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Adeola AC, Bello SF, Abdussamad AM, Adedokun RAM, Olaogun SC, Abdullahi N, Mark AI, Onoja AB, Sanke OJ, Mangbon GF, Ibrahim J, Dawuda PM, Salako AE, Kdidi S, Yahyaoui MH. Single nucleotide polymorphisms (SNPs) in the open reading frame (ORF) of prion protein gene (PRNP) in Nigerian livestock species. BMC Genomics 2024; 25:177. [PMID: 38355406 PMCID: PMC10865551 DOI: 10.1186/s12864-024-10070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Prion diseases, also known as transmissible spongiform encephalopathies (TSEs) remain one of the deleterious disorders, which have affected several animal species. Polymorphism of the prion protein (PRNP) gene majorly determines the susceptibility of animals to TSEs. However, only limited studies have examined the variation in PRNP gene in different Nigerian livestock species. Thus, this study aimed to identify the polymorphism of PRNP gene in Nigerian livestock species (including camel, dog, horse, goat, and sheep). We sequenced the open reading frame (ORF) of 65 camels, 31 village dogs and 12 horses from Nigeria and compared with PRNP sequences of 886 individuals retrieved from public databases. RESULTS All the 994 individuals were assigned into 162 haplotypes. The sheep had the highest number of haplotypes (n = 54), and the camel had the lowest (n = 7). Phylogenetic tree further confirmed clustering of Nigerian individuals into their various species. We detected five non-synonymous SNPs of PRNP comprising of G9A, G10A, C11G, G12C, and T669C shared by all Nigerian livestock species and were in Hardy-Weinberg Equilibrium (HWE). The amino acid changes in these five non-synonymous SNP were all "benign" via Polyphen-2 program. Three SNPs G34C, T699C, and C738G occurred only in Nigerian dogs while C16G, G502A, G503A, and C681A in Nigerian horse. In addition, C50T was detected only in goats and sheep. CONCLUSION Our study serves as the first to simultaneously investigate the polymorphism of PRNP gene in Nigerian livestock species and provides relevant information that could be adopted in programs targeted at breeding for prion diseases resistance.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China
| | - Abdussamad M Abdussamad
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, Nigeria
| | - Rahamon A M Adedokun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Nasiru Abdullahi
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Akanbi I Mark
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Nigeria
| | - Anyebe B Onoja
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | | | - Jebi Ibrahim
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, Maseru, South Africa
| | - Adebowale E Salako
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria
| | - Samia Kdidi
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Route El Djorf, Km 22.5, 4119, Medenine, Tunisia
| | - Mohamed Habib Yahyaoui
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Route El Djorf, Km 22.5, 4119, Medenine, Tunisia
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Adeola AC, Bello SF, Abdussamad AM, Mark AI, Sanke OJ, Onoja AB, Nneji LM, Abdullahi N, Olaogun SC, Rogo LD, Mangbon GF, Pedro SL, Hiinan MP, Mukhtar MM, Ibrahim J, Saidu H, Dawuda PM, Bala RK, Abdullahi HL, Salako AE, Kdidi S, Yahyaoui MH, Yin TT. Polymorphism of prion protein gene (PRNP) in Nigerian sheep. Prion 2023; 17:44-54. [PMID: 36892181 PMCID: PMC10012947 DOI: 10.1080/19336896.2023.2186767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Polymorphism of the prion protein gene (PRNP) gene determines an animal's susceptibility to scrapie. Three polymorphisms at codons 136, 154, and 171 have been linked to classical scrapie susceptibility, although many variants of PRNP have been reported. However, no study has investigated scrapie susceptibility in Nigerian sheep from the drier agro-climate zones. In this study, we aimed to identify PRNP polymorphism in nucleotide sequences of 126 Nigerian sheep by comparing them with public available studies on scrapie-affected sheep. Further, we deployed Polyphen-2, PROVEAN, and AMYCO analyses to determine the structure changes produced by the non-synonymous SNPs. Nineteen (19) SNPs were found in Nigerian sheep with 14 being non-synonymous. Interestingly, one novel SNP (T718C) was identified. There was a significant difference (P < 0.05) in the allele frequencies of PRNP codon 154 between sheep in Italy and Nigeria. Based on the prediction by Polyphen-2, R154H was probably damaging while H171Q was benign. Contrarily, all SNPs were neutral via PROVEAN analysis while two haplotypes (HYKK and HDKK) had similar amyloid propensity of PRNP with resistance haplotype in Nigerian sheep. Our study provides valuable information that could be possibly adopted in programs targeted at breeding for scrapie resistance in sheep from tropical regions.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Abdussamad M Abdussamad
