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Anaya G, Morales R, Demyda-Peyrás S, Moreno-Jiménez S, Jiménez JM, Molina A. Genomic Diversity of the Retinta Breed Derived from Two Ancestral Bovine Lineages. Vet Sci 2024; 11:247. [PMID: 38921994 PMCID: PMC11209511 DOI: 10.3390/vetsci11060247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
The Retinta breed, an autochthonous type of Spanish beef cattle, is highly adapted to breeding in its natural environment, which is characterized by a Mediterranean climate. The origins of this breed can be traced to two ancestral bovine stocks, which gave rise to distinct morphotypes differentiated primarily by coat color, alongside other significant traits such as growth, morphological conformation and temperament. Specifically, one morphotype comprises blond animals (Rubia Andaluza), genetically resembling the ancestral Bos taurus Aquitanicus, while the other encompasses brown- and red-colored animals (Retinta Extremeña) originating from Bos taurus Turdenatus stock. Over decades, these populations have undergone hybridization, leading to a unified population, albeit with the original subpopulations largely maintaining their genetic integrity. The objective of this study was to undertake genealogical and genomic characterization of these genetic lines, including a particular subpopulation within the blond animals (Tamarona cow). To achieve this, the genealogical records of 22,004 active animals were analyzed, and over 63,000 SNPs from a total of 1030 animals were examined for genomic characterization. Genealogical analysis revealed pedigree completeness and a high level of effective population size (Ne) across the entire population, yet relatively low Ne values within each pure line (ranging from 28.38 to 34.47). These findings underscore the ongoing efforts of the National Association of Retinta Breeders (ACRE) over the past decades to mitigate the loss of variability in this breed. The genomic characterization highlights the persistent differences within the original population and the predominant influence of the Retinto line within the current breed, as evidenced by principal component analysis (PCA) and admixture analysis. Furthermore, the identification of the Tamarona subpopulation within the blond lineage underlines its unique genetic composition, warranting its recognition as an official genetic line within the current Retinta breed. Given the small population size of these lines, particularly the Tamarona subpopulation, protective measures are imperative to preserve this distinct gene pool. Such measures would enhance the genetic diversity of the Retinta breed, which is essential for sustainable breeding practices in its natural habitats.
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Affiliation(s)
- Gabriel Anaya
- Department of Genetics, University of Córdoba, CN IV, KM 396, 17071 Córdoba, Spain; (G.A.); (R.M.)
| | - Rosa Morales
- Department of Genetics, University of Córdoba, CN IV, KM 396, 17071 Córdoba, Spain; (G.A.); (R.M.)
| | - Sebastián Demyda-Peyrás
- Department of Genetics, University of Córdoba, CN IV, KM 396, 17071 Córdoba, Spain; (G.A.); (R.M.)
| | - Samuel Moreno-Jiménez
- Department of Genetics, University of Córdoba, CN IV, KM 396, 17071 Córdoba, Spain; (G.A.); (R.M.)
| | - José María Jiménez
- Agricultural and Livestock Experimental Center (CEAG), The Council of Cadiz, 11400 Jerez de la Frontera, Spain
| | - Antonio Molina
- Department of Genetics, University of Córdoba, CN IV, KM 396, 17071 Córdoba, Spain; (G.A.); (R.M.)
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Cartuche Macas LF, Camacho Vallejo ME, González Ariza A, León Jurado JM, Delgado Bermejo JV, Marín Navas C, Navas González FJ. Analysis of Endangered Andalusian Black Cattle (Negra Andaluza) Reveals Genetic Reservoir for Bovine Black Trunk. Animals (Basel) 2024; 14:1131. [PMID: 38612370 PMCID: PMC11010997 DOI: 10.3390/ani14071131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/21/2024] [Accepted: 04/07/2024] [Indexed: 04/14/2024] Open
Abstract
This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed's conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity.
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Affiliation(s)
- Luis Favian Cartuche Macas
- Faculty of Biology, Amazonian State University, Lago Agrio Headquarters, Nueva Loja 210203, Ecuador;
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.V.D.B.); (C.M.N.)
| | | | - Antonio González Ariza
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain; (A.G.A.); (J.M.L.J.)
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain; (A.G.A.); (J.M.L.J.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.V.D.B.); (C.M.N.)
| | - Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.V.D.B.); (C.M.N.)
