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Liu H, Zhai J, Wu H, Wang J, Zhang S, Li J, Niu Z, Shen C, Zhang K, Liu Z, Jiang F, Song E, Sun X, Wang Y, Lan X. Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count. Animals (Basel) 2022; 12:ani12182350. [PMID: 36139210 PMCID: PMC9495067 DOI: 10.3390/ani12182350] [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: 05/18/2022] [Revised: 06/30/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplotypes were identified. Moreover, the nucleotide diversity (π) and haplotype diversity (Hd) were 0.024 ± 0.001 and 0.9794 ± 0.003, respectively, indicating the abundance of genetic resources in Chinese Holstein cows. The results of the median-joining network analysis showed two haplogroups (HG, including HG1 and HG2) that diverged in genetic distance. Furthermore, the two haplogroups were significantly (p < 0.05) correlated with the antral follicle (diameter ≥ 8 mm) count, and HG1 individuals had more antral follicles than HG2 individuals, suggesting that these different genetic variants between HG1 and HG2 correlate with reproductive traits. The construction of a neighbor-joining phylogenetic tree and principal component analysis also revealed two main clades (HG1 and HG2) with different maternal origins: Bos indicus and Bos taurus, respectively. Therefore, HG1 originating from the maternal ancestors of Bos indicus may have a greater reproductive performance, and potential genetic variants discovered may promote the breeding process in the cattle industry.
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Affiliation(s)
- Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Junjun Zhai
- College of Life Science, Yulin University, Yulin 719000, China
| | - Hui Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jingyi Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shaowei Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jie Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhihan Niu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Chenglong Shen
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Kaijuan Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Zhengqing Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250000, China
| | - Enliang Song
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250000, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Correspondence: (Y.W.); (X.L.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Correspondence: (Y.W.); (X.L.)
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Dorji J, Vander Jagt CJ, Chamberlain AJ, Cocks BG, MacLeod IM, Daetwyler HD. Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle. Sci Rep 2022; 12:5582. [PMID: 35379858 PMCID: PMC8980051 DOI: 10.1038/s41598-022-09427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.
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Affiliation(s)
- Jigme Dorji
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Benjamin G Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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Deleterious protein-coding variants in diverse cattle breeds of the world. Genet Sel Evol 2021; 53:80. [PMID: 34654372 PMCID: PMC8518297 DOI: 10.1186/s12711-021-00674-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.
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Mitochondrial genomes from modern and ancient Turano-Mongolian cattle reveal an ancient diversity of taurine maternal lineages in East Asia. Heredity (Edinb) 2021; 126:1000-1008. [PMID: 33782560 PMCID: PMC8178343 DOI: 10.1038/s41437-021-00428-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Turano-Mongolian cattle are a group of taurine cattle from Northern and Eastern Asia with distinct morphological traits, which are known for their ability to tolerate harsh environments, such as the Asian steppe and the Tibetan plateau. Through the analysis of 170 mitogenomes from ten modern breeds, two sub-lineages within T3 (T3119 and T3055) were identified as specific of Turano-Mongolian cattle. These two T3 sub-lineages, together with the previously identified T4, were also present in six Neolithic samples, dated to ~3900 years BP, which might represent the earliest domestic taurine stocks from Southwest Asia. The rare haplogroup Q, found in three Tibetan cattle, testifies for the legacy of ancient migrations from Southwest Asia and suggests that the isolated Tibetan Plateau preserved unique prehistoric genetic resources. These findings confirm the geographic substructure of Turano-Mongolian cattle breeds, which have been shaped by ancient migrations and geographic barriers.
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Wang X, Ju Z, Jiang Q, Zhong J, Liu C, Wang J, Hoff JL, Schnabel RD, Zhao H, Gao Y, Liu W, Wang L, Gao Y, Yang C, Hou M, Huang N, Regitano LCA, Porto-Neto LR, Decker JE, Taylor JF, Huang J. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle. Genomics 2021; 113:1491-1503. [PMID: 33771637 DOI: 10.1016/j.ygeno.2021.03.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 12/30/2022]
Abstract
Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.
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Affiliation(s)
- Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Chengkun Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Han Zhao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Yaping Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Wenhao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Lingling Wang
- Shandong OX Livestock Breeding Co., Ltd., Jinan, Shandong 250131, China
| | - Yundong Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; Shandong OX Livestock Breeding Co., Ltd., Jinan, Shandong 250131, China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Minghai Hou
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Ning Huang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | | | | | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China.
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Liu Y, Xu L, Yang L, Zhao G, Li J, Liu D, Li Y. Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle. Front Genet 2020; 11:533052. [PMID: 33391332 PMCID: PMC7775540 DOI: 10.3389/fgene.2020.533052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 11/27/2020] [Indexed: 01/20/2023] Open
Abstract
Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.
