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Ma X, Liu Y, Sun L, Hanif Q, Qu K, Liu J, Zhang J, Huang B, Lei C. A novel SNP of TECPR2 gene associated with heat tolerance in Chinese cattle. Anim Biotechnol 2023; 34:1050-1057. [PMID: 34877906 DOI: 10.1080/10495398.2021.2011305] [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] [Indexed: 10/19/2022]
Abstract
Heat stress affects the animal production and causes serious economic losses to the husbandry. Tectonin beta-propeller repeat containing 2 (TECPR2) gene plays an important role in autophagy which may affect the temperature sensation in animals. A missense mutation (XM_024981840.1:c.3989 G > A p.Arg1330His) of the transcripts X4 in the bovine TECPR2 gene was identified. In this study, the c.3989 G > A variant in TECPR2 gene was genotyped in a total of 25 cattle breeds (520 individuals). Our results indicated that the frequency of A allele showed a decreasing pattern from southern cattle to northern cattle, while the frequency of G allele showed the opposite pattern, which was consistent with the climate distribution of China. Compared with the GG genotype, southern cattle carried more the AA and AG genotypes. Furthermore, the association results carried out that the frequencies of genotypes (GG, AG, AA) and the value of climate parameters (mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) were significantly correlated (p < 0.01). Hence, we speculated that the c.3989 G > A variant of TECPR2 gene was associated with the heat tolerance trait in Chinese cattle and the locus may be considered as a molecular marker for Chinese cattle breeding.
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Affiliation(s)
- Xiaohui Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yangkai Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Luyang Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, Yunnan, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Wang T, Liu Z, Shi X, Zhang Z, Li Y, Huang B, Ren W, Wang X, Wang C, Chai W. An investigation of genetic diversity in three Dezhou donkey original breeding farms. Sci Rep 2023; 13:11203. [PMID: 37433834 DOI: 10.1038/s41598-023-38219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023] Open
Abstract
Dezhou donkey is one of the excellent large donkey breeds in China. In our study, eight microsatellite markers were used to genotype from each of three populations of Chinese Dezhou donkeys: 67 individuals in Liaocheng (pop1), 103 individuals in Binzhou 1 (pop2), and 102 individuals in Binzhou 2 (pop3), in order to study the genetic diversity of these populations. A total of 213 alleles were detected, and the PIC results showed that eight loci were all highly polymorphic. The means of Ho and He of pop2 were the highest, which were 0.646 and 0.717, respectively. The PCoA analysis demonstrated that the samples from three conservation farms were mixed together. The phylogenetic tree showed that pop 2 and pop 3 were closely related. The phylogenetic tree results clustered that 272 donkeys were divided into six groups. AMOVA analysis showed that the genetic variation was mainly concentrated within the population and the genetic differentiation among the populations was low. Fst values between populations also indicated that genetic differentiation between populations was too small to be considered. This indicated a low probability of inbreeding within the population. And this also showed that the conservation and breeding of Dezhou donkeys in recent years have achieved excellent results. The investigation of genetic diversity in three Dezhou donkey original breeding farms can provide reference data for the selection and breeding of excellent breeds of Dezhou donkey.
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Affiliation(s)
- Tianqi Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Ziwen Liu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Xiaoyuan Shi
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Zhenwei Zhang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Yuhua Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Wei Ren
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Xinrui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China.
| | - Wenqiong Chai
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China.