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González-Cano R, González-Martínez A, Ramón M, González Serrano M, Moreno Millán M, Rubio de Juan A, Rodero Serrano E. Exploring the Effects of Robertsonian Translocation 1/29 (Rob (1;29)) on Genetic Diversity in Minor Breeds of Spanish Berrenda Cattle via Genome-Wide Analysis. Animals (Basel) 2024; 14:793. [PMID: 38473178 DOI: 10.3390/ani14050793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Most of the previous studies on the genetic variability in Spanish "Berrenda" breeds have been carried out using DNA microsatellites. The present work aimed to estimate the genetic diversity, population structure, and potential genetic differences among individuals of both Berrenda breeds and groups based on the presence of the Robertsonian chromosomal translocation, rob (1;29). A total of 373 samples from animals belonging to the two breeds, including 169 cases diagnosed as rob (1;29)-positive, were genotyped using an SNP50K chip. The genetic diversity at the breed level did not show significant differences, but it was significantly lower in those subpopulations containing the rob (1;29). Runs of homozygosity identified a region of homozygosity on chromosome 6, where the KIT (KIT proto-oncogene, receptor tyrosine kinase) gene, which determines the typical spotted coat pattern in both breeds, is located. The four subpopulations considered showed minor genetic differences. The regions of the genome that most determined the differences between the breeds were observed on chromosomes 4, 6, 18, and 22. The presence of this Robertsonian translocation did not result in sub-structuring within each of the breeds considered. To improve the reproductive performance of Berrenda breeds, it would be necessary to implement strategies considering the involvement of potential breeding stock carrying rob (1;29).
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Affiliation(s)
- Rafael González-Cano
- Ministry of Agriculture, Fisheries and Food, Paseo Infanta Isabel 1, 28014 Madrid, Spain
- Regional Center of Animal Breeding and Reproduction (CERSYRA-IRIAF), Avenida del Vino 10, 13300 Ciudad Real, Spain
| | - Ana González-Martínez
- Department of Animal Production, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| | - Manuel Ramón
- Department of Animal Breeding and Genetics, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28040 Madrid, Spain
| | - Miriam González Serrano
- Department of Animal Production, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| | - Miguel Moreno Millán
- Department of Genetic, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| | - Alejandro Rubio de Juan
- Regional Center of Animal Breeding and Reproduction (CERSYRA-IRIAF), Avenida del Vino 10, 13300 Ciudad Real, Spain
| | - Evangelina Rodero Serrano
- Department of Animal Production, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
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Alanzor Puente JM, Pons Barro ÁL, González Ariza A, Martínez Martínez MDA, Delgado Bermejo JV, Navas González FJ. Integrated Discriminant Evaluation of Molecular Genetic Markers and Genetic Diversity Parameters of Endangered Balearic Dog Breeds. Int J Mol Sci 2024; 25:2706. [PMID: 38473952 DOI: 10.3390/ijms25052706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy-Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (Ho) = 0.754, expected heterozygosity (He) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average Ho = 0.313, He = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average Ho = 0.563, He = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average Ho = 0.598, He = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average Ho = 0.611, He = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied.
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Affiliation(s)
- José Manuel Alanzor Puente
- Institut de Reserca i Formaciò Agroalimentaria de les Illes Balears IRFAP, Conselleria d'Agricultura, Pesca i Alimentació, Govern Illes Balears, 07009 Palma, Spain
| | - Águeda Laura Pons Barro
- Institut de Reserca i Formaciò Agroalimentaria de les Illes Balears IRFAP, Conselleria d'Agricultura, Pesca i Alimentació, Govern Illes Balears, 07009 Palma, Spain
| | - Antonio González Ariza
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain
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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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Bhowmik N, Seaborn T, Ringwall KA, Dahlen CR, Swanson KC, Hulsman Hanna LL. Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States. Genes (Basel) 2023; 14:1842. [PMID: 37895190 PMCID: PMC10606367 DOI: 10.3390/genes14101842] [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: 08/11/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.
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Affiliation(s)
- Nayan Bhowmik
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Travis Seaborn
- School of Natural Resource Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Kris A. Ringwall
- Dickinson Research Extension Center, North Dakota State University, Dickinson, ND 58601, USA
| | - Carl R. Dahlen
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Kendall C. Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
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Parra-Bracamonte GM, Magaña-Monforte JG, Jahuey-Martínez FJ, Herrera-Ojeda JB, Vázquez-Armijo JF, Segura-Correa JC. Evidence of differentiation and population structure in Charolais cattle of Mexico. Trop Anim Health Prod 2023; 55:297. [PMID: 37723380 DOI: 10.1007/s11250-023-03729-7] [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: 02/22/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
Charolais is one of the most important beef cattle breeds in the world. In Mexico, it was introduced almost a century ago, and it has been suggested that particular breeding management and genetic material origin have caused a process of divergence among the current population. By a high-density SNP array genome-wide analysis, this study aimed to assess the proposed differentiation and population structure of local populations by genetic distances and structure approaches, and a European Charolais sample was included as a reference population. The differentiation statistics indicated that local populations exhibit moderate divergence, confirming a significant differentiation process between northeastern and northwestern Charolais populations (Fst≥ 0.043, D≥ 0.031). These results were strongly supported by PCA and structure analysis. Genetic isolation and low genetic flow between populations and divergent origins of introduced genetic material (i.e., semen) are likely the main drivers of the outcomes. Some implications are discussed.
