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Kumar C, Song S, Dewani P, Kumar M, Parkash O, Ma Y, Malhi KK, Yang N, Mwacharo JM, He X, Jiang L. Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations. Anim Genet 2018; 49:592-604. [PMID: 30229969 DOI: 10.1111/age.12722] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).
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Affiliation(s)
- C Kumar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan.,Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - S Song
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - P Dewani
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - M Kumar
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - O Parkash
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - Y Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - K K Malhi
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - N Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - J M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - X He
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - L Jiang
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
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Dyomin AG, Danilova MI, Mwacharo JM, Masharsky AE, Panteleev AV, Druzhkova AS, Trifonov VA, Galkina SA. Mitochondrial DNA D-loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia. J Anim Breed Genet 2016; 134:98-108. [PMID: 27988972 DOI: 10.1111/jbg.12248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 06/19/2016] [Accepted: 11/07/2016] [Indexed: 12/22/2022]
Abstract
To elucidate geographical and historical aspects of chicken dispersal across Eastern Europe, we analysed the complete mitochondrial DNA D-loop sequence of 86 representatives from chicken breeds traditionally raised in the territory of the East European Plain (Orloff, Pavlov, Russian White, Yurlov Crower, Uzbek Game and Naked Neck). From the 1231-1232 bp D-loop sequence, 35 variable sites that defined 22 haplotypes were identified in modern chicken. All populations, except Uzbek Game, exhibited high values of haplotype and nucleotide diversity suggesting a wide variation in maternal diversity. Inclusion of mtDNA sequences from other European and Asian countries revealed representatives from this study belonging to haplogroups A, E1 and C1. We also assessed fossil chicken material dated to the 9th-18th century from archaeological sites in Northern and Eastern Europe. Three haplotypes found in the fossil specimens belonged to haplogroup E1, while one sample dated to the 18th century was assigned to the C1 haplogroup. This is the first report of the occurrence of the C1 haplogroup in European chicken populations prior to the 20th century based on the fossil material. These results provide evidence for a relatively recent introduction of all haplotypes other than E1 into the East European chicken gene pool with the significant impact of the C1 haplogroup mainly distributed in Southern China.
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Affiliation(s)
- A G Dyomin
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - M I Danilova
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - J M Mwacharo
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - A E Masharsky
- Research Resource Centre for Molecular and Cell Technologies, Saint Petersburg State University, Saint Petersburg, Russia
| | - A V Panteleev
- The Ornithology Department, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - A S Druzhkova
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V A Trifonov
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Galkina
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
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Mwacharo JM, Elbeltagy AR, Kim ES, Haile A, Rischkowsky B, Rothschild MF. S0124 Indigenous stocks as treasure troves for sustainable livestock production in the 21st century: Insights from small ruminant genomics. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement412a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Kim ES, Elbeltagy AR, Aboul-Naga AM, Rischkowsky B, Sayre B, Mwacharo JM, Rothschild MF. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment. Heredity (Edinb) 2016; 116:255-64. [PMID: 26555032 PMCID: PMC4806575 DOI: 10.1038/hdy.2015.94] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/28/2015] [Accepted: 09/08/2015] [Indexed: 12/31/2022] Open
Abstract
Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.
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Affiliation(s)
- E-S Kim
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - A R Elbeltagy
- Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture, Cairo, Egypt
| | - A M Aboul-Naga
- Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture, Cairo, Egypt
| | - B Rischkowsky
- Small Ruminant Genetics and Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - B Sayre
- Department of Biology, Virginia State University, Petersburg, VA, USA
| | - J M Mwacharo
- Small Ruminant Genetics and Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
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Mwacharo JM, Nomura K, Hanada H, Han JL, Amano T, Hanotte O. Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers. Mol Ecol 2013; 22:2683-97. [PMID: 23611649 PMCID: PMC3664419 DOI: 10.1111/mec.12294] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [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] [Received: 04/04/2011] [Revised: 01/30/2013] [Accepted: 02/13/2013] [Indexed: 11/27/2022]
Abstract
Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long-range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa.
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Affiliation(s)
- J M Mwacharo
- Centre for Genetics and Genomics, School of Biology, University Park, University of Nottingham, Nottingham, UK.
