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Kichamu N, Wanjala G, Cziszter LT, Strausz P, Astuti PK, Bagi Z, Kusza S. Assessing the population structure and genetic variability of Kenyan native goats under extensive production system. Sci Rep 2024; 14:16342. [PMID: 39014189 PMCID: PMC11252283 DOI: 10.1038/s41598-024-67374-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval (GI) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders (fa/fe) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size (Ne) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.
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Affiliation(s)
- Nelly Kichamu
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
- Ministry of Agriculture Livestock, Fisheries and Cooperatives, Directorate of Livestock Development, Naivasha Sheep and Goats Breeding Station, P.O. Box 2238-20117, Naivasha, Kenya
| | - George Wanjala
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
- Ministry of Agriculture, Livestock, Fisheries, Cooperatives and Irrigation, Directorate of Livestock Production, P.O. Box 437-50200, Bungoma, Kenya
| | - Ludovic Toma Cziszter
- Faculty of Bioengineering of Animal Resources, University of Life Sciences "King Mihai I" From Timișoara, 300645, Timișoara, Romania
| | - Péter Strausz
- Institute of Strategy and Management, Department of Management, Corvinus University of Budapest, Budapest, 1093, Hungary
| | - Putri Kusuma Astuti
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary.
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Analysis of the population structure of buffaloes in Brazil. Trop Anim Health Prod 2020; 52:3889-3892. [DOI: 10.1007/s11250-020-02327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/12/2020] [Indexed: 11/29/2022]
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Rego Neto ADA, Rocha Sarmento JL, Pereira da Silva Santos N, Guimarães Campelo JE, Silva Sena L, Biagiotti D, Vieira Dos Santos G. Population genetic structure of Santa Inês sheep in Brazil. Trop Anim Health Prod 2017; 50:503-508. [PMID: 29119378 DOI: 10.1007/s11250-017-1459-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/26/2017] [Indexed: 11/28/2022]
Abstract
This study aimed to describe the population genetic structure and evaluate the state of conservation of the genetic variability of Santa Inês sheep in Brazil. We used pedigree data of the Santa Inês breed available in electronic processing of the Brazilian Association of Sheep Breeders. A file with 20,206 records, which enabled the calculation of the genetic conservation index (GCI), individual inbreeding coefficient (F), change in inbreeding (ΔF), effective population size (Ne), effective number of founders (ƒe), effective number of ancestors (ƒɑ), generation interval (L), average relatedness coefficient of each individual (AR), and Wright's F-statistics (F IT, F IS, and F ST). For pedigree analysis and calculation of population parameters, the program ENDOG was used. The average inbreeding coefficient ([Formula: see text]) was 0.97% and the mean average relatedness ([Formula: see text]) 0.49%. The effective numbers of founders and ancestors were, respectively, 199 and 161. The average values of F and AR increased significantly over the years. The effective population size fluctuated over the years concurrently to oscillations in inbreeding rates, wherein N e reached just 68 in the year 2012. The mean average generation interval was 5.3 years. The Santa Inês breed in Brazil is under genetic drift process, with loss of genetic variation. It requires the implementation of a genetic management plan in the herd, for conservation and improvement of the breed.
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Affiliation(s)
- Aurino de Araújo Rego Neto
- Discente do curso de Pós-Graduação em Ciência Animal, Centro de Ciências Agrárias, Universidade Federal do Piauí, Campus Socopo, Bairro Ininga, Teresina, PI, 64049-550, Brazil.
| | - José Lindenberg Rocha Sarmento
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal do Piauí, Campus Socopo, Bairro Ininga, Teresina, PI, 64049-550, Brazil
| | | | - José Elivalto Guimarães Campelo
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal do Piauí, Campus Socopo, Bairro Ininga, Teresina, PI, 64049-550, Brazil
| | - Luciano Silva Sena
- Discente do curso de Pós-Graduação em Ciência Animal, Centro de Ciências Agrárias, Universidade Federal do Piauí, Campus Socopo, Bairro Ininga, Teresina, PI, 64049-550, Brazil
| | - Daniel Biagiotti
- Colégio Técnico de Bom Jesus, Universidade Federal do Piauí, Planalto Horizonte, Bom Jesus, PI, 64900-000, Brazil
| | - Gleyson Vieira Dos Santos
- Discente do curso de Pós-Graduação em Ciência Animal, Centro de Ciências Agrárias, Universidade Federal do Piauí, Campus Socopo, Bairro Ininga, Teresina, PI, 64049-550, Brazil
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Ghavi Hossein-Zadeh N. Analysis of population structure and genetic variability in Iranian buffaloes (Bubalus bubalis) using pedigree information. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an14738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P < 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.
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Population genetic structure in the Holstein breed in Brazil. Trop Anim Health Prod 2015; 48:331-6. [PMID: 26584942 DOI: 10.1007/s11250-015-0956-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 11/09/2015] [Indexed: 10/22/2022]
Abstract
We evaluated the population genetic structure of the Holstein breed in Brazil through pedigree analysis with the aim of supporting genetic management of extant herds. We used data from genealogical records of 204,511 animals in farms from south and southeast Brazil. Pedigree records between 1943 and 2005 were divided into seven periods of 8 years to estimate the effective population size (N e ). N e varied during the study periods, ranging from 0.19 to 3016.25. There was an increase in the percentage of inbred animals over time, from 0.18 to 5.0 %. However, this figure may be an underestimate due to the low completeness of pedigree, primarily related to paternal pedigree. The effective number of founders (fe) was 473 animals and ancestors (fa) was 471. The genetic contribution of 260 ancestors (founders or not) accounted for 50 % of the genetic variability in the population. The average relatedness coefficient (AR) and inbreeding coefficient indicate that the Holstein breed in Brazil is being effectively managed, despite a moderate founder effect and the low number of animals that are responsible for the population variance.
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Malhado CHM, Malhado ACM, Carneiro PLS, Ramos AA, Carrillo JA, Pala A. Inbreeding depression on production and reproduction traits of buffaloes from Brazil. Anim Sci J 2012; 84:289-95. [PMID: 23590501 DOI: 10.1111/asj.12006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 07/26/2012] [Indexed: 11/30/2022]
Abstract
The objective of this study was to evaluate the influence of inbreeding depression on traits of buffaloes from Brazil. Specifically, the traits studied were body weight at 205 and 365 days of age, average daily gain from birth to 205 days (ADG_205), average daily gain between 205 and 365 days (ADG205_365) in Mediterranean buffaloes, and milk yield, lactation length, age of first calving and calving intervals in Murrah buffaloes. Inbreeding effects on the traits were determined by fitting four regression models (linear, quadratic, exponential and Michaelis-Menten) about the errors generated by the animal model. The linear model was only significant (P < 0.05) for growth traits (exception of ADG205_365). The exponential and Michaelis-Menten models were significant (P < 0.01) for all the studied traits while the quadratic model was not significant (P > 0.05) for any of the traits. Weight at 205 and 365 days of age decreased 0.25 kg and 0.39 kg per 1% of increase in inbreeding, respectively. The inbred animals (F = 0.25) produced less milk than non-inbred individuals: 50.4 kg of milk. Moreover, calving interval increased 0.164 days per 1% of increase in inbreeding. Interestingly, inbreeding had a positive effect on age at first calving and lactation length, decreasing age of first calving and increasing lactation length.
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