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Wang P, Ou G, Li G, Li H, Zhao T. Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip. Anim Biotechnol 2024; 35:2349625. [PMID: 38733367 DOI: 10.1080/10495398.2024.2349625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
This study aimed to evaluate the genetic diversity and structure within the Dengchuan cattle population and effectively protect and utilize their germplasm resources. Herein, the single-nucleotide polymorphisms (SNPs) of 100 Dengchuan cattle (46 bulls and 54 cows) were determined using the GGP Bovine 100K SNP Beadchip. The results showed that among the Dengchuan cattle, a total of 101,220 SNPs were detected, and there were 83,534 SNPs that passed quality control, of which 85.7% were polymorphic. The average genetic distance based on identity-by-state (IBS) within the conservation population of Dengchuan cattle was 0.26 ± 0.02. A total of 3,999 genome-length runs of homozygosity (ROHs) were detected in the Dengchuan cattle, with ROH lengths primarily concentrated in the range of 1-5 Mb, accounting for 87.02% of the total. The average inbreeding coefficient based on ROHs was 4.6%, within the conservation population of Dengchuan cattle, whereas it was 4.9% for bulls, and the Wright inbreeding coefficient (FIS) value was 2.4%, demonstrating a low level of inbreeding within the Dengchuan cattle population. Based on neighbor-joining tree analysis, the Dengchuan cattle could be divided into 16 families. In summary, the conservation population of Dengchuan cattle displays relatively abundant diversity and a moderate genetic relationship. Inbreeding was observed among a few individuals, but the overall inbreeding level of the population remained low. It is important to maintain this low level of inbreeding when introducing purebred bloodlines to expand the core group. This approach will ensure the long-term conservation of Dengchuan cattle germplasm resources and prevent loss of genetic diversity.
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Affiliation(s)
- Pingping Wang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Guoyu Ou
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Genchang Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Huiying Li
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Tianzhang Zhao
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
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Kusza S, Badaoui B, Wanjala G. Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity. Sci Rep 2024; 14:16515. [PMID: 39019985 PMCID: PMC11255268 DOI: 10.1038/s41598-024-67558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
Numerous studies have indicated that Morocco's indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D'man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24-48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1-6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13, and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco. Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds' genomic landscapes and adaptive mechanisms.
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Affiliation(s)
- Szilvia Kusza
- Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary.
| | - Bouabid Badaoui
- Faculty of Sciences, Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI),, Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - George Wanjala
- Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
- Doctoral School of Animal Science, University of Debrecen, Böszörményi út 138., 4032, Debrecen, Hungary
- Institute of Animal Sciences and Wildlife Management, University of Szeged, Andrássy út 15., 6800, Hódmezővásárhely, Hungary
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Ostuni A, Albarella S, Tassoni L, Pugliano M, D'Anza E, Crudele MA, Ciotola F, Beato MS, Iovane V, Cecchini Gualandi S, Frontoso R, De Vendel J, Peretti V, Bavoso A. Circulation of small ruminant lentivirus in endangered goat and sheep breeds of Southern Italy. Heliyon 2024; 10:e33906. [PMID: 39027592 PMCID: PMC11255564 DOI: 10.1016/j.heliyon.2024.e33906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024] Open
Abstract
According to the Domestic Animal Diversity Information System (DAD-IS) of the FAO, Italy has one of the largest numbers of local small ruminant breeds among European countries. In Southern Italy, namely the Campania Region, Bagnolese and Laticauda sheep breeds and Cilentana goat breeds are considered endangered according to the DAD-IS. Conservation of endangered animal breeds is a goal of the European Union (EU). However, the role of infectious diseases as risk factors for endangered breeds has rarely been considered. Small ruminant lentiviruses (SRLV) infect sheep and goats, causing slow-progressive, persistent, and debilitating diseases that can lead to animal death and productivity loss. In this study, we investigated the presence of SRLV in Bagnolese, Laticauda, and Cilentana breeds using a commercial ELISA in parallel with an in-house ELISA. The results of the two tests were in good agreement (Cohen Kappa 0.84, 95 % CI = 0.76-0.93). Discrepancies between the two tests were resolved using western blotting. In total, 430 samples were tested (248 Bagnolese, 125 Laticauda, and 57 Cilentana). The apparent prevalence rates were 12.5 %, 6.4 %, and 1.7 % in Bagnolese, Laticauda, and Cilentana, respectively. In the molecular analysis of 11 proviral partial sequences, subtypes B2 and A24 were identified in two Bagnolese herds. Owing to the beneficial role of sheep and goat breeding in marginal areas, it is important to screen the entire population and implement control/eradication of SRLV infections in conjunction with each conservation program.
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Affiliation(s)
- Angela Ostuni
- Department of Sciences, University of Basilicata, Via dell’ Ateneo Lucano 10, 85100, Potenza, Italy
| | - Sara Albarella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Napoli, Italy
| | - Luca Tassoni
- National Reference Laboratory for Ruminant retroviruses, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM), Via G. Salvemini 1, 06126, Perugia, PG, Italy
| | - Mariagiulia Pugliano
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Napoli, Italy
| | - Emanuele D'Anza
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Napoli, Italy
| | - Maria Antonietta Crudele
- Department of Sciences, University of Basilicata, Via dell’ Ateneo Lucano 10, 85100, Potenza, Italy
| | - Francesca Ciotola
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Napoli, Italy
| | - Maria Serena Beato
- National Reference Laboratory for Ruminant retroviruses, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM), Via G. Salvemini 1, 06126, Perugia, PG, Italy
| | - Valentina Iovane
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Via Università 100, 80055, Portici, NA, Italy
| | | | - Raffaele Frontoso
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 80055, Portici, NA, Italy
- OneHEco APS, 84047, Capaccio Paestum, SA, Italy
| | | | - Vincenzo Peretti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Napoli, Italy
| | - Alfonso Bavoso
- Department of Sciences, University of Basilicata, Via dell’ Ateneo Lucano 10, 85100, Potenza, Italy
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Wang Z, Song B, Yao J, Li X, Zhang Y, Tang Z, Yi G. Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs. J Anim Sci Biotechnol 2024; 15:97. [PMID: 38982489 PMCID: PMC11234542 DOI: 10.1186/s40104-024-01053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear. RESULTS Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments. CONCLUSIONS In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.
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Affiliation(s)
- Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Jianyu Yao
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Yan Zhang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
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Qi L, Xiao L, Fu R, Nie Q, Zhang X, Luo W. Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens. Poult Sci 2024; 103:103863. [PMID: 38810566 PMCID: PMC11166977 DOI: 10.1016/j.psj.2024.103863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.
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Affiliation(s)
- Lin Qi
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Liangchao Xiao
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Rong Fu
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China.
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Min CG, Ma X, Wang YC, Zhong CK, Yuan CS, Zhang KY, Zhan CL, Hou SK, Wang XH, Wang J, Zhao J, Fang Y, Liu HY, Ding H, Guo J, Lu WF. The effects of repeated freezing and thawing on bovine sperm morphometry and function. Cryobiology 2024; 115:104892. [PMID: 38593909 DOI: 10.1016/j.cryobiol.2024.104892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
Refreezing the remaining genetic resources after in vitro fertilization (IVF) can conserve genetic materials. However, the precise damage inflicted by repeated freezing and thawing on bovine sperm and its underlying mechanism remain largely unexplored. Thus, this study investigates the impact of repeated freeze-thaw cycles on sperm. Our findings indicate that such cycles significantly reduce sperm viability and motility. Furthermore, the integrity of the sperm plasma membrane and acrosome is compromised during this process, exacerbating the advanced apoptosis triggered by oxidative stress. Additionally, transmission electron microscopy exposed severe damage to the plasma membranes of both the sperm head and tail. Notably, the "9 + 2" structure of the tail was disrupted, along with a significant decrease in the level of the axonemal protein DNAH10, leading to reduced sperm motility. IVF outcomes revealed that repeated freeze-thaw cycles considerably impair sperm fertilization capability, ultimately reducing the blastocyst rate. In summary, our research demonstrates that repeated freeze-thaw cycles lead to a decline in sperm viability and motility, attributed to oxidative stress-induced apoptosis and DNAH10-related dynamic deficiency. As a result, the utility of semen is compromised after repeated freezing.