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Affiliation(s)
- Yuqiang Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liu Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guoyao Zhao
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
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Barbato M, Reichel MP, Passamonti M, Low WY, Colli L, Tearle R, Williams JL, Ajmone Marsan P. A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel. PLoS One 2020; 15:e0231162. [PMID: 32271816 PMCID: PMC7145104 DOI: 10.1371/journal.pone.0231162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.
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Affiliation(s)
- Mario Barbato
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
| | - Michael P. Reichel
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Matilde Passamonti
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Licia Colli
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rick Tearle
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - John L. Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
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Mkize LS, Zishiri OT. Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA. Trop Anim Health Prod 2020; 52:2079-2089. [PMID: 32048149 DOI: 10.1007/s11250-020-02231-8] [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] [Received: 07/26/2019] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The Nguni cattle breed predominates South Africa and is endowed with traits favourable against environmental stressors such as heat stress and resistance to diseases. Interventions to improve production have led to the erosion of the genetic integrity of local breeds and the introduction of exotic breeds has proved ineffective as they fail to perform well due to different climatic conditions and production systems. In this study, the genetic structure and genetic lineage of Nguni crossbreds from 6 populations were assessed using the mitochondrial cytochrome b gene. Twelve polymorphic sites were detected resulting in 11 haplotypes with haplotype and nucleotide diversities of 0.550 ± 0.135 and 0.0019 ± 0.0011, respectively. Only 2 of the 6 populations displayed recent population expansion events, whereas the majority adhered to neutral evolution. The basal haplotype contained approximately 60% of the studied populations and there were four unique haplotypes that were revealed. A possible Nguni descript haplotype was uncovered, and this haplotype was found in all populations but was however devoid of individuals from around the world. The genetic structure of the populations was rather low (average pairwise FST = 0.066 and Slatkins FST = 0.094), and approximately 96% of the total genetic variation was accounted for by differences within populations. Phylogenetic analyses supported the clustering of all the samples within the Bos taurus clade and no Bos indicus haplotype was detected. Furthermore, no intermediate haplotype of taurine and indicine was detected. Overall, the maternal lineage of the crossbreds points to a taurine origin and the low genetic diversity depicts the retention of the Nguni genetic pool and possibly its superior adaptive traits.
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Affiliation(s)
| | - Oliver Tendayi Zishiri
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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A Novel SNP in EIF2AK4 Gene Is Associated with Thermal Tolerance Traits in Chinese Cattle. Animals (Basel) 2019; 9:ani9060375. [PMID: 31248194 PMCID: PMC6617145 DOI: 10.3390/ani9060375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 12/05/2022] Open
Abstract
Simple Summary China harbors two lineages of cattle (Bos taurus and Bos indicus) that display pronounced geographical distribution differences. Northern Chinese cattle predominantly belong to B. taurus and southern Chinese cattle belong to B. indicus. Both B. taurus and B. indicus contribute to the admixture of cattle in central China. Thermal stress induces oxidative stress and DNA damage in mammals. In general, B. indicus are more resistant to thermal stress than B. taurus. Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4), which pertains to the family of serine–threonine kinase, is a candidate gene for thermal stress. However, the effects of the bovine EIF2AK4 gene on the thermal tolerance traits of Chinese cattle breeds remain unknown. Our results suggest that a variant of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle. Abstract Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4, also known as GCN2), which pertains to the family of serine–threonine kinase, is involved in oxidative stress and DNA damage repair. A missense single-nucleotide polymorphism (SNP) (NC_037337.1 g.35615224 T > G) in exon 6 of the EIF2AK4 gene which encodes a p.Ile205Ser substitution was observed in the Bovine Genome Variation Database and Selective Signatures (BGVD). The purpose of the current study is to determine the allelic frequency distribution of the locus and analyze its association with thermal tolerance in Chinese indigenous cattle. In our study, the allelic frequency distribution of the missense mutation (NC_037337.1 g.35615224 T > G) in Chinese cattle was analyzed by sequencing 1105 individuals of 37 breeds including 35 Chinese indigenous cattle breeds and two exotic breeds. In particular, association analysis was carried out between the genotypes and three environmental parameters including annual mean temperature (T), relative humidity (RH), and temperature–humidity index (THI). The frequency of the mutant allele G (NC_037337.1 g.35615224 T > G) gradually decreased from the southern cattle groups to the northern cattle groups, whereas the frequency of the wild-type allele T showed an opposite pattern, consistent with the distribution of indicine and taurine cattle in China. In accordance with the association analysis, genotypes were significantly associated with T (P < 0.01), RH (P < 0.01), and THI (P < 0.01), suggesting that the cattle with genotype GG were found in regions with higher T, RH, and THI. Thus, our results suggest that the mutation (NC_037337.1 g.35615224 T > G) of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.