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Affiliation(s)
| | - Juan G Magaña-Monforte
- Universidad Autónoma de Yucatán, Facultad de Medicina Veterinaria y Zootecnia, Mérida, Yucatán, México
| | | | - Jessica B Herrera-Ojeda
- Instituto Tecnológico del Valle de Morelia, Tecnológico Nacional de México, Morelia, Michoacán, México
| | | | - José C Segura-Correa
- Universidad Autónoma de Yucatán, Facultad de Medicina Veterinaria y Zootecnia, Mérida, Yucatán, México
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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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Genetic Differentiation among Livestock Breeds—Values for Fst. Animals (Basel) 2022; 12:ani12091115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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
Simple Summary The degree of relationship among livestock breeds can be quantified by the Fst statistic, which measures the extent of genetic differentiation between them. An Fst value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, Fst values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that Fst > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of Fst data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds. 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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Investigation of genetic diversity and selection signatures in Czech cattle genetic resources revealed by genome-wide analysis. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dixit SP, Bhatia AK, Ganguly I, Singh S, Dash S, Sharma A, Anandkumar N, Dang AK, Jayakumar S. Genome analyses revealed genetic admixture and selection signatures in Bos indicus. Sci Rep 2021; 11:21924. [PMID: 34753978 PMCID: PMC8578574 DOI: 10.1038/s41598-021-01144-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.
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Affiliation(s)
- S P Dixit
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
| | - A K Bhatia
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Indrajit Ganguly
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Sanjeev Singh
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Soumya Dash
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anurodh Sharma
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - N Anandkumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - A K Dang
- ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S Jayakumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
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Fan H, Wang T, Li Y, Liu H, Dong Y, Zhang R, Wang H, Shang L, Xing X. Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip. BMC Genom Data 2021; 22:35. [PMID: 34535071 PMCID: PMC8447661 DOI: 10.1186/s12863-021-00994-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background China is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easily distinguished. Therefore, the development of a SNP identification chip is urgently required. Results In this study, 250 sika deer, 206 red deer, 23 first-generation hybrid deer (F1), 20 s-generation hybrid deer (F2), and 20 third-generation hybrid deer (F3) were resequenced. Using the chromosome-level sika deer genome as the reference sequence, mutation detection was performed on all individuals, and a total of 130,306,923 SNP loci were generated. After quality control filtering was performed, the remaining 31,140,900 loci were confirmed. From molecular-level and morphological analyses, the sika deer reference population and the red deer reference population were established. The Fst values of all SNPs in the two reference populations were calculated. According to customized algorithms and strict screening principles, 1000 red deer-specific SNP sites were finally selected for chip design, and 63 hybrid individuals were determined to contain red deer-specific SNP loci. The results showed that the gene content of red deer gradually decreased in subsequent hybrid generations, and this decrease roughly conformed to the law of statistical genetics. Reaction probes were designed according to the screening sites. All candidate sites met the requirements of the Illumina chip scoring system. The average score was 0.99, and the MAF was in the range of 0.3277 to 0.3621. Furthermore, 266 deer (125 sika deer, 39 red deer, 56 F1, 29 F2,17 F3) were randomly selected for 1 K SNP chip verification. The results showed that among the 1000 SNP sites, 995 probes were synthesized, 4 of which could not be typed, while 973 loci were polymorphic. PCA, random forest and ADMIXTURE results showed that the 1 K sika deer SNP chip was able to clearly distinguish sika deer, red deer, and hybrid deer and that this 1 K SNP chip technology may provide technical support for the protection and utilization of pure sika deer species resources. Conclusion We successfully developed a low-density identification chip that can quickly and accurately distinguish sika deer from their hybrid offspring, thereby providing technical support for the protection and utilization of pure sika deer germplasm resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00994-z.
