAT enhancer binding protein alpha (Cebpα), Peroxisome proliferator activated receptor gamma (Pparg), Sterol regulatory element binding protein isoform 1c (Srebp1c), Fatty acids binding protein (aP2) and Lipoprotein lipase (Lpl). Next, adenovirus overexpression of LXRα does not affect intramuscular adipocytes adipogenesis manifested by Oil Red O signal measurement and adipogenic specific genes detection. Mechanically, we found that both CCAAT enhancer binding protein beta (Cebpβ) and Kruppel like factor 8 (Klf8) are potential targets of LXRα, indicated by having putative binding sites of LXRα at the promoter of these genes and similar expression pattern during adipogenesis comparing to LXRα. Importantly, mRNA levels of Cebpβ and Klf8 are downregulated significantly in goat LXRα knockdown intramuscular adipocyte. These results demonstrate that loss function of LXRα inhibits intramuscular adipogenesis possibly through down-regulation of Cebpβ and Klf8. Our research will provide new insights into mechanical regulation of goat IMF deposition.
Collapse
|
40
|
Abstract
Natriuretic peptides are structurally similar, but genetically distinct, hormones that participate in cardiovascular homeostasis by regulating blood and extracellular fluid volume and blood pressure. We investigated the distribution of natriuretic peptides and their receptors in goat (Capra hircus) heart tissue using the peroxidase-anti-peroxidase (PAP) immunohistochemical method. Strong staining of atrial natriuretic peptide (ANP) was observed in atrial cardiomyocytes, while strong staining for brain natriuretic peptide (BNP) was observed in ventricular cardiomyocytes. Slightly stronger cytoplasmic C-type natriuretic peptide (CNP) immunostaining was detected in the ventricles compared to the atria. Natriuretic peptide receptor-A (NPR-A) immunoreactivity was more prominent in the atria, while natriuretic peptide receptor-B (NPR-B) immunoreactivity was stronger in the ventricles. Cytoplasmic natriuretic peptide receptor-C (NPR-C) immunoreactivity was observed in both the atria and ventricles, although staining was more prominent in the ventricles. ANP immunoreactivity ranged from weak to strong in endothelial and vascular smooth muscle cells. Endothelial cells exhibited moderate to strong BNP immunoreactivity, while vascular smooth cells displayed weak to strong staining. Endothelial cells exhibited weak to strong cytoplasmic CNP immunoreactivity. Vascular smooth muscle cells were labeled moderately to strongly for CNP. Weak to strong cytoplasmic NPR-A immunoreactivity was found in the endothelial cells and vascular smooth muscle cells stained weakly to moderately for NPR-A. Endothelial and vascular smooth cells exhibited weak to strong cytoplasmic NPR-B immunoreactivity. Moderate to strong NPR-C immunoreactivity was observed in the endothelial and smooth muscle cells. Small gender differences in the immunohistochemical distribution of natriuretic peptides and receptors were observed. Our findings suggest that endothelial cells, vascular smooth cells and cardiomyocytes express both natriuretic peptides and their receptors.
Collapse
Affiliation(s)
- M Öztop
- a Department of Biology , Mehmet Akif Ersoy University , Burdur
| | - K Cinar
- b Department of Biology , Süleyman Demirel University , Isparta , Turkey
| | - S Turk
- b Department of Biology , Süleyman Demirel University , Isparta , Turkey
| |
Collapse
|
41
|
Onzima RB, Upadhyay MR, Doekes HP, Brito LF, Bosse M, Kanis E, Groenen MAM, Crooijmans RPMA. Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds. Front Genet 2018; 9:318. [PMID: 30154830 PMCID: PMC6102322 DOI: 10.3389/fgene.2018.00318] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023] Open
Abstract
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
Collapse
Affiliation(s)
- Robert B. Onzima
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Maulik R. Upadhyay
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harmen P. Doekes
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Luiz. F. Brito
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, Guelph, ON, Canada
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Egbert Kanis
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Martien A. M. Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | | |
Collapse
|
42
|
Zhou G, Kang D, Ma S, Wang X, Gao Y, Yang Y, Wang X, Chen Y. Integrative analysis reveals ncRNA-mediated molecular regulatory network driving secondary hair follicle regression in cashmere goats. BMC Genomics 2018; 19:222. [PMID: 29587631 PMCID: PMC5870523 DOI: 10.1186/s12864-018-4603-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/13/2018] [Indexed: 02/06/2023] Open
Abstract