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Affiliation(s)
- Chang-Guo Min
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Xin Ma
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu-Chan Wang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Cheng-Kun Zhong
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Chong-Shan Yuan
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Kai-Yan Zhang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Cheng-Lin Zhan
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Sheng-Kui Hou
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Xin-Hai Wang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jun Wang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Zhao
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Yi Fang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Hong-Yu Liu
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - He Ding
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Guo
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China.
| | - Wen-Fa Lu
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China; Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China.
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7
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Alipanah M, Mazloom SM, Gharari F. Detection of selective sweep in European wild sheep breeds. 3 Biotech 2024; 14:122. [PMID: 38560387 PMCID: PMC10978567 DOI: 10.1007/s13205-024-03964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
In wild animal populations, there is a differentiation between populations due to natural selection. The direction and pressure of natural selection in the wild sheep are different in the various geographic areas. Linkage disequilibrium studies showed that regions of the genome in whole wild sheep are under natural selection and that natural selection can affect immune or reproductive or metabolic traits. The study aimed to identify genomic regions under natural selection in wild sheep. For this purpose, the genetic information of 24 European wild sheep and 24 Sardinian wild sheep was used. The genotypes were determined using Illumina 50 K SNPChip arrays based on Oar_4.0 version of the sheep genome. After quality control steps, finally, 31,560 SNP markers were analyzed. The value of LD was calculated by calculating the r2 statistic between all pairs of locations through PLINK software. To identify signs of selection based on linkage disequilibrium methods, an extended haplotype homozygosity test of XP-EHH crossing population and iHS intrapopulation was used. The results of iHS studies showed that in European and Sardinian wild sheep, the highest iHS coefficient under natural selection was observed on 3 and 2 chromosome numbers, respectively. Also, the results of XP-EHH studies showed that the largest XP-EHH coefficients under natural selection in European wild sheep compared to Sardinian and vice versa in Sardinian wild sheep compared to European wild sheep were observed on 3 and 16 chromosome numbers, respectively. In addition, the results of gene cycle studies showed that COPB1, SEC24D, ZDHHC17, BBS4, RFX3, SLC26A8, CAMK2D, GRIA1, GRM1, GRID2, PPP2R1A, CPEB4, PLEKHA5 and KIF13A, VPS39, VPS53, DTNBP1, DYNC1I1, FAM91A genes are under natural selection in Sardinian and European wild sheeps, respectively. The direction and selection pressure of natural selection in the two breeds of wild sheep is different due to different geographic conditions.
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Affiliation(s)
- Masoud Alipanah
- Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595 Iran
| | - Seyed Mostafa Mazloom
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974 Iran
| | - Faezeh Gharari
- Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595 Iran
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974 Iran
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8
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Janák V, Novák K, Kyselý R. Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives. Animals (Basel) 2024; 14:645. [PMID: 38396613 PMCID: PMC10886113 DOI: 10.3390/ani14040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.
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Affiliation(s)
- Vojtěch Janák
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
- Department of Archaeology, Faculty of Arts, Charles University, Nám. Jana Palacha 2, 116 38 Praha, Czech Republic
| | - Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
| | - René Kyselý
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
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9
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Li J, Li Y, Xiao H, Li W, Ye F, Wang L, Li Y, Wang C, Wu Y, Xuan R, Huang Y, Huang J. The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China. Poult Sci 2024; 103:103198. [PMID: 38016408 PMCID: PMC10696398 DOI: 10.1016/j.psj.2023.103198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 11/30/2023] Open
Abstract
Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.
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Affiliation(s)
- Jiawei Li
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yuping Li
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Huiyuan Xiao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Wen Li
- Changsheng Town People's Government of Ningdu County, Ganzhou, China
| | - Fengchun Ye
- Jiangxi Yifeng County Qiaoxi Veterinary Station, Yichun, China
| | - Liping Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yuhang Li
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Cong Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yan Wu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Rui Xuan
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yuxuan Huang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jianhua Huang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China.
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10
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Mereu P, Pirastru M, Sanna D, Bassu G, Naitana S, Leoni GG. Phenotype transition from wild mouflon to domestic sheep. Genet Sel Evol 2024; 56:1. [PMID: 38166592 PMCID: PMC10763062 DOI: 10.1186/s12711-023-00871-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
The domestication of animals started around 12,000 years ago in the Near East region. This "endless process" is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today's domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.
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Affiliation(s)
- Paolo Mereu
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100, Sassari, Italy
| | - Monica Pirastru
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100, Sassari, Italy.
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100, Sassari, Italy
| | - Giovanni Bassu
- Agenzia FoReSTAS, Regione autonoma della Sardegna, 09123, Cagliari, Italy
| | - Salvatore Naitana
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100, Sassari, Italy
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11
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Blondeau Da Silva S, Mwacharo JM, Li M, Ahbara A, Muchadeyi FC, Dzomba EF, Lenstra JA, Da Silva A. IBD sharing patterns as intra-breed admixture indicators in small ruminants. Heredity (Edinb) 2024; 132:30-42. [PMID: 37919398 PMCID: PMC10799084 DOI: 10.1038/s41437-023-00658-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
In this study, we investigated how IBD patterns shared between individuals of the same breed could be informative of its admixture level, with the underlying assumption that the most admixed breeds, i.e. the least genetically isolated, should have a much more fragmented genome. We considered 111 goat breeds (i.e. 2501 individuals) and 156 sheep breeds (i.e. 3304 individuals) from Europe, Africa and Asia, for which beadchip SNP genotypes had been performed. We inferred the breed's level of admixture from: (i) the proportion of the genome shared by breed's members (i.e. "genetic integrity level" assessed from ADMIXTURE software analyses), and (ii) the "AV index" (calculated from Reynolds' genetic distances), used as a proxy for the "genetic distinctiveness". In both goat and sheep datasets, the statistical analyses (comparison of means, Spearman correlations, LM and GAM models) revealed that the most genetically isolated breeds, also showed IBD profiles made up of more shared IBD segments, which were also longer. These results pave the way for further research that could lead to the development of admixture indicators, based on the characterization of intra-breed shared IBD segments, particularly effective as they would be independent of the knowledge of the whole genetic landscape in which the breeds evolve. Finally, by highlighting the fragmentation experienced by the genomes subjected to crossbreeding carried out over the last few generations, the study reminds us of the need to preserve local breeds and the integrity of their adaptive architectures that have been shaped over the centuries.
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Affiliation(s)
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotlands Rural College (SRUC) and Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, EH25 9RG, Midlothian, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Menghua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Abulgasim Ahbara
- Animal and Veterinary Sciences, Scotlands Rural College (SRUC) and Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, EH25 9RG, Midlothian, UK
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | | | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Da Silva
- Faculté des Sciences et Techniques de Limoges, E2LIM, 87000, Limoges, France.