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Affiliation(s)
- Huanhuan Fan
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tianjiao Wang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yang Li
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Huitao Liu
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yimeng Dong
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Ranran Zhang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Hongliang Wang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Liyuan Shang
- Jilin Animal Husbandry and Veterinary Research Institute Changchun, Changchun, 130112, China
| | - Xiumei Xing
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds. Animals (Basel) 2021; 11:ani11072016. [PMID: 34359144 PMCID: PMC8300386 DOI: 10.3390/ani11072016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity. Abstract Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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15
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Casellas J, Id-Lahoucine S, Cánovas A. Discriminating between allele- and genotype-specific transmission ratio distortion. Anim Genet 2020; 51:847-854. [PMID: 32996622 DOI: 10.1111/age.13007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 11/30/2022]
Abstract
Transmission ratio distortion (TRD) is defined as the observed deviation from the expected Mendelian inheritance of alleles from heterozygous parents. This phenomenon is attributed to various biological mechanisms acting on germ cells, embryos or fetuses, or even in early postnatal life. Current statistical approaches typically use two independent parametrizations assuming that TRD relies on allele- or genotype-related mechanisms, although they have never been tested and compared. This study compared allele- and genotype-related TRD models on simulated datasets with 1000 genotyped offspring and real data from 168 sire-dam-offspring beef cattle trios. The analysis of simulated datasets favored the true model of analysis in most cases (>93%), and a low percentage of missidentification occurred under (almost) null dominance (genotype-related model) or similar and moderate-to-low sire- and dam-specific TRD parameters (allele-related model). Moreover, the correlation between simulated and predicted distortion parameters was high (>0.97) under the true model. The comparison of allele- and genotype-related TRD models is an appealing tool to infer the biological source of TRD (i.e. haploid vs. diploid cells) when screening the whole genome. The analysis of beef cattle data corroborated a TRD region previously reported in chromosome 4, although discarding allele-related mechanisms and favoring the genotype-related model as the more reliable one. The results of this study highlight the relevance of implementing and comparing different parametrizations to capture all kinds of TRD, and to compare them using appropriate statistical methods.
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Affiliation(s)
- J Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - S Id-Lahoucine
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
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16
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Alam MZ, Lee YM, Son HJ, Hanna LH, Riley DG, Mannen H, Sasazaki S, Park SP, Kim JJ. Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms. Anim Biosci 2020; 34:789-800. [PMID: 32882779 PMCID: PMC8100474 DOI: 10.5713/ajas.19.0888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/29/2020] [Indexed: 11/27/2022] Open
Abstract
Objective Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei’s genetic distance and Weir and Cockerham’s FST. Results Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was −0.076 for Jeju Black, while −0.018 to −0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.
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Affiliation(s)
- M Zahangir Alam
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Hyo-Jung Son
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Lauren H Hanna
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58105, USA
| | - David G Riley
- Department of Animal Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Shinji Sasazaki
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Se Pill Park
- Faculty of Biotechnology, Jeju National University, Jeju 13557, Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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17
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Rodríguez-Vázquez R, Mato A, López-Pedrouso M, Franco D, Sentandreu MA, Zapata C. Measuring quantitative proteomic distance between Spanish beef breeds. Food Chem 2020; 315:126293. [PMID: 32028200 DOI: 10.1016/j.foodchem.2020.126293] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 01/11/2023]
Abstract
Estimates of quantitative proteomic distance between populations have not been reported to date. Here, quantitative proteomic distances between three Spanish bovine breeds (Asturiana de los Valles, AV; Retinta, RE; and Rubia Gallega, RG) were estimated from two-dimensional electrophoresis profiles of meat samples of longissimus thoracis muscle at 2 h post-mortem. Statistically significant distances were detected between AV/RG and the most genetically different RE breed, using the novel QD measure of quantitative proteomic distance. In total, 18 differentially abundant myofibrillar and sarcoplasmic proteins/isoforms contributing to proteomic distances between breeds were confidently identified by tandem mass spectrometry. The fast skeletal myosin regulatory light chain 2 followed by other five interacting proteins exhibited the most pronounced relative change between breeds. In addition, most differentially represented proteins could be associated with variations in meat tenderness. Therefore, they could be candidate biomarkers for molecular breeding programs and authentication of the three Spanish beef breeds.
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Affiliation(s)
- R Rodríguez-Vázquez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A Mato
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - D Franco
- Meat Technology Center of Galicia, 32900 San Cibrao das Viñas, Ourense, Spain
| | - M A Sentandreu
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), 46980 Paterna, Valencia, Spain
| | - C Zapata
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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18
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Smaragdov MG, Kudinov AA. Assessing the power of principal components and wright's fixation index analyzes applied to reveal the genome-wide genetic differences between herds of Holstein cows. BMC Genet 2020; 21:47. [PMID: 32345235 PMCID: PMC7189535 DOI: 10.1186/s12863-020-00848-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 03/27/2020] [Indexed: 11/30/2022] Open
Abstract
Background Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright’s fixation index (Fst) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. Results Comparative analysis of the power Principal Components Analysis (PCA) and Fst were carried out to reveal genetic differences between herds of Holsteinized cows. Totally, 803 BovineSNP50 genotypes of cows from 13 herds were used in current study. Obtained Fst values were in the range of 0.002–0.012 (mean 0.0049) while for rare SNPs with MAF 0.0001–0.005 they were even smaller in the range of 0.001–0.01 (mean 0.0027). Genetic relatedness of the cows in the herds was the cause of such small Fst values. The contribution of rare alleles with MAF 0.0001–0.01 to the Fst values was much less than common alleles and this effect depends on linkage disequilibrium (LD). Despite of substantial change in the MAF spectrum and the number of SNPs we observed small effect size of LD - based pruning on Fst data. PCA analysis confirmed the mutual admixture and small genetic difference between herds. Moreover, PCA analysis of the herds based on the visualization the results of a single eigenvector cannot be used to significantly differentiate herds. Only summed eigenvectors should be used to realize full power of PCA to differentiate small between herds genetic difference. Finally, we presented evidences that the significance of Fst data far exceeds the significance of PCA data when these methods are used to reveal genetic differences between herds. Conclusions LD - based pruning had a small effect on findings of Fst and PCA analyzes. Therefore, for weakly structured populations the LD - based pruning is not effective. In addition, our results show that the significance of genetic differences between herds obtained by Fst analysis exceeds the values of PCA. Proposed, to differentiate herds or low structured populations we recommend primarily using the Fst approach and only then PCA.