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Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle. BMC Genomics 2019; 20:494. [PMID: 31200634 PMCID: PMC6570941 DOI: 10.1186/s12864-019-5822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Background Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. Results We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions. Conclusions Our results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5822-y) contains supplementary material, which is available to authorized users.
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Yan L, She Y, Elzo MA, Zhang C, Fang X, Chen H. Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA. Arch Anim Breed 2019; 62:325-333. [PMID: 31807643 PMCID: PMC6852867 DOI: 10.5194/aab-62-325-2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/09/2019] [Indexed: 11/11/2022] Open
Abstract
The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A + T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was 0.903 ± 0.077 , while the nucleotide diversity was 0.0071 ± 0.0039 . Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.
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Affiliation(s)
- Linjun Yan
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China.,School of Environmental and Biological Engineering, Nantong College of Science and Technology, Nantong, Jiangsu 226007, China
| | - Yifan She
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Mauricio A Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611-0910, USA
| | - Chunlei Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xingtang Fang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Hong Chen
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
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12
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Zhang W, Gao X, Zhang Y, Zhao Y, Zhang J, Jia Y, Zhu B, Xu L, Zhang L, Gao H, Li J, Chen Y. Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle. BMC Genet 2018; 19:114. [PMID: 30572824 PMCID: PMC6302425 DOI: 10.1186/s12863-018-0705-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022] Open
Abstract
Background China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K). Results In principal component analysis (PCA) and neighbour-joining (NJ) tree analysis, samples of the same breeds were grouped together, leading to clear separation from other breeds. And Chinese indigenous cattle were clustered into two groups of southern and northern breeds, originated from Asian Bos indicus lineage and Eurasian Bos taurus lineage, respectively. In STRUCTURE K = 2, a clear transition occurred from the northern breeds to the southern breeds. Additionally, the northern breeds contained a smaller Eurasian taurine (62.5%) descent proportion than that reported previously (more than 90%). In STRUCTURE K = 3, a distinct descent was detected in the southern Chinese breeds, which could reflect a long-term selection history of Chinese indigenous cattle. The results from TreeMix and f3 statistic provided the evidence of an admixture history between southern breeds and northern breeds. Conclusions Consistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds. Electronic supplementary material The online version of this article (10.1186/s12863-018-0705-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wengang Zhang
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue Gao
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yang Zhang
- Xinjiang Academy of Animal Science, Urumqi, 830011, China
| | - Yumin Zhao
- Jilin Academy of Animal Science, Changchun, 130124, China
| | | | - Yutang Jia
- Institute of Animal Husbandry and Veterinary Medicine, AnhuiAcademyof Agricultural Sciences, Hefei, 230031, China
| | - Bo Zhu
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lingyang Xu
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lupei Zhang
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Huijiang Gao
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Junya Li
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Yan Chen
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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13
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Xu L, Zhang W, Shen H, Zhang Y, Zhao Y, Jia Y, Gao X, Zhu B, Xu L, Zhang L, Gao H, Li J, Chen Y. Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Pramod RK, Velayutham D, P K S, P S B, Zachariah A, Zachariah A, B C, S S S, P G, Dhinoth Kumar B, Iype S, Gupta R, Santhosh S, Thomas G. Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle ( Bos indicus) breeds. Anim Biotechnol 2018; 30:219-232. [PMID: 29938580 DOI: 10.1080/10495398.2018.1476376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.
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Affiliation(s)
| | | | - Sajesh P K
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Beena P S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | | | - Arun Zachariah
- c Department of Forest and Wildlife , Wayanad , Kerala , India
| | - Chandramohan B
- d National Institute of Science Education and Research , Jatni , India
| | - Sujith S S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Ganapathi P
- e Bargur Cattle Research Station, Tamil Nadu Veterinary Animal Sciences University , Chennai , India
| | | | | | - Ravi Gupta
- f Medgenome Labs Pvt. Ltd. , Narayana Health City , Bommasandra , Bengaluru , India
| | - Sam Santhosh
- g SciGenom Research Foundation , Cheruthuruthy , India
| | - George Thomas
- g SciGenom Research Foundation , Cheruthuruthy , India
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15
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Tarekegn GM, Ji XY, Bai X, Liu B, Zhang W, Birungi J, Djikeng A, Tesfaye K. Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1393-1400. [PMID: 29642685 PMCID: PMC6127579 DOI: 10.5713/ajas.17.0596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/13/2018] [Indexed: 01/09/2023]
Abstract
Objective This study was carried out to assess the haplotype diversity and population dynamics in cattle populations of Ethiopia. Methods We sequenced the complete mitochondrial cytochrome b gene of 76 animals from five indigenous and one Holstein Friesian×Barka cross bred cattle populations. Results In the sequence analysis, 18 haplotypes were generated from 18 segregating sites and the average haplotype and nucleotide diversities were 0.7540±0.043 and 0.0010±0.000, respectively. The population differentiation analysis shows a weak population structure (4.55%) among the populations studied. Majority of the variation (95.45%) is observed by within populations. The overall average pair-wise distance (FST) was 0.049539 with the highest (FST = 0.1245) and the lowest (FST = 0.011) FST distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. No haplotype in Ethiopian cattle was observed clustered with the reference Bos indicus group. The mismatch distribution analysis indicates a single population expansion event among the cattle populations. Conclusion Overall, high haplotype variability was observed among Ethiopian cattle populations and they share a common ancestor with Bos taurus.