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria.,Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, Nigeria
| | - Akanbi I Mark
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Anyebe B Onoja
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nasiru Abdullahi
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lawal D Rogo
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | | | | | - Manasseh P Hiinan
- Small Ruminant Section, Solomon Kesinton Agro-Allied Limited Iperu-Remo, Ogun State, Nigeria
| | - Muhammad M Mukhtar
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Jebi Ibrahim
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Hayatu Saidu
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, Lesotho, Southern Africa
| | - Rukayya K Bala
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Hadiza L Abdullahi
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, Nigeria
| | - Adebowale E Salako
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria
| | - Samia Kdidi
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Medenine, Tunisia
| | - Mohamed Habib Yahyaoui
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Medenine, Tunisia
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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3
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Li WL, Liu YH, Li JX, Ding MT, Adeola AC, Isakova J, Aldashev AA, Peng MS, Huang X, Xie G, Chen X, Yang WK, Zhou WW, Ghanatsaman ZA, Olaogun SC, Sanke OJ, Dawuda PM, Hytönen MK, Lohi H, Esmailizadeh A, Poyarkov AD, Savolainen P, Wang GD, Zhang YP. Multiple Origins and Genomic Basis of Complex Traits in Sighthounds. Mol Biol Evol 2023; 40:msad158. [PMID: 37433053 PMCID: PMC10401622 DOI: 10.1093/molbev/msad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.
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Affiliation(s)
- Wu-Lue Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jin-Xiu Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Meng-Ting Ding
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Jainagul Isakova
- Laboratory of Molecular and Cell Biology, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan
| | - Almaz A Aldashev
- Laboratory of Molecular and Cell Biology, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Xuezhen Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Guoli Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J Sanke
- Ministry of Agriculture and Natural Resources, Taraba State Government, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, Roma, Southern Africa
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Andrey D Poyarkov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | - Peter Savolainen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, Solna, Sweden
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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4
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Adeola AC, Luka PD, Jiang XX, Cai ZF, Oluwole OO, Shi X, Oladele BM, Olorungbounmi TO, Boladuro B, Omotosho O, Okoro VMO, Dawuda PM, Olaogun SC, Sanke OJ, Xie HB, Bishop RP, Han J, Li J, Zhang YP, Peng MS. Target capture sequencing for the first Nigerian genotype I ASFV genome. Microb Genom 2023; 9:mgen001069. [PMID: 37489884 PMCID: PMC10438811 DOI: 10.1099/mgen.0.001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023] Open
Abstract
African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is important to understand the genotype and phylogenetic relationship of ASF viruses (ASFVs). Recent genetic analysis of Nigerian ASFV isolates has revealed the presence of both genotypes I and II; this is based on analysis of a few selected genes. Phylogenetic analysis of ASFV whole genomes highlights virus origins and evolution in greater depth. However, there is currently no information on the ASFV genome from Nigerian isolates. Two ASFV-positive samples were detected during a random survey of 150 Nigerian indigenous pig samples collected in 2016. We assembled near-complete genomes of the two ASFV-positive samples using in-solution hybrid capture sequencing. The genome-wide phylogenetic tree assigned these two genomes into p72 genotype I, particularly close to the virulent Benin 97/1 strain. The two ASFVs share 99.94 and 99.92 % genomic sequence identity to Benin97/1. This provides insight into the origin and relationship of ASFV strains from Nigeria and Italy. The study reports for the first time the determination of near-complete genomes of ASFV using in-solution hybrid capture sequencing, which represents an important advance in understanding the global evolutionary landscape of ASFVs.
