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Susana Lopes M, Azevedo AR, Mendonça D, Rojer H, Cabral V, Ceraolo F, Canto Brum C, Mendes B, da Câmara Machado A. Morphological and genetic characterization of the Graciosa donkey breed. JOURNAL OF APPLIED ANIMAL RESEARCH 2023. [DOI: 10.1080/09712119.2023.2171421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Maria Susana Lopes
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Ana Rita Azevedo
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Duarte Mendonça
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Horst Rojer
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Verónica Cabral
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Franco Ceraolo
- Associação de Criadores e Amigos do Burro Anão da Ilha Graciosa, Açores, Portugal
| | - Carlos Canto Brum
- Associação de Criadores e Amigos do Burro Anão da Ilha Graciosa, Açores, Portugal
| | - Bruno Mendes
- CRL, Unicol-Cooperativa Agrícola, Açores, Portugal
| | - Artur da Câmara Machado
- Centro de Biotecnologia dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
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Orazymbetova Z, Ualiyeva D, Dossybayev K, Torekhanov A, Sydykov D, Mussayeva A, Baktybayev G. Genetic Diversity of Kazakhstani Equus caballus (Linnaeus, 1758) Horse Breeds Inferred from Microsatellite Markers. Vet Sci 2023; 10:598. [PMID: 37888550 PMCID: PMC10611244 DOI: 10.3390/vetsci10100598] [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: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Understanding the genetic diversity and structure of domesticated horse (Equus caballus) populations is critical for long-term herd management and breeding programs. This study examines 435 horses from Kazakhstan, covering seven groups in three geographic areas using 11 STR markers. Identified are 136 alleles, with the mean number of alleles per locus ranging from 9 to 19. VHL20 is the most variable locus across groups, while loci HTG4, AHT4, AHT5, HTG7, and HMS3 are variable in most populations. The locus AHT5 in the Emba population shows the highest frequency of rare alleles, while the lowest frequency, 0.005, is observed in the Kulandy population. All loci were highly informative for the Kazakhstani populations of E. caballus, with PIC values higher than 0.5. Pairwise variations in Wright's FST distances show that the examined varieties have little genetic differentiation (0.05%), indicating a high degree of admixture and a continuing lineage sorting process. Phylogenetic and population structure analyses reveal three major clusters of Kazakh horses, representing (I) the Uralsk population of the Kushum breed and the monophyly of two groups: (II) the Kozhamberdy population of the Mugalzhar breed, and (III) the Mugalzhar-Kushum breed populations. Kazakhstani horse populations, while being regionally isolated, were recently in contact with each other.
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Affiliation(s)
- Zarina Orazymbetova
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Daniya Ualiyeva
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
- Institute of Zoology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Kairat Dossybayev
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Aibyn Torekhanov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| | - Dauren Sydykov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| | - Aizhan Mussayeva
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Gabiden Baktybayev
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
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Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys. Genes (Basel) 2022; 13:1945. [PMID: 36360182 PMCID: PMC9689456 DOI: 10.3390/genes13111945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 08/11/2023] Open
Abstract
Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.
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Direct and indirect contributions of molecular genetics to farm animal welfare: a review. Anim Health Res Rev 2021; 22:177-186. [PMID: 34842522 DOI: 10.1017/s1466252321000104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Since domestication, farm animals have played a key role to increase the prosperity of humankind, while animal welfare (AW) is debated even today. This paper aims to comprehensively review the contributions of developing molecular genetics to farm animal welfare (FAW) and to raise awareness among both scientists and farmers about AW. Welfare is a complex trait affected by genetic structure and environmental factors. Therefore, the best welfare status can be achieved not only to enhance environmental factors such as management and feeding practices, but also the genetic structure of animals must be improved. In this regard, advances in molecular genetics have made great contributions to improve the genetic structure of farm animals, which has increased AW. Today, by sequencing and/or molecular markers, genetic diseases may be detected and eliminated in local herds. Additionally, genes related to diseases or adaptations are investigated by molecular techniques, and the frequencies of desired genotypes are increased in farm animals to keep welfare at an optimized level. Furthermore, stress on animals can be reduced with DNA extraction from stool and feather samples which reduces physical contact between animals and veterinarians. Together with molecular genetics, advances in genome editing tools and biotechnology are promising to improve FAW in the future.