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Affiliation(s)
- M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the l.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia. .,, St. Petersburg, Russian Federation.
| | - A A Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the l.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia.,Department of Agricultural Science, University of Helsinki, FI-00014, Helsinki, Finland
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19
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López-Pedrouso M, Rodríguez-Vázquez R, Purriños L, Oliván M, García-Torres S, Sentandreu MÁ, Lorenzo JM, Zapata C, Franco D. Sensory and Physicochemical Analysis of Meat from Bovine Breeds in Different Livestock Production Systems, Pre-Slaughter Handling Conditions and Ageing Time. Foods 2020; 9:E176. [PMID: 32054070 PMCID: PMC7074555 DOI: 10.3390/foods9020176] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/25/2020] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
Different bovine breeds and production systems are used worldwide, giving rise to differences in intrinsic and extrinsic characteristics of beef. In order to meet the consumer requirements, new approaches are currently being developed to guarantee tenderness, taste, and juiciness of beef. However, the final consumer perception is complex, and it is also affected by several interrelated variables. This study aimed to evaluate the physicochemical parameters and sensory profile of three Spanish cattle breeds under different livestock production systems (extensive and intensive) and pre-slaughter handling conditions (mixing and not mixing with unfamiliar individuals at pre-mortem time). Meat samples from each group were also studied at different ageing times (7 and 14 days). Regarding sensory attributes, twelve panelists assessed meat samples and an exhaustive statistical analysis was carried out. The most evident and strongest effect was the breed type, allowing a great differentiation among them using principal components and discriminant analysis. The livestock production system was the second most important parameter, significantly affecting odor, flavor, and textural profile (fibrousness). It can be concluded that there were marked differences in the traits of these beef that could be modified by other factors in order to fulfill consumer tastes.
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Affiliation(s)
- María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain; (M.L.-P.); (R.R.-V.); (C.Z.)
| | - Raquel Rodríguez-Vázquez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain; (M.L.-P.); (R.R.-V.); (C.Z.)
| | - Laura Purriños
- Centro Tecnológico de la Carne de Galicia, Rúa Galicia N° 4, Parque Tecnológico de Galicia, 32900 San Cibrao das Viñas, Spain; (L.P.); (J.M.L.)
| | - Mamen Oliván
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Apdo. 13, 33300 Villaviciosa, Spain;
- ISPA, Avda Roma s/n, 33011 Oviedo, Spain
| | - Susana García-Torres
- CICYTEX (Centro de Investigaciones Científicas y Tecnológicas de Extremadura), Junta de Extremadura. Ctra. A-V, Km372, 06187 Guadajira, Spain;
| | - Miguel Ángel Sentandreu
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Avenida Agustín Escardino, 7, Paterna, 46980 Valencia, Spain;
| | - José Manuel Lorenzo
- Centro Tecnológico de la Carne de Galicia, Rúa Galicia N° 4, Parque Tecnológico de Galicia, 32900 San Cibrao das Viñas, Spain; (L.P.); (J.M.L.)
| | - Carlos Zapata
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain; (M.L.-P.); (R.R.-V.); (C.Z.)
| | - Daniel Franco
- Centro Tecnológico de la Carne de Galicia, Rúa Galicia N° 4, Parque Tecnológico de Galicia, 32900 San Cibrao das Viñas, Spain; (L.P.); (J.M.L.)