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Siwek M, Wragg D, Sławińska A, Malek M, Hanotte O, Mwacharo JM. Insights into the genetic history of Green-legged Partridgelike fowl: mtDNA and genome-wide SNP analysis. Anim Genet 2013; 44:522-32. [PMID: 23611337 PMCID: PMC3793231 DOI: 10.1111/age.12046] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 02/26/2013] [Indexed: 11/27/2022]
Abstract
The Green-legged Partridgelike (GP) fowl, an old native Polish breed, is characterised by reseda green-coloured shanks rather than yellow, white, slate or black commonly observed across most domestic breeds of chicken. Here, we investigate the origin, genetic relationships and structure of the GP fowl using mtDNA D-loop sequencing and genome-wide SNP analysis. Genome-wide association analysis between breeds enables us to verify the genetic control of the reseda green shank phenotype, a defining trait for the breed. Two mtDNA D-loop haplogroups and three autosomal genetic backgrounds are revealed. Significant associations of SNPs on chromosomes GGA24 and GGAZ indicate that the reseda green leg phenotype is associated with recessive alleles linked to the W and Id loci. Our results provide new insights into the genetic history of European chicken, indicating an admixd origin of East European traditional breeds of chicken on the continent, as supported by the presence of the reseda green phenotype and the knowledge that the GP fowl as a breed was developed before the advent of commercial stocks.
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Affiliation(s)
- M Siwek
- Department of Animal Biotechnology, University of Technology and Life Sciences, Mazowiecka 28, Bydgoszcz, Poland.
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Mwacharo JM, Bjørnstad G, Han JL, Hanotte O. The History of African Village Chickens: an Archaeological and Molecular Perspective. Afr Archaeol Rev 2013; 30:97-114. [PMID: 27212780 PMCID: PMC4851118 DOI: 10.1007/s10437-013-9128-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The history of the introduction and dispersal of village chickens across the African continent is a subject of intense debate and speculation among scholars. Here, we synthesize and summarise the current scientific genetic and nongenetic knowledge in relation to the history of the species on the continent. Sociocultural, linguistic, archaeological and historic data all suggest a complex history for the species in Africa, characterized by multiple maritime and/or terrestrial introductions over time and several dispersal routes towards and within Africa. Molecular genetics information supports these observations and in addition suggests possible Asian centers of origin for African domestic chickens, including South Asia and Island Southeast Asia. However, both sets of data were until now too limited in their geographic scope, both within Africa and in comparison with chickens from Asia, to unravel the history of the species in detail. We anticipate that further continent-wide studies combining archaeological, ancient and/or modern genetic information may shed new insights on the history of the species. These will contribute to a deeper understanding of the history of trading networks and human interactions within Africa and between African and Asian societies, at the root of the development and expansion of African civilizations.
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Affiliation(s)
- J. M. Mwacharo
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - G. Bjørnstad
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100 Kenya
- Department of Archaeology, Conservation and History, University of Oslo, P.O. Box 1008, Blindern, 0315 Oslo, Norway
| | - J. L. Han
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100094 China
| | - O. Hanotte
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100 Kenya
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Abstract
In this study, 30 microsatellite markers recommended by the International Society for Animal Genetics and the Food and Agriculture Organization were used to determine the extent of genetic differentiation and phylogenetic relationships among indigenous chicken populations sampled in Kenya, Uganda, Ethiopia and Sudan. Genetic differentiation (F(ST)) and chord genetic distances (D(C)) indicated that the indigenous chickens were genetically related but distinct from commercial broiler and egg layer lines. Genetic divergence among the indigenous chickens determined using the Mantel test was significantly influenced (P < 0.001) by geographic (reproductive) isolation. Genetic subdivisions were found between the Kenyan/Ugandan chicken populations and Ethiopian/Sudanese chicken populations. The Marsabit chicken population from northern Kenya was the most genetically distinct population within the Kenyan and Ugandan chicken cluster, thus warranting further investigation.