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Affiliation(s)
- Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala P.O. Box 7070, Sweden.,Department of Animal Production and Technology, Bahir Dar University, Bahir Dar P.O. Box 79, Ethiopia
| | - Xiao-Yang Ji
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xue Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bin Liu
- Nei Mongol BioNew Technology Co. Ltd, Hohhot 010020, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Josephine Birungi
- Biosciences Eastern and Central Africa (BecA) Hub - International Livestock Research Institute, PO Box 30709, Nairobi 00100, Kenya
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Kassahun Tesfaye
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa P.O. Box, 1176, Ethiopia
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16
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Chen N, Huang J, Zulfiqar A, Li R, Xi Y, Zhang M, Dang R, Lan X, Chen H, Ma Y, Lei C. Population structure and ancestry of Qinchuan cattle. Anim Genet 2018; 49:246-248. [DOI: 10.1111/age.12658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2018] [Indexed: 12/22/2022]
Affiliation(s)
- N. Chen
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - J. Huang
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
- College of Life Science; Xinyang Normal University; Xinyang Henan 464000 China
| | - A. Zulfiqar
- University of Poonch; Rawalakot Azad Jammu Kashmir 12350 Pakistan
| | - R. Li
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Y. Xi
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - M. Zhang
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
- College of Life Science; Xinyang Normal University; Xinyang Henan 464000 China
| | - R. Dang
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - X. Lan
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - H. Chen
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Y. Ma
- College of Life Science; Xinyang Normal University; Xinyang Henan 464000 China
| | - C. Lei
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
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17
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Abdoli R, Zamani P, Ghasemi M. Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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18
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Mei C, Wang H, Liao Q, Wang L, Cheng G, Wang H, Zhao C, Zhao S, Song J, Guang X, Liu GE, Li A, Wu X, Wang C, Fang X, Zhao X, Smith SB, Yang W, Tian W, Gui L, Zhang Y, Hill RA, Jiang Z, Xin Y, Jia C, Sun X, Wang S, Yang H, Wang J, Zhu W, Zan L. Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing. Mol Biol Evol 2017; 35:688-699. [PMID: 29294071 DOI: 10.1093/molbev/msx322] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analyzed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle genomes, 11 Japanese black cattle genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus. Moreover, we found that the level of genetic variation in Chinese cattle depends upon the degree of indicine content. We also discovered many potential selective sweep regions associated with domestication related to breed-specific characteristics, with selective sweep regions including genes associated with coat color (ERCC2, MC1R, ZBTB17, and MAP2K1), dairy traits (NCAPG, MAPK7, FST, ITFG1, SETMAR, PAG1, CSN3, and RPL37A), and meat production/quality traits (such as BBS2, R3HDM1, IGFBP2, IGFBP5, MYH9, MYH4, and MC5R). These findings substantially expand the catalogue of genetic variants in cattle and reveal new insights into the evolutionary history and domestication traits of Chinese cattle.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hongcheng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qijun Liao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, Maryland, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Maryland, USA
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xueli Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal Science, McGill University, Montreal, Canada
| | - Stephen B Smith
- Department of Animal Science, Texas A&M University, Texas, USA
| | - Wucai Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wanqiang Tian
- Yangling Vocational & Technical College, Yangling, China
| | - Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yingying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rodney A Hill
- School of Biomedical Sciences, Charles Sturt University, New South Wales, Australia
| | - Zhongliang Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yaping Xin
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cunling Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | | | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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19
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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20
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Nuclear and mitochondrial DNA analysis reveals that hybridization between Fasciola hepatica and Fasciola gigantica occurred in China. Parasitology 2016; 144:206-213. [PMID: 27804894 DOI: 10.1017/s003118201600161x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The well-known pathogens of fasciolosis, Fasciola hepatica (Fh) and Fasciola Gigantica (Fg), possess abundant mature sperms in their seminal vesicles, and thus, they reproduce bisexually. On the other hand, aspermic Fasciola flukes reported from Asian countries, which have no sperm in their seminal vesicles, probably reproduce parthenogenetically. The aim of this study was to reveal the origin of aspermic Fasciola flukes. The nuclear single copy markers, phosphoenolpyruvate carboxykinase and DNA polymerase delta, were employed for analysis of Fasciola species from China. The hybrid origin of aspermic Fasciola flukes was strongly suggested by the presence of the Fh/Fg type, which includes DNA fragments of both F. hepatica and F. gigantica. China can be regarded as the cradle of the interspecific hybridization because F. hepatica and F. gigantica were detected in the northern and southern parts of China, respectively, and hybrids flukes were distributed between the habitats of the two species. The Chinese origin was supported by the fact that a larger number of mitochondrial NADH dehydrogenase subunit 1 (nad1) haplotypes was detected in Chinese aspermic Fasciola populations than in aspermic populations from the neighbouring countries. Hereafter, 'aspermic' Fasciola flukes should be termed as 'hybrid' Fasciola flukes.