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20
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Bohórquez MD, Ordoñez D, Suárez CF, Vicente B, Vieira C, López-Abán J, Muro A, Ordóñez I, Patarroyo MA. Major Histocompatibility Complex Class II (DRB3) Genetic Diversity in Spanish Morucha and Colombian Normande Cattle Compared to Taurine and Zebu Populations. Front Genet 2020; 10:1293. [PMID: 31998362 PMCID: PMC6965167 DOI: 10.3389/fgene.2019.01293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/25/2019] [Indexed: 11/13/2022] Open
Abstract
Bovine leukocyte antigens (BoLA) have been used as disease markers and immunological traits in cattle due to their primary role in pathogen recognition by the immune system. A higher MHC allele diversity in a population will allow presenting a broader peptide repertoire. However, loss of overall diversity due to domestication process can decrease a population's peptide repertoire. Within the context of zebu and taurine cattle populations, BoLA-DRB3 genetic diversity in Spanish Morucha and Colombian Normande cattle was analyzed and an approach to estimate functional diversity was performed. Sequence-based typing was used for identifying 29, 23, 27, and 28 alleles in Spanish Morucha, Nariño-, Boyacá-, and Cundinamarca-Normande cattle, respectively. These breeds had remarkably low heterozygosity levels and the Hardy-Weinberg principle revealed significant heterozygote deficiency. FST and DA genetic distance showed that Colombian Normande populations had greater variability than other phenotypically homogeneous breeds, such as Holstein. It was also found that Spanish Morucha cattle were strongly differentiated from other cattle breeds. Spanish Morucha had greater divergence in the peptide-binding region regarding other cattle breeds. However, peptide-binding region covariation indicated that the potential peptide repertoire seemed equivalent among cattle breeds. Despite the genetic divergence observed, the extent of the potential peptide repertoire in the cattle populations studied appears to be similar and thus their pathogen recognition potential should be equivalent, suggesting that functional diversity might persist in the face of bottlenecks imposed by domestication and breeding.
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Affiliation(s)
- Michel David Bohórquez
- Microbiology Postgraduate Programme, Universidad Nacional de Colombia, Bogotá, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Diego Ordoñez
- PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia.,Faculty of Agricultural Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Carlos Fernando Suárez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Belén Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Carmen Vieira
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Julio López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Iván Ordóñez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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21
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Mouresan EF, González-Rodríguez A, Cañas-Álvarez JJ, Munilla S, Altarriba J, Díaz C, Baró JA, Molina A, Lopez-Buesa P, Piedrafita J, Varona L. Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain. Front Genet 2019; 10:1170. [PMID: 31824571 PMCID: PMC6880760 DOI: 10.3389/fgene.2019.01170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/23/2019] [Indexed: 01/14/2023] Open
Abstract
In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely related populations. The biological material comprised 171 triplets (sire/dam/offspring) from seven populations of autochthonous beef cattle in Spain (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta, and Rubia Gallega), which were genotyped for 777,962 SNPs with the BovineHD BeadChip. After standard quality filtering, we reconstructed the haplotype phases in the parental individuals and calculated the LD by the correlation -r- between each pair of markers that had a genetic distance < 1 Mb. Subsequently, these correlations were used to calculate the persistency of LD phase between each pair of populations along the autosomal genome. Therefore, the distribution of the recombination rate along the genome can be inferred since the effect of the number of generations of divergence should be equivalent throughout the genome. In our study, the recombination rate was highest in the largest chromosomes and at the distal portion of the chromosomes. In addition, the persistency of LD phase was highly heterogeneous throughout the genome, with a ratio of 25.4 times between the estimates of the recombination rates from the genomic regions that had the highest (BTA18-7.1 Mb) and the lowest (BTA12-42.4 Mb) estimates. Finally, an overrepresentation enrichment analysis (ORA) showed differences in the enriched gene ontology (GO) terms between the genes located in the genomic regions with estimates of the recombination rate over (or below) the 95th (or 5th) percentile throughout the autosomal genome.
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Affiliation(s)
- Elena Flavia Mouresan
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | - Sebastián Munilla
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Juan Altarriba
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Clara Díaz
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Jesús A Baró
- Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | - Antonio Molina
- Departamento de Ciencias Agroforestales, Universidad de Valladolid, Valladolid, Spain
| | - Pascual Lopez-Buesa
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Jesús Piedrafita
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luis Varona
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
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Li R, Li C, Chen H, Liu X, Xiao H, Chen S. Genomic diversity and admixture patterns among six Chinese indigenous cattle breeds in Yunnan. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1069-1076. [PMID: 30744361 PMCID: PMC6599958 DOI: 10.5713/ajas.18.0605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/08/2018] [Indexed: 11/27/2022]
Abstract
Objective Yunnan is not only a frontier zone that connects China with South and Southeast Asia, but also represents an admixture zone between taurine (Bos taurus) and zebu (Bos indicus) cattle. The purpose of this study is to understand the level of genomic diversity and the extent of admixture in each Yunnan native cattle breed. Methods All 120 individuals were genotyped using Illumina BovineHD BeadChip (777,962 single nucleotide polymorphisms [SNPs]). Quality control and genomic diversity indexes were calculated using PLINK software. The principal component analysis (PCA) was assessed using SMARTPCA program implemented in EIGENSOFT software. The ADMIXTURE software was used to reveal admixture patterns among breeds. Results A total of 604,630 SNPs was obtained after quality control procedures. Among six breeds, the highest level of mean heterozygosity was found in Zhaotong cattle from Northeastern Yunnan, whereas the lowest level of heterozygosity was detected in Dehong humped cattle from Western Yunnan. The PCA based on a pruned dataset of 233,788 SNPs clearly separated Dehong humped cattle (supposed to be a pure zebu breed) from other five breeds. The admixture analysis further revealed two clusters (K = 2 with the lowest cross validation error), corresponding to taurine and zebu cattle lineages. All six breeds except for Dehong humped cattle showed different degrees of admixture between taurine and zebu cattle. As expected, Dehong humped cattle showed no signature of taurine cattle influence. Conclusion Overall, considerable genomic diversity was found in six Yunnan native cattle breeds except for Dehong humped cattle from Western Yunnan. Dehong humped cattle is a pure zebu breed, while other five breeds had admixed origins with different extents of admixture between taurine and zebu cattle. Such admixture by crossbreeding between zebu and taurine cattle facilitated the spread of zebu cattle from tropical and subtropical regions to other highland regions in Yunnan.