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12
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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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13
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Smith WJ, Jezierski MT, Dunn JC, Clegg SM. Parasite exchange and hybridisation at a wild-feral-domestic interface. Int J Parasitol 2023; 53:797-808. [PMID: 37474096 DOI: 10.1016/j.ijpara.2023.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/27/2023] [Accepted: 06/06/2023] [Indexed: 07/22/2023]
Abstract
Interactions between wild, feral, and domestic animals are of economic and conservation significance. The pigeon Columba livia is a synanthropic species in a feral form, but it also includes the rare Rock Dove. Columba livia is an important player at the wild-domestic interface, acting as a carrier of avian diseases, and the feral form threatens Rock Doves with extinction via hybridisation. Despite its abundance, little is known about drivers of disease prevalence in C. livia, or how disease and hybridisation represent synergistic threats to Rock Doves. We focused on infection by the parasite Trichomonas, first collating prevalence estimates in domestic and free-living populations from relevant studies of C. livia. Second, we characterised variation in the diversity and prevalence of Trichomonas among three C. livia populations in the United Kingdom: a feral, a Rock Dove, and a feral-wild hybrid population. Across multiple continents, free-living pigeons had lower Trichomonas infection than captive conspecifics, but the effect was weak. Environmental factors which could impact Trichomonas infection status did not explain variation in infection among populations. Among the British populations, strain diversity varied, and there was lower parasite prevalence in Rock Doves than feral pigeons. Individual infection status was not explained by the available covariates, including hybrid score and site. The drivers of Trichomonas prevalence are unclear, perhaps due to idiosyncratic local-scale drivers. However, given the population-level variation in both infection prevalence and introgressive hybridisation, the potential combined effects could accelerate the extinction of the Rock Dove. Further study of the synergistic effects of multiple types of biotic interactions at the wild-feral-domestic interface is warranted, especially where vagile, globally distributed and superabundant animals are involved.
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Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, UK.
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, UK
| | - Jenny C Dunn
- School of Life and Environmental Sciences, University of Lincoln, UK; School of Biology, University of Leeds, UK
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, UK
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14
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Zago FC, Schütz LF, Gerger RPDC, de Aguiar LH, Pinzón-Osorio CA, Mezzallira A, Rodrigues JL, Forell F, Bertolini M. In vitro and in vivo embryo production efficiency in Flemish and Holstein donor females. Anim Reprod 2023; 20:e20230080. [PMID: 38025999 PMCID: PMC10681134 DOI: 10.1590/1984-3143-ar2023-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/10/2023] [Indexed: 12/01/2023] Open
Abstract
The aim of this study was to compare embryo production efficiency in Flemish and Holstein donor females using ovum pick-up and in vitro fertilization (OPU-IVF) or in vivo production (superovulation; SOV) procedures. The study was conducted using a split-plot design, with eight Flemish and eight Holstein non-lactating cycling females. Females were subjected to ten weekly OPU/IVF sessions and/or two SOV/embryo collections sessions at a 63-day interval, for a total of 160 OPU-IVF and 32 SOV sessions. Mean numbers of follicles and corpora lutea, and cumulus-oocyte complex (COC) recovery rates were similar between breeds after the OPU and SOV sessions. However, Flemish donors yielded better quality grade II COCs (301, 41.9%) than Holstein females (609, and 202, 33.1%). Also, cleavage and blastocyst rates, and the total number and the mean number of viable embryos obtained after OPU-IVF were higher in Flemish (49.6% and 11.8%, and 63 and 11.8 per donor, respectively) than in Holstein (32.8% and 7.2%, and 34 and 7.2 per donor, respectively) females. Flemish females were also more efficient in yielding viable embryos after SOV (111, 7.3 per donor) than Holstein (48, 3.3 per donor) females. Overall, Flemish donor females had better responses to OPU-IVF or SOV procedures than Holstein counterparts. Irrespective of the breeds, SOV procedures were more efficient than OPU-IVF in yielding more viable embryos, under the conditions of this study. Both reproductive procedures were useful tools for the genetic conservation of the Flemish cattle breed in Southern Brazil.
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Affiliation(s)
- Fabiano Carminatti Zago
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Lages, SC, Brasil
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brasil
| | - Luís Fernando Schütz
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brasil
| | | | - Luís Henrique de Aguiar
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brasil
- Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | | | - Alceu Mezzallira
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brasil
| | - José Luiz Rodrigues
- Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Fabiana Forell
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brasil
| | - Marcelo Bertolini
- Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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15
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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. ROYAL SOCIETY OPEN SCIENCE 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] [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.
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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
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Amiri Ghanatsaman Z, Ayatolahi Mehrgardi A, Asadollahpour Nanaei H, Esmailizadeh A. Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds. Sci Rep 2023; 13:8722. [PMID: 37253766 DOI: 10.1038/s41598-023-35973-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/26/2023] [Indexed: 06/01/2023] Open
Abstract
During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Ahmad Ayatolahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
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Carrier A, Gilbert I, Leclerc P, Duchesne M, Robert C. Characterization of the genetic pool of the Canadienne dairy cattle breed. Genet Sel Evol 2023; 55:32. [PMID: 37161364 PMCID: PMC10170705 DOI: 10.1186/s12711-023-00793-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/15/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Canadienne cattle are the oldest breed of dairy cattle in North America. The Canadienne breed originates from cattle that were brought to America by the mid-seventeenth century French settlers. The herd book was established in 1886 and the current breed characteristics include dark coat color, small size compared to the modern Holstein breed, and overall rusticity shaped by the harsh environmental conditions that were prevalent during the settlement of North America. The Canadienne breed is an invaluable genetic resource due to its high resilience, longevity and fertility. However, it is heavily threatened with a current herd limited to an estimated 1200 registered animals, of which less than 300 are fullblood. To date, no effort has been made to document the genetic pool of this heritage breed in order to preserve it. RESULTS In this project, we used genomic data, which allow a precise description of the genetic makeup of a population, to provide valuable information on the genetic diversity of this heritage breed and suggest management options for its long-term viability. Using a panel that includes 640,000 single nucleotide polymorphisms (SNPs), we genotyped 190 animals grouped into six purity ranges. Unsupervised clustering analyses revealed three genetically distinct groups among those with the higher levels of purity. The observed heterozygosity was higher than expected even in the 100% purebreds. Comparison with Holstein genotypes showed significantly shorter runs of homozygosity for the Canadienne breed, which was unexpected due to the high inbreeding value calculated from pedigree data. CONCLUSIONS Overall, our data indicate that the fullblood gene pool of the Canadienne breed is more diversified than expected and that bloodline management could promote breed sustainability. In its current state, the Canadienne is not a dead-end breed but remains highly vulnerable due to its small population size.
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Affiliation(s)
- Alexandra Carrier
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Isabelle Gilbert
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Pierre Leclerc
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Dé̇partement d'obstétrique, gynécologie et reproduction, Faculté de médecine, Université Laval, QC, Québec, Canada
| | - Mario Duchesne
- Association de Mise en Valeur de La Race Bovine Canadienne (AVRBC), Québec, QC, Canada
| | - Claude Robert
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada.
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada.
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
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SHARMA REKHA, SEHRAWAT RENUKA, AHLAWAT SONIKA, GURJAR ML, TANTIA MS. Genetic diversity evaluation of Sojat goat population of India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i12.117981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sojat goat forms the part and parcel of the lives of the farmers in the Barmer region of Rajasthan. These are large-sized goats, white in colour, and have dual utility. These goats fetch premium price during the Eid festival. Assessment of diversity is essential for germplasm characterization and management. Genomic microsatellite markers being a valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in the Sojat goat population. The standard metrics of genomic diversity detected moderate variability with a total of 162 alleles across 22 loci in this lesser-known population. The expected number of alleles had a mean value of 3.40±0.39. Similarly, a moderate magnitude of diversity was recorded in the Sojat population as the mean observed heterozygosity was 0.54±0.05. Expected heterozygosity was higher than the observed (0.60±0.06), indicating a deviation from Hardy-Weinberg Equilibrium (HWE) and the possibility of inbreeding due to the non-random mating in the population. Accordingly, significant heterozygote deficiency was noticed (F=0.08±0.03). The population did not suffer a reduction in effective population size in the last few generations. Mutation drift equilibrium did not reveal significant heterozygosity excess under different models of microsatellite evolution and no shift was recorded in the frequency distribution of alleles. To conclude, the results provided the first insights into the genetic diversity of Sojat goats. A moderate genetic variability with heterozygote deficiency within the population warrants immediate attention for scientific management of this unique goat population to conserve the existing genetic variation and to avoid any escalation of inbreeding.