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Meng S, Zhang Y, Lv S, Zhang Z, Liu X, Jiang L. Comparison of muscle metabolomics between two Chinese horse breeds. Front Vet Sci 2023; 10:1162953. [PMID: 37215482 PMCID: PMC10196265 DOI: 10.3389/fvets.2023.1162953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/03/2023] [Indexed: 05/24/2023] Open
Abstract
With their enormous muscle mass and athletic ability, horses are well-positioned as model organisms for understanding muscle metabolism. There are two different types of horse breeds-Guanzhong (GZ) horses, an athletic breed with a larger body height (~148.7 cm), and the Ningqiang pony (NQ) horses, a lower height breed generally used for ornamental purposes-both inhabited in the same region of China with obvious differences in muscle content. The main objective of this study was to evaluate the breed-specific mechanisms controlling muscle metabolism. In this study, we observed muscle glycogen, enzyme activities, and LC-MS/MS untargeted metabolomics in the gluteus medius muscle of six, each of GZ and NQ horses, to explore differentiated metabolites that are related to the development of two muscles. As expected, the glycogen content, citrate synthase, and hexokinase activity of muscle were significantly higher in GZ horses. To alleviate the false positive rate, we used both MS1 and MS2 ions for metabolite classification and differential analysis. As a result, a total of 51,535 MS1 and 541 MS2 metabolites were identified, and these metabolites can separate these two groups from each other. Notably, 40% of these metabolites were clustered into lipids and lipid-like molecules. Furthermore, 13 significant metabolites were differentially detected between GZ and NQ horses (fold change [FC] value ≥ 2, variable important in projection value ≥1, and Q value ≤ 0.05). They are primarily clustered into glutathione metabolism (GSH, p = 0.01), taurine, and hypotaurine metabolism (p < 0.05) pathways. Seven of the 13 metabolites were also found in thoroughbred racing horses, suggesting that metabolites related to antioxidants, amino acids, and lipids played a key role in the development of skeleton muscle in horses. Those metabolites related to muscle development shed a light on racing horses' routine maintenance and improvement of athletic performance.
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Affiliation(s)
- Sihan Meng
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yanli Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Shipeng Lv
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Zhengkai Zhang
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xuexue Liu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Genetic Diversity and Structure of the Main Danubian Horse Paternal Genealogical Lineages Based on Microsatellite Genotyping. Vet Sci 2022; 9:vetsci9070333. [PMID: 35878350 PMCID: PMC9322366 DOI: 10.3390/vetsci9070333] [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: 06/14/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Danubian horse was created on the former Klementina stud farm near Pleven to satisfy the demands of the Bulgarian Army for light draft horses and to improve the working capacity of the local horse population. The privatization of the Klementina stud farm in the late 1990s and the lack of economic activity have led to a sharp reduction in the number of mares and stallions and their sale to private owners. At present, only six of the main paternal lines which participated in the creation of the Danubian horse breed are preserved: Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar. This is the first study on the genetic and population diversity of the Danubian horse paternal lines based on microsatellite markers (STRs). The results showed that the studied Danubian horse population was characterized by a high level of genetic diversity with a medium value of 0.84. The fixation index (FST) was 0.08 for all studied markers, which is indicative of the low genetic differentiation of the Danubian horse population. Our analysis also confirmed the low level of inbreeding and heterozygous deficiency among the animals selected from the six paternal lineages of the Danubian horse. The present research could be helpful for the development of breeding and conservation programs for the Danubian horse, as well as for making informed decisions on the management of paternal lines. Abstract The Danubian horse, together with the Pleven and the Eastern Bulgarian horse breeds, is one of the modern breeds in Bulgaria. The objective of this study was to compare the genetic structure and genetic diversity of six paternal genealogical lineages of the Danubian horse breed (Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar). In total, 166 individuals from the six genealogical lines were investigated, based on 15 STR markers (short tandem repeats, also known as microsatellites). In total, 184 alleles were found in the six populations, using 15 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphic information content (PIC) values per locus were 12.28, 9.48, and 0.73, respectively. In a comparison of the allelic diversity among sire lineages, the highest genetic diversity (Na) was observed in Lider and Kalifa (14.60 ± 0.21), while the lowest value of this parameter was observed in the Zdravko lineage 4.20 ± 0.35. The largest genetic diversity was found in loci HMS3 and HMS7, with 13 alleles, and the smallest polymorphism was noted for the locus ASB17, with 10 alleles. The level of observed heterozygosity was in the range of 0.65 ± 0.069 for the Zdravko lineage to 0.93 ± 0.01 for the Torpedo lineage. The expected heterozygosity level range was from 0.57 ± 0.048 to 0.91 ± 0.01 for all horse lineages. Structure analysis revealed three main gene pools in the study population. The first pool included the Zdravko lineage; the second had the NONIUS XVII-30, Torpedo, Lider, and Kalifa lineages; and the third defined the Hrabar lineage, which was significantly differentiated from the other genealogical lineages.