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Affiliation(s)
- Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Pam D. Luka
- National Veterinary Research Institute, Vom, Nigeria
| | - Xiang-Xiang Jiang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- College of Life Sciences, Anhui Normal University, Wuhu, PR China
| | - Zheng-Fei Cai
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, PR China
| | - Olufunke O. Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Xian Shi
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China
| | - Bukola M. Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Oladipo Omotosho
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Victor M. O. Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | | | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science Chinese Academy of Agricultural Sciences(CAAS), Beijing, PR China
| | - Jianbo Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, PR China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
- Sino‐Africa Joint Research Center, Chinese Academy of Sciences, Kunming, PR China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, PR China
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5
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Adeola AC, Bello SF, Abdussamad AM, Mark AI, Sanke OJ, Onoja AB, Nneji LM, Abdullahi N, Olaogun SC, Rogo LD, Mangbon GF, Pedro SL, Hiinan MP, Mukhtar MM, Ibrahim J, Saidu H, Dawuda PM, Bala RK, Abdullahi HL, Salako AE, Kdidi S, Yahyaoui MH, Yin TT. Scrapie-associated polymorphisms of the prion protein gene (PRNP) in Nigerian native goats. Gene X 2023; 855:147121. [PMID: 36535463 DOI: 10.1016/j.gene.2022.147121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Scrapie is a fatal prion protein disease stiffly associated with single nucleotide polymorphism (SNPs) of the prion protein gene (PRNP). The prevalence of this deadly disease has been reported in small ruminants, including goats. The Nigerian goats are hardy, trypano-tolerant, and contribute to the protein intake of the increasing population. Although scrapie has been reported in Nigerian goats, there is no study on the polymorphism of the PRNP gene. Herein, we evaluated the genetic and allele distributions of PRNP polymorphism in 132 Nigerian goats and compared them with publicly available studies on scrapie-affected goats. We utilized Polyphen-2, PROVEAN and AMYCO programs to examine structural variations produced by the non-synonymous SNPs. Our study revealed 29 SNPs in Nigerian goats, of which 14 were non-synonymous, and 23 were novel. There were significant differences (P < 0.001) in the allele frequencies of PRNP codons 139, 146, 154 and 193 in Nigerian goats compared with scrapie-affected goats, except for Northern Italian goats at codon 154. Based on the prediction by Polyphen-2, R139S and N146S were 'benign', R154H was 'probably damaging', and T193I was 'possibly damaging'. In contrast, PROVEAN predicted 'neutral' for all non-synonymous SNPs, while AMYCO showed a similar amyloid propensity of PRNP for resistant haplotype and two haplotypes of Nigerian goats. Our study is the first to investigate the polymorphism of scrapie-related genes in Nigerian goats.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China; Centre for Biotechnology Research, Bayero University, Kano, Nigeria.