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19
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Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle. PLoS One 2022; 17:e0278681. [PMID: 36490290 PMCID: PMC9733863 DOI: 10.1371/journal.pone.0278681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.
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20
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Lashmar SF, Visser C, Okpeku M, Muchadeyi FC, Mapholi NO, van Marle-Köster E. A within- and across-country assessment of the genomic diversity and autozygosity of South African and eSwatini Nguni cattle. Trop Anim Health Prod 2022; 54:365. [DOI: 10.1007/s11250-022-03373-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
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Strandén I, Kantanen J, Lidauer MH, Mehtiö T, Negussie E. Animal board invited review: Genomic-based improvement of cattle in response to climate change. Animal 2022; 16:100673. [PMID: 36402112 DOI: 10.1016/j.animal.2022.100673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 12/24/2022] Open
Abstract
Climate change brings challenges to cattle production, such as the need to adapt to new climates and pressure to reduce greenhouse emissions (GHG). In general, the improvement of traits in current breeding goals is favourably correlated with the reduction of GHG. Current breeding goals and tools for increasing cattle production efficiency have reduced GHG. The same amount of production can be achieved by a much smaller number of animals. Genomic selection (GS) may offer a cost-effective way of using an efficient breeding approach, even in low- and middle-income countries. As climate change increases the intensity of heatwaves, adaptation to heat stress leads to lower efficiency of production and, thus, is unfavourable to the goal of reducing GHG. Furthermore, there is evidence that heat stress during cow pregnancy can have many generation-long lowering effects on milk production. Both adaptation and reduction of GHG are among the difficult-to-measure traits for which GS is more efficient and suitable than the traditional non-genomic breeding evaluation approach. Nevertheless, the commonly used within-breed selection may be insufficient to meet the new challenges; thus, cross-breeding based on selecting highly efficient and highly adaptive breeds may be needed. Genomic introgression offers an efficient approach for cross-breeding that is expected to provide high genetic progress with a low rate of inbreeding. However, well-adapted breeds may have a small number of animals, which is a source of concern from a genetic biodiversity point of view. Furthermore, low animal numbers also limit the efficiency of genomic introgression. Sustainable cattle production in countries that have already intensified production is likely to emphasise better health, reproduction, feed efficiency, heat stress and other adaptation traits instead of higher production. This may require the application of innovative technologies for phenotyping and further use of new big data techniques to extract information for breeding.
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Affiliation(s)
- I Strandén
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland.
| | - J Kantanen
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - M H Lidauer
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - T Mehtiö
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - E Negussie
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
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22
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Nyman S, Johansson AM, Palucci V, Schönherz AA, Guldbrandtsen B, Hinrichs D, de Koning DJ. Inbreeding and pedigree analysis of the European red dairy cattle. Genet Sel Evol 2022; 54:70. [PMID: 36274137 PMCID: PMC9590155 DOI: 10.1186/s12711-022-00761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/12/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Red dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals with the highest genetic contributions were identified. Pedigree data included 9,073,403 animals that were born between 1900 and 2019 from Denmark, Finland, Germany, Latvia, Lithuania, the Netherlands, Norway, Poland, and Sweden, and covered 32 breeds. The numerically largest breeds were Red Dairy Cattle and Meuse-Rhine-Yssel. RESULTS The deepest average complete generation equivalent (9.39) was found for Red Dairy Cattle in 2017. Mean pedigree completeness ranged from 0.6 for Finncattle to 7.51 for Red Dairy Cattle. An effective population size of 166 animals was estimated for the total pedigree and ranged from 35 (Rotes Höhenvieh) to 226 (Red Dairy Cattle). Average generation intervals were between 5 and 7 years. The mean inbreeding coefficient for animals born between 1960 and 2018 was 1.5%, with the highest inbreeding coefficients observed for Traditional Angler (4.2%) and Rotes Höhenvieh (4.1%). The most influential animal was a Dutch Meuse-Rhine-Yssel bull born in 1960. The mean inbreeding level for animals born between 2016 and 2018 was 2% and highest for the Meuse-Rhine-Yssel (4.64%) and Rotes Hohenvieh breeds (3.80%). CONCLUSIONS We provide the first detailed analysis of the genetic diversity and inbreeding levels of the European red dairy cattle breeds. Rotes Höhenvieh and Traditional Angler have high inbreeding levels and are either close to or below the minimal recommended effective population size, thus it is necessary to implement tools to monitor the selection process in order to control inbreeding in these breeds. Red Dairy Cattle, Vorderwälder, Swedish Polled and Hinterwälder hold more genetic diversity. Regarding the Meuse-Rhine-Yssel breed, given its decreased population size, increased inbreeding and low effective population size, we recommend implementation of a breeding program to prevent further loss in its genetic diversity.
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Affiliation(s)
- Sofia Nyman
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna M. Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Valentina Palucci
- Interbull Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Bernt Guldbrandtsen
- Department of Animal Science, Aarhus University, Tjele, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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23
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Drzaic I, Curik I, Lukic B, Shihabi M, Li MH, Kantanen J, Mastrangelo S, Ciani E, Lenstra JA, Cubric-Curik V. High-Density Genomic Characterization of Native Croatian Sheep Breeds. Front Genet 2022; 13:940736. [PMID: 35910220 PMCID: PMC9337876 DOI: 10.3389/fgene.2022.940736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.
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Affiliation(s)
- Ivana Drzaic
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
- *Correspondence: Ivana Drzaic, ; Vlatka Cubric-Curik,
| | - Ino Curik
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Boris Lukic
- Department of Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, Chair for Domestic Animal Breeding and Genetics, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Universita Degli Studi di Bari “Aldo Moro”, Bari, Italy
| | | | - Vlatka Cubric-Curik
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
- *Correspondence: Ivana Drzaic, ; Vlatka Cubric-Curik,
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Comparison of Female Verzaschese and Camosciata delle Alpi Goats' Hematological Parameters in The Context of Adaptation to Local Environmental Conditions in Semi-Extensive Systems in Italy. Animals (Basel) 2022; 12:ani12131703. [PMID: 35804602 PMCID: PMC9264801 DOI: 10.3390/ani12131703] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 01/15/2023] Open
Abstract
Local livestock breeds are pivotal to ensure sustainable agriculture and represent a real genetic resource in the context of genetic variability reduction. This study aimed at broadening the knowledge about hematological values in female Verzaschese and Camosciata delle Alpi goats (an Italian local and a cosmopolitan goat breed, respectively) and investigating factors affecting them (i.e., breed, age, season). Blood samples were collected monthly from 34 Verzaschese and 37 Camosciata delle Alpi female goats kept under the same semi-extensive farming system for a whole year. The main hematological parameters were evaluated, and descriptive as well as inferential statistical analyses were performed. Reference intervals for complete blood cell count were established and several inter-breed differences were found. In particular, most of the red blood cell parameters were higher in Verzaschese than Camosciata delle Alpi (p < 0.05) suggesting a greater gastrointestinal parasites’ resilience of the local breed. The age effect (p < 0.05) was consistent with the literature while the season effect (p < 0.05) could be explained by the melatonin immunostimulant action and gastrointestinal parasitism influence. Overall, differences in blood values could be attributed to physiological changes and adaptive strategies developed through centuries highlighting the remarkable rusticity and adaptation to the environment and farming system of the local breed.