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Affiliation(s)
- J M Mwacharo
- Laboratory of Animal Genetics and Breeding, Department of Animal Science, Tokyo University of Agriculture, 1737 Funako Atsugi-shi, Kanagawa 243-0034, Japan
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Abstract
Assessment of genetic diversity is a prerequisite for the management and conservation of animal genetic resources. Appropriate design of breeding programmes is therefore impossible for breeds that have not been adequately characterized either phenotypically and/or genetically. Phenotypic characteristics are important in breed identification and classification in ways that farming communities can relate with. This study phenotypically characterized two breeds of zebu cattle in Kenya. A total of 12 measurements (face length, ear length, horn length, heart girth, height at withers, chest depth, body length, height at rump, pelvis width, corpus length, pin bone width and tail length) were collected on 373 Maasai and 277 Kamba zebu kept by traditional farmers in south-east Kenya. The data were classified on the basis of breed group, age group, sex and coat colour pattern. Breed group, age group and sex significantly influenced all measurements. Coat colour pattern significantly influenced only height at withers, corpus length, ear length and tail length. Except for horn and ear length, all the other measurements were significantly higher for the Maasai zebu. Additionally, the Maasai zebu was taller than it was long. The opposite was true for the Kamba zebu. The Maasai and Kamba zebus can be classified as medium-sized breeds; however, great variations exist in their body sizes within and between the breeds.
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Affiliation(s)
- J M Mwacharo
- Kenya Agricultural Research Institute, P.O. Box 12, Makindu, Kenya.
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Mwacharo JM, Drucker AG. Production objectives and management strategies of livestock keepers in south-east Kenya: implications for a breeding programme. Trop Anim Health Prod 2006; 37:635-52. [PMID: 16619880 DOI: 10.1007/s11250-005-4253-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A survey of pastoralist and agropastoralist households in south-east Kenya was conducted to determine their production objectives and management strategies in order to optimize and extend a breeding programme for indigenous small East African Shorthorn Zebu cattle. The reasons for keeping cattle and the breed/trait preferences identified reflect the multiple objectives of the livestock keepers, with both adaptive traits and productive/reproductive traits rated as important. Although the Maasai and Kamba zebu (M&KZ) breeds were ranked highly with regard to adaptive traits, the population is considered to have been in decline over recent years. In order to promote the conservation and sustainable use of the M&KZ cattle, the formation of an open nucleus breeding scheme is recommended. In particular, such a scheme would be able to address several existing constraints (e.g. individual herds are very small and communal use of pastures/water makes controlled mating difficult). Such interventions would require the full participation of the livestock keepers, as well as ensuring that a holistic approach to species and breed attributes is taken into account in setting breeding goals, such that the full array of contributions that livestock make to livelihoods and the genetic characteristics related to these contributions are fully incorporated into the programme.
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Affiliation(s)
- J M Mwacharo
- Kenya Agricultural Research Institute, Kiboko Research Centre, Makindu.
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Mwacharo JM, Otieno CJ, Okeyo AM, Aman RA. Characterization of indigenous fat-tailed and fat-rumped hair sheep in Kenya: diversity in blood proteins. Trop Anim Health Prod 2002; 34:515-24. [PMID: 12537389 DOI: 10.1023/a:1021231204414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This paper reports the variation in five blood proteins from five populations of sheep found in Kenya. Blood samples were collected from a total of 309 adult sheep of both sexes in Kwale, Makueni and Kakamega districts for the fat-tailed sheep and in Isiolo district for the fat-rumped hair sheep. Fine-wooled Merino sheep were used in this study as the reference population. Transferrin, esterase-A and esterase-C were polymorphic in all the populations investigated, while albumin was monomorphic for the S allele in the fat-tailed sheep and haemoglobin was fixed for the B allele in the Kwale, Makueni and Isiolo populations. Phylogenies derived from the pairwise genetic distance estimates showed a clear separation between the indigenous sheep populations and the exotic Merino. However, the topology of the former showed rather poor consistency with their morphological classification based on the localization of their fat deposits, namely fat-tailed or fat-rumped hair sheep.
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Affiliation(s)
- J M Mwacharo
- University of Nairobi, Department of Animal Production, PO Box 29053, Nairobi, Kenya.
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