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King F, Visser C, Banga C. Genetic characterization of Mozambican Nguni cattle and their relationship with indigenous populations of South Africa. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hall SJG. Genetic Differentiation among Livestock Breeds-Values for F st. Animals (Basel) 2022; 12:1115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Affiliation(s)
- Stephen J G Hall
- Department of Environmental Protection and Landscape, Estonian University of Life Sciences, Kreutzwaldi 5, 51014 Tartu, Estonia
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van Marle-Köster E, Lashmar SF, Retief A, Visser C. Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations. Front Genet 2021; 12:714194. [PMID: 34777459 PMCID: PMC8581043 DOI: 10.3389/fgene.2021.714194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek® Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina® Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean Ho ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (FROH range: 0.018–0.104), than for sheep populations (FROH range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of <4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment.
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Affiliation(s)
| | | | - Anel Retief
- Department of Animal Science, University of Pretoria, Pretoria, South Africa
| | - Carina Visser
- Department of Animal Science, University of Pretoria, Pretoria, South Africa
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Molina Flores B, Camacho Vallejo ME, Delgado Bermejo JV, Navas González FJ, Martínez MDA. Do Pharaohs' cattle still graze the Nile Valley? Genetic characterization of the Egyptian Baladi cattle breed. Anim Biotechnol 2021:1-13. [PMID: 34694188 DOI: 10.1080/10495398.2021.1991938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Egyptian Baladi cattle is one of the few native taurine breeds which remain in the original domestication area of Bos taurus, the Nile Valley (Upper Egypt). Apart from its evolutive relevance, the breed is well-adapted and integrated into the traditional family farming systems, with great potentialities for local sustainable rural development. The diversity and structure of the Baladi population were assessed using 28 genetic microsatellite markers. Within and between-breeds diversity, its relations with other cattle breeds, and an inference on its origin and evolution, were analyzed. Results reported high levels of diversity, with an average number of alleles (Na) of 11.39, observed heterozygosity (Ho) of 0.68, and expected heterozygosity (He) of 0.75. The studied population was in Hardy-Weinberg disequilibrium, which could be ascribed to its internal structure. The comparison between breeds using factorial correspondence analysis, Reynolds genetic distance evaluation, and genetic structure analysis suggested slight influences of Bos indicus. Upper Egypt's rural communities have preserved the Baladi cattle breed, protecting this historical and biological heritage against the constant and indiscriminate introduction of exotic genetic resources along the history of development of the breed. Developing and implementing conservation and breeding programs is crucial for the preservation and improvement of the breed.HIGHLIGHTSBaladi cattle breed is a well-defined and highly diverse breed.Higher diversity levels are found in northern and central governorates.A clear geographical cluster is formed around the Nile Delta.Baladi cattle may be reminiscent of the ancient 'pharaoh' cattle.Assiut's population acted as the most ancestral population nucleus.
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Affiliation(s)
| | | | | | - Francisco Javier Navas González
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, Córdoba, Spain
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van der Nest MA, Hlongwane N, Hadebe K, Chan WY, van der Merwe NA, De Vos L, Greyling B, Kooverjee BB, Soma P, Dzomba EF, Bradfield M, Muchadeyi FC. Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed. Front Genet 2021; 11:608650. [PMID: 33584805 PMCID: PMC7876384 DOI: 10.3389/fgene.2020.608650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022] Open
Abstract
In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.
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Affiliation(s)
| | - Nompilo Hlongwane
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Wai-Yin Chan
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Nicolaas A van der Merwe
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Ben Greyling
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | | | - Pranisha Soma
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | - Edgar F Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
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