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Smith WJ, Quilodrán CS, Jezierski MT, Sendell-Price AT, Clegg SM. The wild ancestors of domestic animals as a neglected and threatened component of biodiversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13867. [PMID: 34811819 DOI: 10.1111/cobi.13867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.
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Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
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Capturing Genetic Diversity and Selection Signatures of the Endangered Kosovar Balusha Sheep Breed. Genes (Basel) 2022; 13:genes13050866. [PMID: 35627251 PMCID: PMC9140571 DOI: 10.3390/genes13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
There is a growing concern about the loss of animal genetic resources. The aim of this study was to analyze the genetic diversity and potential peculiarity of the endangered Kosovar sheep breed Balusha. For this purpose, a dataset consisting of medium-density SNP chip genotypes (39,879 SNPs) from 45 Balusha sheep was generated and compared with SNP chip genotypes from 29 individuals of a second Kosovar breed, Bardhoka. Publicly available SNP genotypes from 39 individuals of the relatively closely located sheep breeds Istrian Pramenka and Ruda were additionally included in the analyses. Analysis of heterozygosity, allelic richness and effective population size was used to assess the genetic diversity. Inbreeding was evaluated using two different methods (FIS, FROH). The standardized FST (di) and cross-population extended haplotype homozygosity (XPEHH) methods were used to detect signatures of selection. We observed the lowest heterozygosity (HO = 0.351) and effective population size (Ne5 = 25, Ne50 = 228) for the Balusha breed. The mean allelic richness levels (1.780–1.876) across all analyzed breeds were similar and also comparable with those in worldwide breeds. FROH estimates (0.023–0.077) were highest for the Balusha population, although evidence of decreased inbreeding was observed in FIS results for the Balusha breed. Two Gene Ontology (GO) TERMs were strongly enriched for Balusha, and involved genes belonging to the melanogenesis and T cell receptor signaling pathways, respectively. This could result from selection for the special coat color pattern of Balusha (black head) and resistance to certain infectious diseases. The analyzed diversity parameters highlight the urgency to preserve the local Kosovar Balusha sheep as it is clearly distinguished from other sheep of Southeastern Europe, has the lowest diversity level and may harbor valuable genetic variants, e.g., for resistance to infectious diseases.
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Waineina RW, Okeno TO, Ilatsia ED, Ngeno K. Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. Front Genet 2022; 13:858923. [PMID: 35528543 PMCID: PMC9068939 DOI: 10.3389/fgene.2022.858923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.
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Affiliation(s)
- Ruth W Waineina
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya.,Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Tobias O Okeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| | - Evans D Ilatsia
- Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Kiplangat Ngeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
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Abstract
This study is part of a project (Sheep Al.L. Chain, RDP Veneto Region) aiming to improve the competitiveness of local sheep breed farms through valorization of their links with mountain agroecosystems. We considered two local sheep breeds of the eastern Italian Alps, “Alpagota” and “Lamon”, which have a population of 400 and 3000 heads, respectively, and are used to produce lambs for typical products. A total of 35 farms (17 for Alpagota, with a total of 1652 heads; 18 for Lamon, with a total of 337 heads) were surveyed to collect data on farm organization, flock structure and management (farm questionnaire), land use management (GIS approach), and value chain organization (participatory processes). The link between the two local sheep breeds and mountain agroecosystems is very strong: land use is characterized by a large number of small patches of grasslands in marginal areas. Moving from the results of this study, a set of strategies aiming at improving the competitiveness of these systems have been proposed. Communication to the consumers and to the relevant stakeholders of the added value of local sheep breeds in marginal mountain agroecosystems can contribute to favor the resilience of small ruminant farms and the conservation of Alpine sheep breeds.
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Genetic diversity in some domestic and wild sheep and goats in Iran. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Single nucleotide polymorphisms and metabolic biochemical profile of productive markers characterize three European breeds of dairy cattle. ACTA VET BRNO 2022. [DOI: 10.2754/avb202291040317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The objective of this study was to investigate polymorphisms of DGAT1, FABP, OLR1 and ATP1A1 genes using PCR-DNA sequencing, and to associate these genetic structures to changes in metabolic biochemical markers and milk composition indicators in a total of 90 dairy cows of the Holstein, Simmental, and Brown Swiss breeds (30 cows each). PCR was carried out for amplification of 411-bp of DGAT1, 525-bp of FABP, 582-bp of OLR1, and 300-bp of ATP1A1 genes. Three breeds’ nucleotide sequence variations in the form of single nucleotide polymorphisms (SNPs) were detailed by DNA sequencing analysis. Chisquare analysis showed that the distribution of all discovered SNPs varied significantly (P < 0.001). Biochemical indices in cow’s serum revealed no significant difference in serum total protein, albumin, and total cholesterol among the three breeds. However, triglyceride showed a significant increase in Simmental compared to either Holsteins or Brown Swiss, while the highest mean value of triiodothyronine (T3) and tetraiodothyronine (T4) was detected in Holstein dairy cows The milk composition indicators analysis revealed that milk protein, sugar, and density were significantly higher in Holsteins than both Simmental and Brown Swiss. Meanwhile, milk fat and total solids revealed a significantly higher increase in Simmental than both brown Swiss and Holstein. As a result, the metabolic biochemical markers profile along with the identified SNPs could be used as a candidate and a reference guide for effective characterization of the Holstein, Simmental, and Brown Swiss breeds, leading to the creation of a marker-assisted selection system for production traits in dairy cattle breeds.
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31
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Ouhrouch A, Boitard S, Boyer F, Servin B, Da Silva A, Pompanon F, Haddioui A, Benjelloun B. Genomic Uniqueness of Local Sheep Breeds From Morocco. Front Genet 2021; 12:723599. [PMID: 34925440 PMCID: PMC8675355 DOI: 10.3389/fgene.2021.723599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2021] [Indexed: 01/17/2023] Open
Abstract
Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.
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Affiliation(s)
- Abdessamad Ouhrouch
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco.,Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Simon Boitard
- CBGP, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Anne Da Silva
- PEREINE/E2LIM, Faculty of Science and Technics, Limoges, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Abdelmajid Haddioui
- Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
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Serranito B, Cavalazzi M, Vidal P, Taurisson-Mouret D, Ciani E, Bal M, Rouvellac E, Servin B, Moreno-Romieux C, Tosser-Klopp G, Hall SJG, Lenstra JA, Pompanon F, Benjelloun B, Da Silva A. Local adaptations of Mediterranean sheep and goats through an integrative approach. Sci Rep 2021; 11:21363. [PMID: 34725398 PMCID: PMC8560853 DOI: 10.1038/s41598-021-00682-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Small ruminants are suited to a wide variety of habitats and thus represent promising study models for identifying genes underlying adaptations. Here, we considered local Mediterranean breeds of goats (n = 17) and sheep (n = 25) from Italy, France and Spain. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original cradle (i.e., the geographical area in which the breed has emerged), including transhumant pastoral areas. We then used the programs PCAdapt and LFMM to identify signatures of artificial and environmental selection. Considering cradles instead of current GPS coordinates resulted in a greater number of signatures identified by the LFMM analysis. The results, combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles in relation to the gradient of aridity and altitude. Some of these genes have been previously implicated in lipid metabolism (SUCLG2, BMP2), hypoxia stress/lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). Selection signatures involving the PCDH9 and KLH1 genes, as well as NBEA/NBEAL1, were identified in both species and thus could play an important adaptive role.