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21
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Kwon D, Koo OJ, Kim MJ, Jang G, Lee BC. Nuclear-mitochondrial incompatibility in interorder rhesus monkey-cow embryos derived from somatic cell nuclear transfer. Primates 2016; 57:471-8. [PMID: 27165688 DOI: 10.1007/s10329-016-0538-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 04/07/2016] [Indexed: 01/08/2023]
Abstract
Monkey interorder somatic cell nuclear transfer (iSCNT) using enucleated cow oocytes yielded poor blastocysts development and contradictory results among research groups. Determining the reason for this low blastocyst development is a prerequisite for optimizing iSCNT in rhesus monkeys. The aim of this study was to elucidate nuclear-mitochondrial incompatibility of rhesus monkey-cow iSCNT embryos and its relationship to low blastocyst development. Cytochrome b is a protein of complex III of the electron transport chain (ETC). According to meta-analysis of amino acid sequences, the homology of cytochrome b is 75 % between rhesus monkeys and cattle. To maintain the function of ETC after iSCNT, 4n iSCNT embryos were produced by fusion of non-enucleated cow oocytes and rhesus monkey somatic cells. The blastocyst development rate of 4n iSCNT embryos was higher than that of 2n embryos (P < 0.01). Formation of reactive oxygen species (ROS) is an indirect indicator of ETC activity of cells. The ROS levels of 4n iSCNT embryos was higher than that of 2n embryos (P < 0.01). Collectively, rhesus monkey iSCNT embryos reconstructed with cow oocytes have nuclear-mitochondrial incompatibility due to fundamental species differences between rhesus monkeys and cattle. Nuclear-mitochondrial incompatibility seems to correlate with low ETC activity and extremely low blastocyst development of rhesus monkey-cow iSCNT embryos.
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Affiliation(s)
- Daekee Kwon
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Korea
| | - Ok-Jae Koo
- Laboratory Animal Research Center, Samsung Biomedical Research Institute, Suwon, 440-746, Korea
| | - Min-Jung Kim
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Korea
| | - Goo Jang
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Korea.,Emergency Center for Personalized Food-Medicine Therapy System, Advanced Institutes of Convergence Technology, Seoul National University, Suwon, 443-270, Korea
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Korea. .,Institute of Green Bio Science Technology, Seoul National University, Pyeongchang, 232-916, Korea.
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22
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Han SH, Oh HS, Cho IC. Identifying the species of origin in commercial sausages in South Korea. JOURNAL OF APPLIED ANIMAL RESEARCH 2016. [DOI: 10.1080/09712119.2015.1124334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Sang-Hyun Han
- Department of Science Education, Jeju National University, Jeju, South Korea
- Educational Science Research Institute, Jeju National University, Jeju, South Korea
| | - Hong-Shik Oh
- Department of Science Education, Jeju National University, Jeju, South Korea
| | - In-Cheol Cho
- Subtropical Animal Experiment Station, National Institute of Animal Science, RDA, Jeju, South Korea
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23
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Kim JH, Byun MJ, Kim MJ, Suh SW, Ko YG, Lee CW, Jung KS, Kim ES, Yu DJ, Kim WH, Choi SB. mtDNA Diversity and Phylogenetic State of Korean Cattle Breed, Chikso. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:163-70. [PMID: 25049772 PMCID: PMC4093160 DOI: 10.5713/ajas.2012.12499] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/19/2012] [Accepted: 10/11/2012] [Indexed: 11/27/2022]
Abstract
In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1–C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3–C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.
