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Marcuzzi O, Calcaterra F, Loza Vega A, Ortega Masagué MF, Armstrong E, Pereira Rico JA, Jara E, Olivera LH, Peral García P, Giovambattista G. Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America. Anim Genet 2024; 55:527-539. [PMID: 38716584 DOI: 10.1111/age.13435] [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: 03/25/2024] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 07/04/2024]
Abstract
The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.
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Affiliation(s)
- O Marcuzzi
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - F Calcaterra
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - A Loza Vega
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - M F Ortega Masagué
- Instituto de Investigación Animal del Chaco Semiárido, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Leales, Tucumán, Argentina
| | - E Armstrong
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - J A Pereira Rico
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - E Jara
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - L H Olivera
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - P Peral García
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
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Bhardwaj S, Togla O, Mumtaz S, Yadav N, Tiwari J, Muansangi L, Illa SK, Wani YM, Mukherjee S, Mukherjee A. Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics. Anim Biosci 2024; 37:795-806. [PMID: 37946419 PMCID: PMC11065711 DOI: 10.5713/ab.23.0263] [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: 07/15/2023] [Revised: 08/21/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the longterm sustainability of these breeds. METHODS The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. RESULTS The average LD between single nucleotide polymorphisms (SNPs) was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based Ne of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for Ne estimation), respectively. CONCLUSION KF cattle have an Ne exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for longterm sustainable development.
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Affiliation(s)
- Shivam Bhardwaj
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Oshin Togla
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Shabahat Mumtaz
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Nistha Yadav
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
- Department of Animal Genetics and Breeding, CVAS, RAJUVAS, Bikaner 334001, Rajasthan,
India
| | - Jigyasha Tiwari
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Lal Muansangi
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Satish Kumar Illa
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
- Livestock Research Station, Garividi Sri Venkateswara Veterinary University, Andhra Pradesh 535101,
India
| | - Yaser Mushtaq Wani
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Sabyasachi Mukherjee
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
| | - Anupama Mukherjee
- Animal Genetics and Breeding Division, ICAR- National Dairy Research Institute (NDRI), Karnal 132001, Haryana,
India
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Novo I, Ordás P, Moraga N, Santiago E, Quesada H, Caballero A. Impact of population structure in the estimation of recent historical effective population size by the software GONE. Genet Sel Evol 2023; 55:86. [PMID: 38049712 PMCID: PMC10694967 DOI: 10.1186/s12711-023-00859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Effective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration or confluence of other populations. If this occurs, the estimates of Ne can be heavily biased. In this paper, we evaluate the impact of migration and admixture on the estimates of historical Ne provided by GONE through a series of computer simulations considering several scenarios: (a) the mixture of two or more ancestral populations; (b) subpopulations that continuously exchange individuals through migration; (c) populations receiving migrants from a large source; and (d) populations with balanced systems of chromosomal inversions, which also generate genetic structure. RESULTS Our results indicate that the estimates of historical Ne provided by GONE may be substantially biased when there has been a recent mixture of populations that were previously separated for a long period of time. Similarly, biases may occur when the rate of continued migration between populations is low, or when chromosomal inversions are present at high frequencies. However, some biases due to population structuring can be eliminated by conducting population structure analyses and restricting the estimation to the differentiated groups. In addition, disregarding the genomic regions that are involved in inversions can also remove biases in the estimates of Ne. CONCLUSIONS Different kinds of deviations from isolation and panmixia of the populations can generate biases in the recent historical estimates of Ne. Therefore, estimation of past demography could benefit from performing population structure analyses beforehand, by mitigating the impact of these biases on historical Ne estimates.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain.
| | - Pilar Ordás
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Natalia Moraga
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Humberto Quesada
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
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Novo I, Pérez-Pereira N, Santiago E, Quesada H, Caballero A. An empirical test of the estimation of historical effective population size using Drosophila melanogaster. Mol Ecol Resour 2023; 23:1632-1640. [PMID: 37455584 DOI: 10.1111/1755-0998.13837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The availability of a large number of high-density markers (SNPs) allows the estimation of historical effective population size (Ne ) from linkage disequilibrium between loci. A recent refinement of methods to estimate historical Ne from the recent past has been shown to be rather accurate with simulation data. The method has also been applied to real data for numerous species. However, the simulation data cannot encompass all the complexities of real genomes, and the performance of any estimation method with real data is always uncertain, as the true demography of the populations is not known. Here, we carried out an experimental design with Drosophila melanogaster to test the method with real data following a known demographic history. We used a population maintained in the laboratory with a constant census size of about 2800 individuals and subjected the population to a drastic decline to a size of 100 individuals. After a few generations, the population was expanded back to the previous size and after a few further generations again expanded to twice the initial size. Estimates of historical Ne were obtained with the software GONE both for autosomal and X chromosomes from samples of 17 individuals sequenced for the whole genome. Estimates of the historical effective size were able to infer the patterns of changes that occurred in the populations showing generally good performance of the method. We discuss the limitations of the method and the application of the software carried out so far.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Noelia Pérez-Pereira
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Humberto Quesada
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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Hu M, Jiang H, Lai W, Shi L, Yi W, Sun H, Chen C, Yuan B, Yan S, Zhang J. Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array. Animals (Basel) 2023; 13:ani13101717. [PMID: 37238146 DOI: 10.3390/ani13101717] [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: 03/08/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.
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Affiliation(s)
- Mingyue Hu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Chengzhen Chen
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Bao Yuan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Jiabao Zhang
- College of Animal Science, Jilin University, Changchun 130062, China
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