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Affiliation(s)
- Rong Li
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - Chunqing Li
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China.,National Demonstration Center for Experimental Life Sciences Education, Yunnan University, Kunming Yunnan 650500, China
| | - Hongyu Chen
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - Xuehong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650221, China
| | - Heng Xiao
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - Shanyuan Chen
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China.,National Demonstration Center for Experimental Life Sciences Education, Yunnan University, Kunming Yunnan 650500, China
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23
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Mastrangelo S, Ciani E, Ajmone Marsan P, Bagnato A, Battaglini L, Bozzi R, Carta A, Catillo G, Cassandro M, Casu S, Ciampolini R, Crepaldi P, D'Andrea M, Di Gerlando R, Fontanesi L, Longeri M, Macciotta NP, Mantovani R, Marletta D, Matassino D, Mele M, Pagnacco G, Pieramati C, Portolano B, Sarti FM, Tolone M, Pilla F. Conservation status and historical relatedness of Italian cattle breeds. Genet Sel Evol 2018; 50:35. [PMID: 29940848 PMCID: PMC6019226 DOI: 10.1186/s12711-018-0406-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/11/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
| | | | - Alessandro Bagnato
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095, Grugliasco, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, University of Firenze, 50144, Florence, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015, Monterotondo, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100, Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e tecnologie Agroalimentari, University of Bologna, 40127, Bologna, Italy
| | - Maria Longeri
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione, Ambiente, University of Catania, 95125, Catania, Italy
| | - Donato Matassino
- Divulgazione e Applicazione di Biotecniche Innovative, Consorzio per la Sperimentazione, 82100, Benevento, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, 56124, Pisa, Italy
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Camillo Pieramati
- Dipartimento di Medicina Veterinaria, University of Perugia, 06126, Perugia, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari, Ambientali, University of Perugia, 06121, Perugia, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, University of Molise, 86100, Campobasso, Italy.,Centro Risorse Bio-Culturali e Sviluppo Locale, University of Molise, 86100, Campobasso, Italy
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Evaluation of the potential use of a meta-population for genomic selection in autochthonous beef cattle populations. Animal 2017; 12:1350-1357. [PMID: 29094666 DOI: 10.1017/s175173111700283x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip. Purebred and combined reference sets were used for the genomic evaluation and several scenarios of different genetic architecture of the trait were investigated. The single-breed evaluations yielded the highest within-breed accuracies. Across breed accuracies were found low but positive on average confirming the genetic connectedness between the populations. If the same genotyping effort is split in several populations, the accuracies were lower when compared with single-breed evaluation, but showed a small advantage over small-sized purebred reference sets over the accuracies of subsequent generations. Besides, the genetic architecture of the trait did not show any relevant effect on the accuracy with the exception of rare variants, which yielded slightly lower results and higher loss of predictive ability over the generations.
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25
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Mouresan E, González-Rodríguez A, Cañas-Álvarez J, Díaz C, Altarriba J, Baro J, Piedrafita J, Molina A, Toro M, Varona L. On the haplotype diversity along the genome in Spanish beef cattle populations. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Cañas-Álvarez JJ, Mouresan EF, Varona L, Díaz C, Molina A, Baro JA, Altarriba J, Carabaño MJ, Casellas J, Piedrafita J. Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip. J Anim Sci 2017; 94:2779-88. [PMID: 27482665 DOI: 10.2527/jas.2016-0425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.