Background Cashmere is a keratinized product derived from the secondary hair follicles (SHFs) of cashmere goat skins. The cashmere fiber stops growing following the transition from the actively proliferating anagen stage to the apoptosis-driven catagen stage. However, little is known regarding the molecular mechanisms responsible for the occurrence of apoptosis in SHFs, especially as pertains to the role of non-coding RNAs (ncRNAs) and their interactions with other molecules. Hair follicle (HF) degeneration is caused by localized apoptosis in the skin, while anti-apoptosis pathways may coexist in adjacent HFs. Thus, elucidating the molecular interactions responsible for apoptosis and anti-apoptosis in the skin will provide insights into HF regression. Results We used multiple-omics approaches to systematically identify long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs expressed in cashmere goat skins in two crucial phases (catagen vs. anagen) of HF growth. Skin samples were collected from three cashmere goats at the anagen (September) and catagen (February) stages, and six lncRNA libraries and six miRNA libraries were constructed for further analysis. We identified 1122 known and 403 novel lncRNAs in the goat skins, 173 of which were differentially expressed between the anagen and catagen stages. We further identified 3500 gene-encoding transcripts that were differentially expressed between these two phases. We also identified 411 known miRNAs and 307 novel miRNAs, including 72 differentially expressed miRNAs. We further investigated the target genes of lncRNAs via both cis- and trans-regulation during HF growth. Our data suggest that lncRNAs and miRNAs act synergistically in the HF growth transition, and the catagen inducer factors (TGFβ1 and BDNF) were regulated by miR-873 and lnc108635596 in the lncRNA-miRNA-mRNA networks. Conclusion This study enriches the repertoire of ncRNAs in goats and other mammals, and contributes to a better understanding of the molecular mechanisms of ncRNAs involved in the regulation of HF growth and regression in goats and other hair-producing species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4603-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Danju Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Sen Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xingtao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ye Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yuxin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
43
|
Onzima RB, Upadhyay MR, Mukiibi R, Kanis E, Groenen MAM, Crooijmans RPMA. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds. Anim Genet 2018; 49:59-70. [PMID: 29344947 PMCID: PMC5838551 DOI: 10.1111/age.12631] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2017] [Indexed: 12/18/2022]
Abstract
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.
Collapse
Affiliation(s)
- R B Onzima
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands.,National Agricultural Research Organization (NARO), P O Box 295, Entebbe, Uganda
| | - M R Upadhyay
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - R Mukiibi
- Department of Agriculture, Food and Nutritional Sciences (AFNS), Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, 1416 College Plaza Edmonton, T6G 2C8, Alberta, Canada
| | - E Kanis
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| | - M A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| |
Collapse
|
44
|
Sevane N, Cortés O, Gama LT, Martínez A, Zaragoza P, Amills M, Bedotti DO, Bruno de Sousa C, Cañon J, Dunner S, Ginja C, Lanari MR, Landi V, Sponenberg P, Delgado JV; BioGoat Consortium. Dissection of ancestral genetic contributions to Creole goat populations. Animal 2018; 12:2017-26. [PMID: 29306351 DOI: 10.1017/S1751731117003627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus' arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.
Collapse
|
45
|
Cassidy LM, Teasdale MD, Carolan S, Enright R, Werner R, Bradley DG, Finlay EK, Mattiangeli V. Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland. Biol Lett 2017; 13:rsbl.2016.0876. [PMID: 28250207 DOI: 10.1098/rsbl.2016.0876] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 11/07/2016] [Accepted: 02/07/2017] [Indexed: 11/12/2022] Open
Abstract
The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous 'Old Goat' populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral 'Old Goats' of Ireland and Britain.
Collapse
Affiliation(s)
- Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | | | | | - Ruth Enright
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | | | | | - Emma K Finlay
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | |
Collapse
|
46
|
Costa RC, Mesquita LP, Nunes MVL, Oliveira IM, Oliveira LFS, Souza AR, Maiorka PC, Varaschin MS. Neospora caninum bioassay in gerbils using placental tissues from naturally infected goats. Vet Parasitol 2017; 249:70-73. [PMID: 29279089 DOI: 10.1016/j.vetpar.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 02/13/2017] [Revised: 10/25/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022]
Abstract
Neospora caninum is one of the main agents that causes abortions in cattle worldwide. However, little is known about the pathogenesis of neosporosis in small ruminants, especially goats. Gerbils (Meriones unguiculatus) have been used as a model for neosporosis, and this species is highly susceptible to infection by bovine N. caninum strains. The present study aimed to evaluate the susceptibility of gerbils to a N. caninum isolate from goats. The placentas were obtained from naturally infected goats, that presented with mild to severe lymphoplasmacytic and histiocytic infiltrate, foci of necrosis, calcification and protozoan-like structures. Immunosuppressed gerbils bioassayed with N. caninum-infected placental tissues showed severe neurological signs. Microscopic lesions in these gerbils were characterized by encephalitis, myocarditis, myositis and pancreatitis. These lesions were often associated with a small to moderate number of N. caninum tachyzoites, confirmed by immunohistochemistry and PCR. This is the first report showing that goat N. caninum strains could infect immunocompetent gerbils and cause severe lesions and clinical signs in immunosuppressed gerbils.