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Abdussamad M Abdussamad
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria; Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, Nigeria
| | - Akanbi I Mark
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Anyebe B Onoja
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, United States
| | - Nasiru Abdullahi
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lawal D Rogo
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | | | | | - Manasseh P Hiinan
- Small Ruminant Section, Solomon Kesinton Agro-Allied Limited Iperu-Remo, Ogun State, Nigeria
| | - Muhammad M Mukhtar
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Jebi Ibrahim
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Hayatu Saidu
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, South Africa
| | - Rukayya K Bala
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Hadiza L Abdullahi
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, Nigeria; Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Adebowale E Salako
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria
| | - Samia Kdidi
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Route El Djorf, Km 22.5, Medenine 4119, Tunisia
| | - Mohamed Habib Yahyaoui
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Route El Djorf, Km 22.5, Medenine 4119, Tunisia
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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6
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Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng'ang'a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023; 14:1041103. [PMID: 36923796 PMCID: PMC10010571 DOI: 10.3389/fgene.2023.1041103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - George Niba
- National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon
| | - Ndifor K Wanzie
- Department of Zoology, University of Douala, Douala, Cameroon.,Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Ayotunde O Adebambo
- Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Said I Ng'ang'a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wasiu A Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Victor M O Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | | | - Omotoso Olatunde
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
| | - Moise M Matouke
- Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Saidu O Oseni
- Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Christopher D Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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7
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Xie HB, Yan C, Adeola AC, Wang K, Huang CP, Xu MM, Qiu Q, Yin X, Fan CY, Ma YF, Yin TT, Gao Y, Deng JK, Okeyoyin AO, Oluwole OO, Omotosho O, Okoro VMO, Omitogun OG, Dawuda PM, Olaogun SC, Nneji LM, Ayoola AO, Sanke OJ, Luka PD, Okoth E, Lekolool I, Mijele D, Bishop RP, Han J, Wang W, Peng MS, Zhang YP. African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments. Mol Biol Evol 2022; 39:6840307. [PMID: 36413509 PMCID: PMC9733430 DOI: 10.1093/molbev/msac256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed that common warthog and red river hog diverged from their common ancestor around the Miocene/Pliocene boundary, putatively predating their entry into Africa. We detected species-specific selective signals associated with sensory perception and interferon signaling pathways in common warthog and red river hog, respectively, which contributed to their local adaptation to savannah and tropical rainforest environments, respectively. The structural variation and evolving signals in genes involved in T-cell immunity, viral infection, and lymphoid development were identified in their ancestral lineage. Our results provide new insights into the evolutionary histories and divergent genetic adaptations of African suids.
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Affiliation(s)
| | | | | | | | | | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710129, China
| | - Xue Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Chen-Yu Fan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yun-Fei Ma
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Jia-Kun Deng
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja 900108, Nigeria
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Oladipo Omotosho
- Department of Veterinary Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Victor M O Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri 460114, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife 220282, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi 970001, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming 650204, China
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming 650204, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660213, Nigeria
| | - Pam D Luka
- National Veterinary Research Institute, Vom 930103, Nigeria
| | - Edward Okoth
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | | | | | - Richard P Bishop
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | | | - Wen Wang
- Corresponding authors: E-mails: ; ; ;
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8
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Adeola AC, Sola-Ojo FE, Opeyemi YA, Oguntunji AO, Nneji LM, Ewuola MK, Bello SF, Olaniyi WA, Adesoji AT, Karuno AP, Sanke OJ, Daniel EL. Genetic diversity and population structure of muscovy duck ( Cairina moschata) from Nigeria. PeerJ 2022; 10:e13236. [PMID: 35444865 PMCID: PMC9014852 DOI: 10.7717/peerj.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 01/15/2023] Open
Abstract
The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (F ST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
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Affiliation(s)
- Adeniyi C. Adeola
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Foluke E. Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Yusuf A. Opeyemi
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Abel O. Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, Osun, Nigeria
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States
| | - Muslim K. Ewuola
- Animal Breeding and Genetics Unit/Department of Animal Science, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics/Breeding and Reproduction/College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adeosun T. Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, Kano, Nigeria
| | - Alex P. Karuno
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
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9
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Mauki DH, Tijjani A, Ma C, Ng’ang’a SI, Mark AI, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Kazwala RR, Gwakisa PS, Yin TT, Li Y, Peng MS, Adeola AC, Zhang YP. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics. BMC Genomics 2022; 23:306. [PMID: 35428239 PMCID: PMC9012019 DOI: 10.1186/s12864-022-08512-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region. Results The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities. Conclusion The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08512-w.