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Affiliation(s)
- Jae-Hwan Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Mi Jeong Byun
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Myung-Jick Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Sang Won Suh
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Chang Woo Lee
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Kyoung-Sub Jung
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Eun Sung Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Dae Jung Yu
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Woo Hyun Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Seong-Bok Choi
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
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Yue X, Li R, Liu L, Zhang Y, Huang J, Chang Z, Dang R, Lan X, Chen H, Lei C. When and how did Bos indicus introgress into Mongolian cattle? Gene 2014; 537:214-9. [DOI: 10.1016/j.gene.2013.12.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 12/31/2013] [Indexed: 11/28/2022]
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Zhang R, Cheng M, Li X, Chen F, Zheng J, Wang X, Meng Q. Y-SNPs Haplotype Diversity in Four Chinese Cattle Breeds. Anim Biotechnol 2013; 24:288-92. [DOI: 10.1080/10495398.2013.800531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Syed-Shabthar SMF, Rosli MKA, Mohd-Zin NAA, Romaino SMN, Fazly-Ann ZA, Mahani MC, Abas-Mazni O, Zainuddin R, Yaakop S, Md-Zain BM. The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers. Mol Biol Rep 2013; 40:5165-76. [PMID: 23686165 DOI: 10.1007/s11033-013-2619-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 04/30/2013] [Indexed: 11/28/2022]
Abstract
Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
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Affiliation(s)
- S M F Syed-Shabthar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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27
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Li R, Zhang XM, Campana MG, Huang JP, Chang ZH, Qi XB, Shi H, Su B, Zhang RF, Lan XY, Chen H, Lei CZ. Paternal origins of Chinese cattle. Anim Genet 2013; 44:446-9. [DOI: 10.1111/age.12022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2012] [Indexed: 11/28/2022]
Affiliation(s)
- R. Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling; Shaanxi; 712100; China
| | - X. M. Zhang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology and Kunming Primate Research Centre; Chinese Academy of Sciences; Kunming; Yunnan; 650223; China
| | - M. G. Campana
- Department of Human Evolutionary Biology; Harvard University; Cambridge; MA; 02138; USA
| | - J. P. Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling; Shaanxi; 712100; China
| | - Z. H. Chang
- Weinan Vocational and Technical College; Weinan; Shaanxi; 714000; China
| | - X. B. Qi
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology and Kunming Primate Research Centre; Chinese Academy of Sciences; Kunming; Yunnan; 650223; China
| | - H. Shi
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology and Kunming Primate Research Centre; Chinese Academy of Sciences; Kunming; Yunnan; 650223; China
| | - B. Su
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology and Kunming Primate Research Centre; Chinese Academy of Sciences; Kunming; Yunnan; 650223; China
| | - R. F. Zhang
- College of Life Science; National Experiment Teaching Center of Biology; Hubei Normal University; Huangshi; Hubei; 435002; China
| | - X. Y. Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling; Shaanxi; 712100; China
| | - H. Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling; Shaanxi; 712100; China
| | - C. Z. Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling; Shaanxi; 712100; China
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28
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Rosli MKA, Zamzuriada AS, Syed-Shabthar SMF, Mahani MC, Abas-Mazni O, Md-Zain BM. Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA. GENETICS AND MOLECULAR RESEARCH 2011; 10:2554-68. [PMID: 22033937 DOI: 10.4238/2011.october.19.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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29
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Rosli MKA, Zakaria SS, Syed-Shabthar SMF, Zainal ZZ, Shukor MN, Mahani MC, Abas-Mazni O, Md-Zain BM. Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences. GENETICS AND MOLECULAR RESEARCH 2011; 10:482-93. [PMID: 21476194 DOI: 10.4238/vol10-1gmr1002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy? PLoS One 2010; 5:e15760. [PMID: 21209945 PMCID: PMC3011016 DOI: 10.1371/journal.pone.0015760] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/23/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. METHODOLOGY The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. CONCLUSIONS Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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31
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Tanaka K, Takizawa T, Murakoshi H, Dorji T, Nyunt MM, Maeda Y, Yamamoto Y, Namikawa T. Molecular phylogeny and diversity of Myanmar and Bhutan mithun based on mtDNA sequences. Anim Sci J 2010; 82:52-6. [PMID: 21269359 DOI: 10.1111/j.1740-0929.2010.00819.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mithun (Bos frontalis), synonymous with mithan and gayal, is considered to be a domesticated form of gaur (B. gaurus). However, there has been a controversy concerning its origin. In an effort to address this issue, the mitochondrial cytochrome b (cytb) genes of 20 mithun from Myanmar and 13 from Bhutan were sequenced to trace its maternal origin. Seven cytb haplotypes were found in the 33 mithun, and the phylogenetic tree for these haplotypes clearly showed three embranchments involving five gaur types, a B. indicus type, and a B. taurus type. Sixteen Myanmar and 12 Bhutan mithun had gaur haplotypes, while a B. indicus haplotype was found in three Myanmar and one Bhutan mithun. The B. taurus haplotype was detected in a single Myanmar animal. These results demonstrated that the principal maternal origin of mithun was gaur and suggested that it was directly domesticated from gaur. However, some introgression of domestic cattle existed in current mithun populations. The presence of cattle mtDNA raised the question of how many cattle nuclear genes might have been integrated into the gene pool of mithun.