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Affiliation(s)
- Bruno Serranito
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France
- CRESCO, Museum National d'Histoire Naturelle (MNHN), 35800, Dinard, France
| | | | - Pablo Vidal
- Universidad Catolica de Valencia, Valencia, Spain
| | - Dominique Taurisson-Mouret
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
- CNRS, UMR 5815, Dynamiques du droit, Université de Montpellier, Montpellier, France
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Marie Bal
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
| | | | - Bertrand Servin
- GenPhySE, INRAE, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | | | | | - Stephen J G Hall
- Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands
| | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
| | - Badr Benjelloun
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
- National Institute of Agronomic Research (INRA), Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Anne Da Silva
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France.
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Denoyelle L, de Villemereuil P, Boyer F, Khelifi M, Gaffet C, Alberto F, Benjelloun B, Pompanon F. Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats. Front Genet 2021; 12:745284. [PMID: 34650601 PMCID: PMC8508783 DOI: 10.3389/fgene.2021.745284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (FST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.
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Affiliation(s)
- Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France.,GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études
- PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Meidhi Khelifi
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Clément Gaffet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Florian Alberto
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Badr Benjelloun
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France.,Institut National de la Recherche Agronomique Maroc (INRA-Maroc), Centre Régional de Beni Mellal, Beni Mellal, Morocco
| | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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34
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Naturally Occurring Glycosidases in Milk from Native Cattle Breeds: Activity and Consequences on Free and Protein Bound-Glycans. Metabolites 2021; 11:metabo11100662. [PMID: 34677377 PMCID: PMC8540597 DOI: 10.3390/metabo11100662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the extent of variation and activity of naturally occurring milk glycosidases and their potential to degrade milk glycans. A multi-omics approach was used to investigate the relationship between glycosidases and important bioactive compounds such as free oligosaccharides and O-linked glycans in bovine milk. Using 4-methylumbelliferone (4-MU) assays activities of eight indigenous glycosidases were determined, and by mass spectrometry and 1H NMR spectroscopy various substrates and metabolite products were quantified in a subset of milk samples from eight native North European cattle breeds. The results showed a clear variation in glycosidase activities among the native breeds. Interestingly, negative correlations between some glycosidases including β-galactosidase, N-acetyl-β-d-glucosaminidase, certain oligosaccharide isomers as well as O-linked glycans of κ-casein were revealed. Further, a positive correlation was found for free fucose content and α-fucosidase activity (r = 0.37, p-value < 0.001) indicating cleavage of fucosylated glycans in milk at room temperature. The results obtained suggest that milk glycosidases might partially degrade valuable glycans, which would result in lower recovery of glycans and thus represent a loss for the dairy ingredients industry if these activities are pronounced.
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35
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Disentangling the Multidimensional Relationship between Livestock Breeds and Ecosystem Services. Animals (Basel) 2021; 11:ani11092548. [PMID: 34573513 PMCID: PMC8467734 DOI: 10.3390/ani11092548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/26/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Livestock breeds represent the diversity of livestock animals. They participate in the delivery of ecosystem services (ES), i.e., the benefits to humans provided by nature. In recent years, the contribution of livestock breeds to ES has received attention in livestock research. Additionally, there is increasing interest in integrating this knowledge into policies to make agriculture more sustainable. In this work, we elaborate on livestock breed characteristics that are key to the study of livestock breed contributions to ES. Thus, we explore the natural and human factors that have produced livestock breeds as ecologically and culturally mediated entities. In addition, we review the different roles of livestock breeds as biodiversity components. Finally, we examine how livestock breeds participate in livestock system heterogeneity. By integrating these aspects, we might better understand how livestock breeds provide and modulate ES provision and, therefore, how to improve breed conservation and livestock policies toward more sustainable farming. Abstract There is an increasing interest in assessing livestock breed contributions to ecosystem services (ES) and including this knowledge in decision making. However, this task has been limited due to the complexity of the multidimensional relationship between livestock diversity and ecosystem services. In this work, we elaborate on the livestock breed characteristics central to developing a comprehensive approach to livestock breed inclusion in the ecosystem services framework. Thus, we explore the multidimensional nature of livestock breeds, i.e., as eco-cultural entities, biodiversity components, and drivers of livestock system heterogeneity and functioning. First, anthropogenic and natural factors have acted jointly to develop breeds as eco-cultural entities. This fact represents an opportunity to move toward farming system sustainability by Nature-Based Solutions and Nature’s Contribution to People paradigms. Second, livestock breeds are components of biodiversity, and as such, can be framed as goods, as final ecosystem services, and as regulators of ecosystem processes. Third, livestock breeds contribute to livestock system heterogeneity and resilience. By integrating these aspects, we might better understand how livestock breeds provide and modulate ecosystem service provision and, therefore, how to improve breed conservation and livestock policies toward farming system sustainability.
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36
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Vohra V, Singh NP, Chhotaray S, Raina VS, Chopra A, Kataria RS. Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India. PeerJ 2021; 9:e11846. [PMID: 34447621 PMCID: PMC8364325 DOI: 10.7717/peerj.11846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/01/2021] [Indexed: 12/02/2022] Open
Abstract
To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.
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Affiliation(s)
- Vikas Vohra
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Narendra Pratap Singh
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Varinder Singh Raina
- Department of Animal Husbandry and Dairying, Ministry of Fisheries, Animal Husbandry and Dairying, New Delhi, New Delhi, India
| | - Alka Chopra
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Ranjit Singh Kataria
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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37
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Suezawa R, Nikadori H, Sasaki S. Genetic diversity and genomic inbreeding in Japanese Black cows in the islands of Okinawa Prefecture evaluated using single-nucleotide polymorphism array. Anim Sci J 2021; 92:e13525. [PMID: 33599382 DOI: 10.1111/asj.13525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 11/30/2022]
Abstract
Maintaining genetic diversity and inbreeding control are important in Japanese Black cattle production, especially in remote areas such as the islands of Okinawa Prefecture. Using a single-nucleotide polymorphism (SNP) array, we evaluated the genetic diversity and genomic inbreeding in Japanese Black cows from the islands of Okinawa Prefecture and compared them to those from other locations across Japan. Linkage disequilibrium decay was slower in cows in the islands of Okinawa Prefecture. The estimated effective population size declined over time in both populations. The genomic inbreeding coefficient (FROH ) was estimated using long stretches of consecutive homozygous SNPs (runs of homozygosity; ROH). FROH was higher in the cows on the islands of Okinawa Prefecture than on other locations. In total, 818 ROH fragments, including those containing NCAPG and PLAG1, which are major quantitative trait loci for carcass weight in Japanese Black cattle, were present at significantly higher frequencies in cows in the islands of Okinawa Prefecture. This suggests that the ROH fragments are under strong selection and that cows in the islands of Okinawa Prefecture have low genetic diversity and high genomic inbreeding relative to those at other locations. SNP arrays are useful tools for evaluating genetic diversity and genomic inbreeding in cattle.