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27
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Genomic differentiation between Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega cattle breeds. Animal 2017; 11:1667-1679. [PMID: 28270253 DOI: 10.1017/s1751731117000398] [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] [Indexed: 12/29/2022] Open
Abstract
The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous populations (Asturiana de los Valles (AV), Avileña-Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG)). The BovineHD 777K BeadChip was used on 342 individuals (AV, n=50; ANI, n=48; BP, n=50; Mo, n=50; Pi, n=48; Re, n=48; RG, n=48) chosen to be as unrelated as possible. We calculated the fixation index (F ST ) and performed a Bayesian analysis named SelEstim. The output of both procedures was very similar, although the Bayesian analysis provided a richer inference and allowed us to calculate significance thresholds by generating a pseudo-observed data set from the estimated posterior distributions. We identified a very large number of genomic regions, but when a very restrictive significance threshold was applied these regions were reduced to only 10. Among them, four regions can be highlighted because they comprised a large number of single nucleotide polymorphisms and showed extremely high signals (Kullback-Leiber divergence (KLD)>6). They are located in BTA 2 (5 575 950 to 10 152 228 base pairs (bp)), BTA 5 (17 596 734 to 18 850 702 bp), BTA 6 (37 853 912 to 39 441 548 bp) and BTA 18 (13 345 515 to 15 243 838 bp) and harbor, among others, the MSTN (Myostatin), KIT-LG (KIT Ligand), LAP3 (leucine aminopeptidase 3), NAPCG (non-SMC condensing I complex, subunit G), LCORL (ligand dependent nuclear receptor corepressor-like) and MC1R (Melanocortin 1 receptor) genes. Knowledge on these genomic regions allows to identify potential targets of recent selection and helps to define potential candidate genes associated with traits of interest, such as coat color, muscle development, fertility, growth, carcass and immunological response.
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28
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González-Rodríguez A, Munilla S, Mouresan EF, Cañas-Álvarez JJ, Díaz C, Piedrafita J, Altarriba J, Baro JÁ, Molina A, Varona L. On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations. Genet Sel Evol 2016; 48:81. [PMID: 27793093 PMCID: PMC5084421 DOI: 10.1186/s12711-016-0258-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 10/18/2016] [Indexed: 01/05/2023] Open
Abstract
Background Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations. Results Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic–pituitary–thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors. Conclusions We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0258-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sebastián Munilla
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.,Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, 1417, Buenos Aires, Argentina
| | - Elena F Mouresan
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain
| | - Jhon J Cañas-Álvarez
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Clara Díaz
- Departamento de Mejora Genética Animal, INIA, 28040, Madrid, Spain
| | - Jesús Piedrafita
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Juan Altarriba
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.,Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain
| | - Jesús Á Baro
- Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004, Palencia, Spain
| | | | - Luis Varona
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain. .,Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain.
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29
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Upadhyay MR, Chen W, Lenstra JA, Goderie CRJ, MacHugh DE, Park SDE, Magee DA, Matassino D, Ciani F, Megens HJ, van Arendonk JAM, Groenen MAM. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity (Edinb) 2016; 118:169-176. [PMID: 27677498 PMCID: PMC5234481 DOI: 10.1038/hdy.2016.79] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/10/2023] Open
Abstract
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.
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Affiliation(s)
- M R Upadhyay
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish Institute of Agricultural Sciences, Uppsala, Sweden
| | - W Chen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, CM Utrecht, The Netherlands
| | | | - D E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - S D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Dublin 2, Ireland
| | - D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - D Matassino
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - F Ciani
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - H-J Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A M van Arendonk
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - M A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
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30
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Sánchez-Molano E, Tsiokos D, Chatziplis D, Jorjani H, Degano L, Diaz C, Rossoni A, Schwarzenbacher H, Seefried F, Varona L, Vicario D, Nicolazzi EL, Banos G. A practical approach to detect ancestral haplotypes in livestock populations. BMC Genet 2016; 17:91. [PMID: 27342071 PMCID: PMC4921009 DOI: 10.1186/s12863-016-0405-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/21/2016] [Indexed: 12/04/2022] Open
Abstract
Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0405-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Sánchez-Molano
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Dimitrios Tsiokos
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece
| | | | - Lorenzo Degano
- Associazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy
| | - Clara Diaz
- Departamento de Mejora Genética Animal, INIA, Madrid, 28040, Spain
| | - Attilio Rossoni
- Associazione Nazionale Allevatori Bovini della Razza Bruna, Verona, Italy
| | | | | | - Luis Varona
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, Zaragoza, 50013, Spain.,Instituto Agroalimentario de Aragón (IA2), Zaragoza, 50013, Spain
| | - Daniele Vicario
- Associazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy
| | - Ezequiel L Nicolazzi
- Bioinformatics core facility, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. CascinaCodazza, Lodi, 26900, Italy
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.,SRUC,The Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, Edinburgh, UK.,School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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