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10
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Erratum to: Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa. Genome Biol Evol 2021; 13:6355925. [PMID: 34417609 PMCID: PMC8379371 DOI: 10.1093/gbe/evab174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Zeng L, Liu HQ, Tu XL, Ji CM, Gou X, Esmailizadeh A, Wang S, Wang MS, Wang MC, Li XL, Charati H, Adeola AC, Moshood Adedokun RA, Oladipo O, Olaogun SC, Sanke OJ, Godwin F M, Cecily Ommeh S, Agwanda B, Kasiiti Lichoti J, Han JL, Zheng HK, Wang CF, Zhang YP, Frantz LAF, Wu DD. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zool Res 2021; 42:450-460. [PMID: 34156172 PMCID: PMC8317180 DOI: 10.24272/j.issn.2095-8137.2021.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xiao-Long Tu
- Annoroad Gene Tech. (Beijing) Co., Ltd., Beijing 100176, China
| | - Chang-Mian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,Biomarker Technologies Corporation, Beijing 101300, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Xiao-Long Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hadi Charati
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Olatunbosun Oladipo
- Federal College of Animal Health and Production Technology, Moor-Plantation, Ibadan, Nigeria
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
| | | | - Sheila Cecily Ommeh
- Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, Kenya.,Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Jacqueline Kasiiti Lichoti
- State Department of Livestock, Ministry of Agriculture, Livestock, Fisheries and Irrigation, Nairobi, Kenya
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Chang-Fa Wang
- Equus Laboratory, Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong 250131, China.,Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, Shandong 252059, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. E-mail:
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Institute of Three-River-Source National Park, Chinese Academy of Sciences, Qinghai 810008, China. E-mail:
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12
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Xueqi W, Abdussamad AM, Ibrahim J, Sanke OJ, Olaniyi WA, Dawuda PM, Pan HC, Peng MS, Adeola AC, Zhang YP. Mitochondrial DNA variation of Nigerian dromedary camel (Camelus dromedarius). Anim Genet 2021; 52:570-572. [PMID: 33934373 DOI: 10.1111/age.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Wang Xueqi
- College of Life Sciences, Anhui Normal University, Wuhu, 241002, China.,State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Abdussamad M Abdussamad
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, 700241, Nigeria.,Centre for Biotechnology Research, Bayero University, Kano, 700241, Nigeria
| | - Jebi Ibrahim
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, 972261, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, 660221, Nigeria
| | - Wasiu A Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, 342111, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, 972261, Nigeria
| | - Hong-Chun Pan
- College of Life Sciences, Anhui Normal University, Wuhu, 241002, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biotechnology Research, Bayero University, Kano, 700241, Nigeria.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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13
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biol Evol 2021; 13:6261762. [PMID: 34009300 PMCID: PMC8214406 DOI: 10.1093/gbe/evab090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/22/2022] Open
Abstract
Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
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Affiliation(s)
- Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Nada M Eltayeb
- Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - John Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Peter Njoroge
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | | | - Rana Pedar
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yuan Du
- Nowbio Biotechnology Company, Kunming, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, California, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheila C Ommeh
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya.,Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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14
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Mauki DH, Adeola AC, Ng’ang’a SI, Tijjani A, Akanbi IM, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Gwakisa PS, Yin TT, Peng MS, Zhang YP. Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers. PeerJ 2021; 9:e10607. [PMID: 33717663 PMCID: PMC7938780 DOI: 10.7717/peerj.10607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/29/2020] [Indexed: 01/29/2023] Open
Abstract
The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.