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Wang X, Bou G, Zhang X, Tao L, Shen Y, Na R, Liu G, Ren H, Ren X, Song L, Su S, Bai D, Zhao Y, Li B, Dugarjaviin M. A Fast PCR Test for the Simultaneous Identification of Species and Gender in Horses, Donkeys, Mules and Hinnies. J Equine Vet Sci 2021; 102:103458. [PMID: 34119210 DOI: 10.1016/j.jevs.2021.103458] [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: 11/04/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 11/30/2022]
Abstract
Having considered that the current methods are costly and time-consuming, we designed an only 3 pairs primer-based PCR test to accurately identify the species and gender in horses, donkeys, mules and hinnies. Through a thorough sequence comparison between horse and donkey's highly similar genomes, and a vast amount of preliminary confirmation, we found that three fragments, CNGB3 gene on an autosome, displacement loop region on mitochondrial DNA and SRY genes on chromosome Y, within these equine DNA, are enough to enable us achieving our goal. The PCR test described here would be an economical, fast and accurate alternative for the most commonly-used methods, polymerase chain reaction-restriction fragment length polymorphism, microsatellite assay, and sequencing.
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Affiliation(s)
- Xisheng Wang
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Gerelchimeg Bou
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Xinzhuang Zhang
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Li Tao
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yingchao Shen
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Riga Na
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Guiqin Liu
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China; College of Agronomy, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, Shandong Province, China
| | - Hong Ren
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China; Vocational and Technical College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiujuan Ren
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Lianjie Song
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Shaofeng Su
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongyi Bai
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yiping Zhao
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Bei Li
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Manglai Dugarjaviin
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China.
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Salinas-Rios T, Hernández-Bautista J, Mariscal-Méndez A, Aquino-Cleto M, Martínez-Martínez A, Rodríguez-Magadán HM. Genetic Characterization of a Sheep Population in Oaxaca, Mexico: The Chocholteca Creole. Animals (Basel) 2021; 11:1172. [PMID: 33923878 PMCID: PMC8073038 DOI: 10.3390/ani11041172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022] Open
Abstract
Creole sheep in México have undergone crossbreeding, provoking the loss of genetic variability. The objective of the present study is to determine the intra-racial genetic diversity, the genetic relationship with other genotypes, and the populational substructure of the Oaxacan Creole sheep. Twenty-nine blood samples were obtained of Creole sheep of the Oaxaca Mixteca region in México. A genetic analysis was made with 41 microsatellites recommended for studies of genetic diversity in sheep. An analysis was made of genetic diversity, populational structure, and genetic distance with 27 other sheep populations. The study found 205 alleles with a range of 2 to 9 by locus and an effective number of 3.33. The intra-racial analysis showed a moderate genetic diversity with values of expected heterozygosity of 0.686 and observed of 0.756, a mean polymorphic information content of 0.609, and a mean coefficient of consanguinity of -0.002. In interracial genetic diversity for the coefficients of consanguinity, the values were FIS = 0.0774, FIT = 0.16993, and FST = 0.10028, showing an elevated genetic distance with other creole breeds, but close to Argentine Creole, to another Creole of México and the Spanish Merino. Its genetic structure showed that it does not have any populational subdivision nor mixes with the others analyzed. It is concluded that it is a distinct and isolated population and is proposed as the creole breed "Chocholteca" for its conservation.
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Affiliation(s)
- Teodulo Salinas-Rios
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68110, Mexico
| | - Jorge Hernández-Bautista
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68110, Mexico
| | - Araceli Mariscal-Méndez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68110, Mexico
| | - Magaly Aquino-Cleto
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca 68110, Mexico
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