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Hsiao C, Lin HH, Kang SR, Hung CY, Sun PY, Yu CC, Toh KL, Yu PJ, Ju YT. Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer. PLoS One 2022; 17:e0265311. [PMID: 35363791 PMCID: PMC8975116 DOI: 10.1371/journal.pone.0265311] [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: 03/19/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.
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Affiliation(s)
- Chen Hsiao
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Hsin-Hung Lin
- Kaohsiung Animal Propagation Station, Pingdong, Taiwan
| | | | - Chien-Yi Hung
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Sun
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chieh-Cheng Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Kok-Lin Toh
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Ju Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ten Ju
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
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Funk SM, Guedaoura S, Juras R, Raziq A, Landolsi F, Luís C, Martínez AM, Musa Mayaki A, Mujica F, Oom MDM, Ouragh L, Stranger Y, Vega‐Pla JL, Cothran EG. Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites. Ecol Evol 2020; 10:4261-4279. [PMID: 32489595 PMCID: PMC7246218 DOI: 10.1002/ece3.6195] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 11/10/2022] Open
Abstract
STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters K opt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (dapc, flock, PCoA, and structure with different run scenarios) all revealed general, broad-scale breed relationships that largely reflect known breed histories but diverged how they characterized small-scale patterns. structure failed to consistently identify K opt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a K opt, was consistent with known breed histories. The over-reliance on K opt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.
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Affiliation(s)
- Stephan Michael Funk
- Centro de Excelencia de Modelación y Computación CientíficaUniversidad de La FronteraTemucoChile
- Nature HeritageSt. LawrenceUK
| | - Sonya Guedaoura
- Faculté des Sciences de la Nature et de la VieUniversité d'El‐TarfEl‐TarfAlgeria
- Faculté de PharmacieUniversité LavalQuébec CityQCCanada
| | - Rytis Juras
- College of Veterinary Medicine and Biomedical ScienceTexas A&M UniversityCollege StationTXUSA
| | - Absul Raziq
- Society of Veterinary, Environment and Agriculture Scientists (SAVES)QuettaPakistan
| | | | - Cristina Luís
- Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT)Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | | | - Fernando Mujica
- Instituto de Producción AnimalUniversidad Austral de ChileValdiviaChile
| | - Maria do Mar Oom
- CE3C – Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | | | - Jose Luis Vega‐Pla
- Laboratorio de Investigación AplicadaCrıa Caballar de las Fuerzas ArmadasCordobaSpain
| | - Ernest Gus Cothran
- College of Veterinary Medicine and Biomedical ScienceTexas A&M UniversityCollege StationTXUSA
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Amano T, Tozaki T, Takasu M, Onogi A, Yamada F, Kawai M, Ueda J. Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses. Anim Sci J 2019; 91:e13318. [PMID: 31755177 DOI: 10.1111/asj.13318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/06/2019] [Accepted: 10/23/2019] [Indexed: 11/29/2022]
Abstract
We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; FIS was -0.07, indicating that the analyzed animals reflected frequent outbreeding and had maintained genetic variation. Based on genetic structural analysis, the number of genetic subpopulations of the animals was estimated to be as 6, and the majority (more than 50%) of each subpopulation corresponded to the progeny of one of the sires used in the breeding farm; these observations suggested that genetic variation in the analyzed animals reflected the genetic differences among sires. Pedigree records indicated that the average co-ancestry coefficient between sires used in the breeding farm was 0.015 corresponding to second cousin. This level of kinship among sires is acceptable for producing HKDs that maintain genetic variation.
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Affiliation(s)
- Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumihiro Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Masahito Kawai
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Junji Ueda
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
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