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Affiliation(s)
- Kazuaki Tanaka
- Laboratory of Animal Biotechnology, School of Veterinary Medicine, Azabu University, Chūō, Sagamihara, Japan.
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32
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Ajmone-Marsan P, Garcia JF, Lenstra JA. On the origin of cattle: How aurochs became cattle and colonized the world. Evol Anthropol 2010. [DOI: 10.1002/evan.20267] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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33
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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34
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Pang Y, Lei C, Zhang C, Lan X, Yue W, Gu C, Chen D, Wang J, Chen H. Analysis of the genetic variation of vascular endothelial growth factor gene in three Chinese indigenous cattle breeds. Mol Biol Rep 2010; 38:3219-25. [PMID: 20191384 DOI: 10.1007/s11033-010-9995-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Accepted: 02/07/2010] [Indexed: 11/30/2022]
Abstract
PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation of vascular endothelial growth factor (VEGF) gene in 675 individuals belonging to three Chinese indigenous cattle breeds including Qinchuan (QC), Jiaxian Red (JX) and Nanyang (NY) breed. Three new single nucleotide polymorphisms (SNPs) (g.6765T > C ss130456744, g.6860A > G ss130456745, g.6893T > C ss130456746) were found. One SNP (g.6765T > C) was detected in intron II of VEGF gene in all three breeds and the other two SNPs (g.6860A > G, g.6893T > C) were in exon III of VEGF gene only in NY breed. Among them, two synonymous mutations of exon III were identified: CCA (Pro) > CCG (Pro) at position 65th amino acid (aa) and TGT (Cys) > TGC (Cys) at position 76th aa of VEGF(190aa) in NY breed. Our study revealed that NY breed exhibited the most abundant genetic diversity in VEGF gene within the three cattle breeds. Furthermore, JX cattle breed was more similar to QC breed than to NY breed. Our genetic data in the present study supported the hypothesis that the distribution pattern of Chinese indigenous cattle breeds was closely related to the geographical and climatic background again.
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Affiliation(s)
- Yonghong Pang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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35
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Cai X, Chen H, Lei C. Matrilineal genetic inter-introgression of Bos taurus and Bos indicus in China. Livest Sci 2010. [DOI: 10.1016/j.livsci.2009.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Hu J, Zhou H, Smyth A, Luo Y, Hickford JGH. Polymorphism of the bovine ADRB3 gene. Mol Biol Rep 2010; 37:3389-92. [PMID: 20091127 DOI: 10.1007/s11033-009-9927-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
The β(3)-adrenergic receptor (ADRB3) is predominantly expressed in white and brown adipose tissue and mediates the lipolytic and thermogenic effects of high catecholamine concentrations. Variation in the ADRB3 gene (ADRB3) has been associated with obesity and the earlier onset of non-insulin-dependent diabetes mellitus in some ethnic groups, as well as some production traits of sheep, but to date variation of bovine ADRB3 has not been reported. In this study, variation in the promoter region of bovine ADRB3 was investigated in 737 cattle by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis. Six PCR-SSCP patterns representing six allelic variations and containing four single nucleotide polymorphisms (SNPs) and three nucleotide deletions/insertions were observed. Allele A was the most common allele (93.83%), whereas alleles C, D, E and F were rare (0.07, 1.09, 0.41, and 0.34%, respectively). The variation identified here might have an impact on both the function and level of expression of bovine ADRB3.
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Affiliation(s)
- Jiang Hu
- Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, People's Republic of China
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37
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Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae). Mol Phylogenet Evol 2009; 54:315-26. [PMID: 19897045 DOI: 10.1016/j.ympev.2009.10.037] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 10/19/2009] [Accepted: 10/29/2009] [Indexed: 11/23/2022]
Abstract
New insights for the systematic and evolution of the wild sheep are provided by molecular phylogenies inferred from Maximum parsimony, Bayesian, Maximum likelihood, and Neighbor-Joining methods. The phylogeny of the wild sheep was based on cytochrome b sequences of 290 samples representative of most of the sub-species described in the genus Ovis. The result was confirmed by a combined tree based on cytochrome b and nuclear sequences for 79 Ovis samples representative of the robust clades established with mitochondrial data. Urial and mouflon, which are either considered as a single or two separate species, form two monophyletic groups (O. orientalis and O. vignei). Their hybrids appear in one or the other group, independently from their geographic origin. The European mouflon O. musimon is clearly in the O. orientalis clade. The others species, O. dalli, O. canadensis, O. nivicola, and O. ammon are monophyletic. The results support an Asiatic origin of the genus Ovis, followed by a migration to North America through North-Eastern Asia and the Bering Strait and a diversification of the genus in Eurasia less than 3 million years ago. Our results show that the evolution of the genus Ovis is a striking example of successive speciation events occurring along the migration routes propagating from the ancestral area.