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Affiliation(s)
- Ryouhei Suezawa
- Okinawa Prefectural Livestock and Grassland Research Center, Okinawa, Japan
| | - Hideki Nikadori
- Okinawa Prefectural Livestock and Grassland Research Center, Okinawa, Japan
| | - Shinji Sasaki
- University of the Ryukyus, Faculty of Agriculture, Okinawa, Japan.,United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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38
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Moosanezhad Khabisi M, Asadi Foozi M, Lv FH, Esmailizadeh A. Genome-wide DNA arrays profiling unravels the genetic structure of Iranian sheep and pattern of admixture with worldwide coarse-wool sheep breeds. Genomics 2021; 113:3501-3511. [PMID: 34293474 DOI: 10.1016/j.ygeno.2021.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/18/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
Archaeological and genetic evidence show that sheep were originally domesticated in area around the North of Zagros mountains, North-west of Iran. The Persian plateau exhibits a variety of native sheep breeds with a common characteristic of coarse-wool production. Therefore, knowledge about the genetic structure and diversity of Iranian sheep and genetic connections with other sheep breeds is of great interest. To this end, we genotyped 154 samples from 11 sheep breeds distributed across Iran with the Ovine Infinium HD SNP 600 K BeadChip array, and analyzed this dataset combined with the retrieved data of 558 samples from 19 worldwide coarse-wool sheep breeds. The average genetic diversity ranged from 0.315 to 0.354, while the FST values ranged from 0.016 to 0.177 indicating a low differentiation of Iranian sheep. Analysis of molecular variance showed that 90.21 and 9.79% of the source of variation were related to differences within and between populations, respectively. Our results indicated that the coarse-wool sheep from Europe were clearly different from those of the Asia. Accordingly, the Asiatic mouflon was positioned between Asian and European countries. In addition, we found that the genetic background of Iranian sheep is present in sheep from China and Kyrgyzstan, as well as India. The revealed admixture patterns of the Iranian sheep and other coarse-wool sheep breeds probably resulted from the expansion of nomads and through the Silk Road trade network.
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Affiliation(s)
- Mozhdeh Moosanezhad Khabisi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133 Kerman, Iran
| | - Masood Asadi Foozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133 Kerman, Iran
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133 Kerman, Iran.
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39
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Abied A, Ahbara AM, Berihulay H, Xu L, Islam R, El-Hag FM, Rekik M, Haile A, Han JL, Ma Y, Zhao Q, Mwacharo JM. Genome Divergence and Dynamics in the Thin-Tailed Desert Sheep From Sudan. Front Genet 2021; 12:659507. [PMID: 34349777 PMCID: PMC8327097 DOI: 10.3389/fgene.2021.659507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
With climate change bound to affect food and feed production, emphasis will shift to resilient and adapted indigenous livestock to sustain animal production. However, indigenous livestock comprise several varieties, strains and ecotypes whose genomes are poorly characterized. Here, we investigated genomic variation in an African thin-tailed Desert Sheep sampled in Sudan, using 600K genotype data generated from 92 individuals representing five ecotypes. We included data from 18 fat-tailed and 45 thin-tailed sheep from China, to investigate shared ancestry and perform comparative genomic analysis. We observed a clear genomic differentiation between the African thin-tailed Desert Sheep and the Chinese thin-tailed and fat-tailed sheep, suggesting a broad genetic structure between the fat-tailed and thin-tailed sheep in general, and that at least two autosomal gene pools comprise the genome profile of the thin-tailed sheep. Further analysis detected two distinct genetic clusters in both the African thin-tailed Desert Sheep and the Chinese thin-tailed sheep, suggesting a fine-scale and complex genome architecture in thin-tailed sheep. Selection signature analysis suggested differences in adaptation, production, reproduction and morphology likely underly the fine-scale genetic structure in the African thin-tailed Desert Sheep. This may need to be considered in designing breeding programs and genome-wide association studies.
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Affiliation(s)
- Adam Abied
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Dry Land Research Centre and Animal Production, Agricultural Research Corporation, Khartoum, Sudan
| | - Abulgasim M Ahbara
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Haile Berihulay
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rabiul Islam
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Faisal M El-Hag
- Dry Land Research Centre and Animal Production, Agricultural Research Corporation, Khartoum, Sudan.,Arid Land Research Centre, Tottori University, Tottori, Japan
| | - Mourad Rekik
- International Center for Agricultural Research in the Dry Areas (ICARDA), Amman, Jordan
| | - Aynalem Haile
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.,Animal and Veterinary Sciences, Scotland Rural College and Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, Midlothian, United Kingdom
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Xiao C, Li J, Xie T, Chen J, Zhang S, Elaksher SH, Jiang F, Jiang Y, Zhang L, Zhang W, Xiang Y, Wu Z, Zhao S, Du X. The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Ecol Evol 2021; 11:7779-7795. [PMID: 34188851 PMCID: PMC8216945 DOI: 10.1002/ece3.7611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 02/05/2023] Open
Abstract
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.
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Affiliation(s)
- Changyi Xiao
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Tanghui Xie
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jianhai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Institutes for Systems GeneticsFrontiers Science Center for Disease‐related Molecular NetworkWest China HospitalSichuan UniversityChengduChina
| | - Sijia Zhang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Salma Hassan Elaksher
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Genetics and Genetic Engineering DepartmentFaculty of AgricultureBenha UniversityMoshtohorEgypt
| | - Fan Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yaoxin Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Wei Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhenyang Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- College of Agroforestry Engineering and PlanningTongren UniversityTongrenChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Xiaoyong Du
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
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Peixoto MGCD, Carvalho MRS, Egito AA, Steinberg RS, Bruneli FÂT, Machado MA, Santos FC, Rosse IC, Fonseca PAS. Genetic Diversity and Population Genetic Structure of a Guzerá ( Bos indicus) Meta-Population. Animals (Basel) 2021; 11:1125. [PMID: 33919992 PMCID: PMC8071051 DOI: 10.3390/ani11041125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 11/16/2022] Open
Abstract
The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021-0.100; lineages = 0.021-0.100), Fis (Farms = -0.007-0.076; lineages = -0.014-0.070), and Fst (Farms = 0.0237-0.032; lineages = 0.029-0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level.
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Affiliation(s)
| | - Maria Raquel S. Carvalho
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.R.S.C.); (R.S.S.); (F.C.S.); (I.C.R.); (P.A.S.F.)
| | | | - Raphael S. Steinberg
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.R.S.C.); (R.S.S.); (F.C.S.); (I.C.R.); (P.A.S.F.)
| | | | | | - Fernanda C. Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.R.S.C.); (R.S.S.); (F.C.S.); (I.C.R.); (P.A.S.F.)
- Centre for Addiction and Mental Health (CAMH), Campbell Family Mental Health Research Institute, Toronto, ON M5T 1R8, Canada
| | - Izinara C. Rosse
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.R.S.C.); (R.S.S.); (F.C.S.); (I.C.R.); (P.A.S.F.)
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Pablo Augusto S. Fonseca
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.R.S.C.); (R.S.S.); (F.C.S.); (I.C.R.); (P.A.S.F.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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van der Nest MA, Hlongwane N, Hadebe K, Chan WY, van der Merwe NA, De Vos L, Greyling B, Kooverjee BB, Soma P, Dzomba EF, Bradfield M, Muchadeyi FC. Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed. Front Genet 2021; 11:608650. [PMID: 33584805 PMCID: PMC7876384 DOI: 10.3389/fgene.2020.608650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022] Open
Abstract
In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.
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Affiliation(s)
| | - Nompilo Hlongwane
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Wai-Yin Chan
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Nicolaas A van der Merwe
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Ben Greyling
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | | | - Pranisha Soma
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | - Edgar F Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
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Mamogobo MD, Mapholi NO, Nephawe KA, Nedambale TL, Mpofu TJ, Sanarana YP, Mtileni BJ. Genetic characterisation of non-descript cattle populations in communal areas of South Africa. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an20030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results High level of genetic diversity was found across the five non-descript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 ≤ K ≤ 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu–Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.