Collapse
Affiliation(s)
- R C Costa
- Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil; Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil.
| | - L P Mesquita
- Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil
| | - M V L Nunes
- Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil
| | - I M Oliveira
- Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil
| | - L F S Oliveira
- Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil
| | - Alinne R Souza
- Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil
| | - P C Maiorka
- Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil
| | - M S Varaschin
- Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil
| |
Collapse
|
47
|
Abstract
Objective: The objective of this study was to characterize the α1-adrenoceptor (α1-AR) subtypes and evaluate the effect of acidosis on α1-AR function and expression in goat superior mesenteric artery (GSMA). Materials and Methods: GSMA rings were mounted in a thermostatically controlled (37.0°C ± 0.5°C) organ bath containing 20 ml of modified Krebs-Henseleit solution, maintained at pHo of 7.4, 6.8, 6.0, 5.5, 5.0, and 4.5. Noradrenaline (NA)- and phenylephrine (PE)-induced contractile response was elicited in the absence or presence of endothelium and prazosin at pHo of 7.4, 6.0, and 5.0. The responses were recorded isometrically by an automatic organ bath connected to PowerLab and analyzed using Labchart 7.1.3 software. Expression of α1D-AR was compared at physiological and acidic pHo using reverse transcription-polymerase chain reaction (RT-PCR). Results: NA- and PE-induced contractile responses were attenuated proportionately with a decrease in extracellular pH (pHo), i.e. 7.4 → 6.8 → 6.0 → 5.5 → 5.0 → 4.5. Endothelium denudation increased the contractile response at both normal and acidic pHo. Prazosin (1 nM, 10 nM, and 0.1 μM) inhibited the NA- and PE-induced contractile response at pHo 7.4 and the blocking effect of prazosin was potentiated at pHo of 6.0 and 5.0. RT-PCR analysis for α1D-AR in GSMA showed that the mRNA expression of α1D-AR was decreased under acidic pHo as compared to physiological pHo. Conclusion: (i) Adrenergic receptor mediates vasoconstriction in GSMA under normal physiological pHo, and α1D is the possible subtype involved in this event (ii) acidosis attenuates the vasocontractile response due to reduced function and expression of α1D-AR and also increased the release of endothelial-relaxing factors.
Collapse
Affiliation(s)
- Ipsita Mohanty
- Department of Pharmacology and Toxicology, Faculty of Veterinary Sciences, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Sujit Suklabaidya
- Tumor Microenvironment and Animal Models, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Subas Chandra Parija
- Department of Pharmacology and Toxicology, College of Veterinary Sciences and Animal Husbandry, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| |
Collapse
|
48
|
Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
49
|
Cosenza G, Iannaccone M, Pico BA, Gallo D, Capparelli R, Pauciullo A. Molecular characterisation, genetic variability and detection of a functional polymorphism influencing the promoter activity of OXT gene in goat and sheep. J DAIRY RES 2017; 84:165-9. [PMID: 28290268 DOI: 10.1017/S0022029917000097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The purpose of the study described in this Research Communication was to report the full characterisation of the goat and sheep oxytocin-neurophysin I gene (OXT), their promoters and amino acid sequences. Using the genomic DNA as template, we sequenced and compared the whole OXT gene (3 exons), plus 958/960 nucleotides at the 5' flanking region and 478/477 nucleotides at the 3' flanking region, in 46 sheep and 24 goats belonging to different breeds/genetic types reared in Italy, Greece and Germany. The comparison of the obtained sequences showed a high degree of genetic variability at these loci. In particular, we focused on the SNP g.438T > C as possible example of trans-specific polymorphism. This SNP alters a putative binding site of the transcription factor Oct-1. The set-up of a luciferase assay confirmed that the C variant of this SNP negatively affects the promoter activity of the sheep OXT gene. The results of this study suggest that the SNP g.438T > C might be useful to promote association studies with traits/physiological processes controlled by this hormone.
Collapse
|
50
|
Zhu L, Chen T, Sui M, Han C, Fang F, Ma Y, Chu M, Zhang X, Liu C, Ling Y. Comparative profiling of differentially expressed microRNAs between the follicular and luteal phases ovaries of goats. Springerplus 2016; 5:1233. [PMID: 27610292 PMCID: PMC4993730 DOI: 10.1186/s40064-016-2902-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/25/2016] [Indexed: 12/12/2022]
Abstract
To explore if the regulation at post-transcriptional level of follicular phase (Fols) to luteal phase (Luts) transition occurs in the ovaries of Anhuai goats, the differentially expressed microRNAs (miRNAs) of ovaries in the Fols and Luts were analyzed using Solexa sequencing in the study. In total, 320 known miRNAs were co-expressed in the two phases, 339 and 353 known miRNAs were expressed in the ovary in the Fols and Luts, respectively. In addition, 45 novel miRNAs were co-expressed in the two phases, 70 and 94 novel miRNAs were expressed in the ovary in the Fols and Luts, respectively. Let-7f was the highest expressed significantly different known miRNA in the two phases, and mir-159 was the highest expressed significantly different novel miRNA in the two phases, which may participate in the follicular-luteal transition of Anhuai goats. GO annotation and KEGG pathway analysis were applied to analyze the target genes of differentially expressed miRNAs detected in the two phases. The results will help to further understand the role of miRNAs in the regulation of follicular to luteal transition in goat ovaries.
Collapse
Affiliation(s)
- Long Zhu
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Tao Chen
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Menghua Sui
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Chunyang Han
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Yuehui Ma
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Institute of Animal Science, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Mingxing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Institute of Animal Science, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Xiaorong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Cuiyan Liu
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| |
Collapse
|