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Affiliation(s)
- David H. Mauki
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | | | - Ibikunle Mark Akanbi
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Oyo, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
| | | | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jebi Ibrahim
- College of veterinary medicine, department of theriogenology, University of agriculture, Makurdi, Makurdi, Benue, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, Nigeria
| | | | - Paul S. Gwakisa
- Department of Microbiology, Parasitology and Biotechnology/ Genome Science Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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15
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Adeola AC, Ewuola MK, Nneji LM, Oguntunji AO, Bello SF, Sola-Ojo FE, Ayoola AO, Adesoji AT, Sanke OJ, Ebiakpo DL, Jonah KN, Jia X, Wu RN, Peng MS, Zhang YP. Mitochondrial DNA variation of Nigerian Muscovy duck (Cairina moschata). Anim Genet 2020; 51:485-486. [PMID: 32100314 DOI: 10.1111/age.12924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Muslim K Ewuola
- Animal Breeding and Genetics Unit, Department of Animal Science, University of Ibadan, Ibadan, 200284, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Abel O Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, 232102, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Foluke E Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, 240213, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Adeosun T Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, 703101, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, 660221, Nigeria
| | - Daniel L Ebiakpo
- Department of Animal Science, University of Benin, Benin City, 300283, Nigeria
| | | | - Xinzheng Jia
- School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Ru-Nian Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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16
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Ma XY, Ning T, Adeola AC, Li J, Esmailizadeh A, Lichoti JK, Agwanda BR, Isakova J, Aldashev AA, Wu SF, Liu HQ, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Adedokun RAM, Olaogun SC, Sanke OJ, Mangbon GF, Chen X, Yang WK, Wang Z, Peng MS, Ommeh SC, Li Y, Zhang YP. Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences. Zool Res 2020; 41:51-60. [PMID: 31709786 PMCID: PMC6956721 DOI: 10.24272/j.issn.2095-8137.2020.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication. However, domestication histories of these two lineages remain enigmatic. We therefore compared several population characteristics between these two lineages based on global sampling, which included 171 sequences obtained in this study (including Middle Asian, East Asian, and African samples) plus 536 published sequences (including European, Asian, and African samples). The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop (D-loop) sequences, respectively. The Clade I lineage experienced an increase in population size more than 8 000 years ago and shows a complex haplotype network. In contrast, the population size of the Clade II lineage has remained relatively constant, with a simpler haplotype network. Although the distribution of the two lineages was almost equal across the Eurasian mainland, they still presented discernible but complex geographic bias in most parts of Africa, which are known as their domestication sites. Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage, whereas the Clade II lineage was dominant along the East and North coasts of Africa. Furthermore, the migration routes inferred from diversity decay suggested different expansion across China between the two lineages. Altogether, these differences indicated non-simultaneous domestication of the two lineages, which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa, respectively.
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Affiliation(s)
- Xi-Yao Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Tiao Ning
- Agriculture College, Kunming University, Kunming, Yunnan 650214, China.,Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, Kunming University, Kunming, Yunnan 650214, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman PB 76169-133, Iran
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock and Fisheries, Nairobi 00100, Kenya
| | - Bernard R Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 00100, Kenya
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Almaz A Aldashev
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | | | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Zhe Wang
- Department of Physiology, Hebei Medical University, Shijiazhuang, Hebei 050017, China.,Hebei Key Laboratory of Animal Science, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Sheila C Ommeh
- Animal Biotechnology Group, Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya. E-mail:
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China.,State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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17
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Liu YH, Wang L, Xu T, Guo X, Li Y, Yin TT, Yang HC, Hu Y, Adeola AC, Sanke OJ, Otecko NO, Wang M, Ma Y, Charles OS, Sinding MHS, Gopalakrishnan S, Alfredo Samaniego J, Hansen AJ, Fernandes C, Gaubert P, Budd J, Dawuda PM, Knispel Rueness E, Jiang L, Zhai W, Gilbert MTP, Peng MS, Qi X, Wang GD, Zhang YP. Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites. Mol Biol Evol 2017; 35:287-298. [DOI: 10.1093/molbev/msx258] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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18
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Adeola AC, Oluwole OO, Oladele BM, Olorungbounmi TO, Boladuro B, Olaogun SC, Nneji LM, Sanke OJ, Dawuda PM, Omitogun OG, Frantz L, Murphy RW, Xie HB, Peng MS, Zhang YP. Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs. Genet Sel Evol 2017. [PMID: 28651519 PMCID: PMC5485568 DOI: 10.1186/s12711-017-0326-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. Results Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes. Conclusions Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0326-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Bukola M Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Laurent Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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