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Peng M, Ichinomiya M, Ohtori M, Ichikawa M, Shibahara T, Itagaki T. Molecular characterization of Fasciola hepatica, Fasciola gigantica, and aspermic Fasciola sp. in China based on nuclear and mitochondrial DNA. Parasitol Res 2009; 105:809-15. [PMID: 19424719 DOI: 10.1007/s00436-009-1459-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 04/24/2009] [Indexed: 11/28/2022]
Abstract
Parthenogenic Fasciola forms as well as bisexual Fasciola hepatica and Fasciola gigantica in mainland China have been identified on the basis of their spermatogenesis and genotypes in nuclear ribosomal internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase I (NDI). The Chinese aspermic Fasciola would include forms originating in interspecific hybrids between F. hepatica and F. gigantica, since they showed the genotype of ITS1-Fh/Fg that had mixed sequences of the two Fasciola species or heterogeneous genotypes in ITS1 and NDI. Additionally, there were Chinese aspermic flukes in which the sequences of ITS1 and NDI genotypes completely coincided with those in aspermic forms from Japan, Korea, and Vietnam, suggesting that the aspermic forms from these four countries are offspring with a common provenance. The Fh-C4 haplotype in NDI was detected in both aspermic specimens and F. hepatica, indicating that aspermic forms showing the haplotype might come into existence in China. The ratio of body length and width in aspermic Fasciola specimens showed intermediate values between those of F. hepatica and F. gigantica.
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Affiliation(s)
- Mao Peng
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550, Japan
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Stock F, Edwards CJ, Bollongino R, Finlay EK, Burger J, Bradley DG. Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations. Anim Genet 2009; 40:694-700. [PMID: 19456314 DOI: 10.1111/j.1365-2052.2009.01905.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA has been the traditional marker for the study of animal domestication, as its high mutation rate allows for the accumulation of molecular diversity within the time frame of domestic history. Additionally, it is exclusively maternally inherited and haplotypes become part of the domestic gene pool via actual capture of a female animal rather than by interbreeding with wild populations. Initial studies of British aurochs identified a haplogroup, designated P, which was found to be highly divergent from all known domestic haplotypes over the most variable portion of the D-loop. Additional analysis of a large and geographically representative sample of aurochs from northern and central Europe found an additional, separate aurochs haplotype, E. Until recently, the European aurochs appeared to have no matrilinear descendants among the publicly available modern cattle control regions sequenced; if aurochs mtDNA was incorporated into the domestic population, aurochs either formed a very small proportion of modern diversity or had been subsequently lost. However, a haplogroup P sequence has recently been found in a modern sample, along with a new divergent haplogroup called Q. Here we confirm the outlying status of the novel Q and E haplogroups and the modern P haplogroup sequence as a descendent of European aurochs, by retrieval and analysis of cytochrome b sequence data from twenty ancient wild and domesticated cattle archaeological samples.
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Affiliation(s)
- F Stock
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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SLC11A1 gene polymorphisms are not associated to somatic cell score and milk yield in Chinese Holstein. Vet Immunol Immunopathol 2008; 127:389-92. [PMID: 19070368 DOI: 10.1016/j.vetimm.2008.10.333] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Revised: 10/26/2008] [Accepted: 10/31/2008] [Indexed: 11/23/2022]
Abstract
It has been well established that mutations of the solute carrier family 11 A1 (SLC11A1) gene are responsible for susceptibility to a number of intracellular pathogens. Mastitis is the most common and most costly disease of dairy cattle, commonly caused by bacteria. As SLC11A1 protein is involved in bacterial killing, we assumed SLC11A1 gene as a candidate gene for bovine mastitis resistance. In this study, polymorphisms in the SLC11A1 gene were identified in the Chinese Holstein population. Genotypes were constructed, and their associations with somatic cell score and milk yield were determined. Single-strand conformation polymorphisms and DNA sequencing were used to reveal polymorphisms in SLC11A1 gene. A SNP in coding region and a variation of GT repeats in 3'-untranslated region were detected. The SNP resulted in an amino acid variation of p.P356A in transmembrane 8 of SLC11A1 peptide, which is the most conserved consecutive region. However, no associations were observed between the detected polymorphisms and somatic cell scores and milk yield in the Chinese Holstein population.
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