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Recent land use and management changes decouple the adaptation of livestock diversity to the environment. Sci Rep 2020; 10:21035. [PMID: 33273517 PMCID: PMC7713044 DOI: 10.1038/s41598-020-77878-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/18/2020] [Indexed: 01/07/2023] Open
Abstract
Native livestock breeds, i.e. those autochthonous to a specific region, are locally adapted domesticated animals that conserve genetic resources, guaranty food security and provide agroecosystem services. Native breeds are largely threatened worldwide by agricultural intensification and rural areas abandonment processes related to recent changes in production schemes and planning. Yet, our gap of knowledge regarding livestock breed-environment relationships may prevent the design of successful conservation measures. In this work, we analyse the links between livestock diversity -i.e. richness of native breeds- and a selection of environmental factors that express at broad scales, with a temporal perspective. We compare native breeds distributional patterns before and after the agricultural intensification, in the context of land-use change in mainland Spain. Our results confirm the existence of strong associations between the distribution of native livestock breeds and environmental factors. These links, however, weaken for contemporary distributions. In fact, changes in breed distribution reflect a shift towards more productive environments. Finally, we found that the areas having higher breed richness are undergoing land abandonment processes. Succeeding in the conservation of threatened native breeds will require going beyond merely genetic and production-oriented views. Ecological and sociocultural perspectives should also be accounted for as global change processes are determinant for livestock agrobiodiversity.
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Bastianetto E, de Oliveira DAA, McManus C, Bagolin DDJ, Leite RC, de Melo CB. Genetic material from buffalo and cattle: crucial importance in the formalization of bilateral trade between India and Brazil. Anim Reprod 2020; 17:e20200031. [PMID: 33791024 PMCID: PMC7995262 DOI: 10.1590/1984-3143-ar2020-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The trade in live animals between India and Brazil dates from the late nineteenth century when European travellers traded animals of Indian origin for display in zoos. Considering the origin of coffee and sugar cane, as well as the expertise related to mineral evaluation, we need to consider that India was involved in important economic cycles of Brazil, even indirectly. This virtuous flow of trade has been maintained and intensified throughout modern history, especially after these two nations gained political independence from their colonisers, thereby becoming independent in mercantile affairs. This paper addresses the main points related to the use of animals of Indian origin in Brazil. We revisit some of the historical aspects of the process of colonisation of Brazil, as well as the importation of animals from India. The restrictions imposed on this process due to the occurrence of diseases in cattle and buffalo in India will be examined. At the end of the text, emphasis will be given to the risks of introducing exotic diseases into Brazil.
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Affiliation(s)
- Eduardo Bastianetto
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | | | - Concepta McManus
- Programa de Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brasil
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Moreno-Sierra AM, Cerón-Muñoz MF, Soto-Calderón ID. Population genetic structure of two herds of Aberdeen Angus cattle breed in Colombia. REV COLOMB CIENC PEC 2020. [DOI: 10.17533/udea.rccp.v34n4a05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: Two biotypes of Aberdeen Angus cattle breed, known as Old Type and New Type, that differ in their origin and beef production are formally recognized. In Colombia, this breed has been commercialized for approximately 80 years. Studies on the origin, kinship and levels of genetic diversity of this breed in Colombian herds are scarce, yet important for planning crossing and management strategies. Objective: To measure the genetic diversity and structure of two Colombian herds of Old Type and New Type biotypes of Aberdeen Angus from Huila and Cundinamarca provinces and assess mitochondrial introgression with other breeds. Methods: A set of ten microsatellites and sequences of the Mitochondrial Control Region were characterized. Estimators of genetic diversity and population differentiation along with tests of population assignment were applied. Results: Nuclear loci were highly polymorphic as shown by the Polymorphic Information Content (0.599) and the Probability of Identity (1.896 10-08). Both populations were highly diverse and clearly differentiated into two groups corresponding to the Old Type and New Type phenotypes. In contrast, mitochondrial data failed to distinguish these two groups and showed extensive admixture. Conclusions: This study optimized a set of ten highly polymorphic nuclear markers that may be used for parentage and population genetic studies of Aberdeen Angus. Genetic differentiation in these loci agreed with phenotypic differences of the Old and New Types. However, mitochondrial data indicated ancestry of multiple European breeds in the origin of Colombian Aberdeen Angus.
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Guo X, Wang ZC, Wang S, Li HF, Suwannapoom C, Wang JX, Zhang C, Shao Y, Wang MS, Jiang RS. Genetic signature of hybridization between Chinese spot-billed ducks and domesticated ducks. Anim Genet 2020; 51:866-875. [PMID: 33020910 DOI: 10.1111/age.13002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022]
Abstract
In this study, we analyzed 93 whole genomes from Chinese spot-billed ducks (CSB), meat-type ducks (MET), and egg and dual purpose-type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical-by-descent method, approximately 10.9 Mb introgression segments containing 140 genes were identified showing the signatures of introgression between CSB and EDT. Meanwhile, nearly 10.6 M introgression regions containing 149 genes were identified between CSB and MET. Based on the haplotypes tree of each segment, we found that the introgression between CSB and domesticated ducks was asymmetric with a high level of gene flow from domestic to CSB and a low level of migration in the opposite direction. Moreover, we identified several genes that were introgressions from CSB and showed the signature of positive selection, which may contribute to the breeding of modern ducks. Our results provide new insight into the evolution and breeding history of domestic ducks and may be useful for the future management of wild and domestic duck populations.
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Affiliation(s)
- X Guo
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Z-C Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - S Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - H-F Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, 58 cangjie Rode, Yangzhou, Jiangsu, 225125, China
| | - C Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, 19 Moo 2 Tambon Maeka, Amphur Muang, Phayao, 56000, Thailand
| | - J-X Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - C Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Y Shao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - M-S Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA
| | - R-S Jiang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
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SHARMA HIMANI, SHARMA REKHA, AHLAWAT SONIKA, N RAJAK, JAIN ASIT, TANTIA MS. Genetic diversity status of only registered cattle breed of Chhattisgarh-Kosali. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i6.104993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Assessment of diversity is essential for germplasm characterization and management. Kosali is the first and only registered breed of Chhattisgarh state which immensely contributes to the local economy of 70% farmers. Genomic microsatellite markers being valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in Kosali cattle population. The standard metrics of genomic diversity detected high variability in this breed. All the loci were polymorphic resulting in 297 alleles. Mean values of observed and expected number of alleles were 11.423±0.877 and 4.989±0.372, respectively. Similarly, higher mean values of observed heterozygosity (0.693±0.031) also corroborated with the allelic diversity. Mean expected heterozygosity (0.765±0.02) under Hardy-Weinberg equilibrium (HWE) was higher than the observed values indicating some deviations from assumptions of the model. It can be attributed to the forces such as inbreeding. In fact a positive FIS value of 0.088±0.038 indicated some heterozygote deficiency in the population. Bottleneck analysis indicated that Kosali cattle have not suffered any population bottleneck event during evolutionary trajectory. This study is first to report the genetic diversity status of Kosali cattle based on microsatellite markers.The results imply the necessity of management programs in order to conserve the existing genetic variation and to avoid any escalation of inbreeding.
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Relatively undisturbed African savannas - an important reference for assessing wildlife responses to livestock grazing systems in European rangelands. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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50
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Papachristou D, Koutsouli P, Laliotis GP, Kunz E, Upadhyay M, Seichter D, Russ I, Gjoko B, Kostaras N, Bizelis I, Medugorac I. Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genet Sel Evol 2020; 52:43. [PMID: 32727375 PMCID: PMC7391618 DOI: 10.1186/s12711-020-00560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
Background The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
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Affiliation(s)
- Dimitris Papachristou
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - George P Laliotis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Bunevski Gjoko
- Livestock Department, Faculty of Agricultural Sciences and Food Institute of Animal Biotechnology, University Ss. Cyril and Methodius, 16-ta Makedonska Brigada 3, 1000, Skopje, North Macedonia
| | - Nikolaos Kostaras
- AMALTHIA, Network for the Protection of Greek Indigenous Farm Animals, 51 Argyrokastrou, 15669, Athens, Greece
| | - Iosif Bizelis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.
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