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Nomura T. Ballou's Ancestral Inbreeding Coefficient: Formulation and New Estimate with Higher Reliability. Animals (Basel) 2024; 14:1844. [PMID: 38997956 PMCID: PMC11240364 DOI: 10.3390/ani14131844] [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: 05/20/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou's ancestral inbreeding coefficient (FBAL-ANC) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for FBAL-ANC has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for FBAL-ANC and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of FBAL-ANC could be remarkably enhanced. The relationship between FBAL-ANC and other pedigree-based parameters is also discussed.
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Affiliation(s)
- Tetsuro Nomura
- Department of Industrial Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
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Vostry L, Vostra-Vydrova H, Moravcikova N, Kasarda R, Margetin M, Rychtarova J, Drzaic I, Shihabi M, Cubric-Curik V, Sölkner J, Curik I. Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds. J Dairy Sci 2024:S0022-0302(24)00937-8. [PMID: 38908686 DOI: 10.3168/jds.2023-24607] [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: 12/23/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
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Affiliation(s)
- Lubos Vostry
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
| | - Hana Vostra-Vydrova
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Nina Moravcikova
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Radovan Kasarda
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Milan Margetin
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Jana Rychtarova
- Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic
| | - Ivana Drzaic
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Mario Shihabi
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Vlatka Cubric-Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Johan Sölkner
- University of Natural Resources & Life Sciences Vienna, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Ino Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
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Nagy I, Nguyen TA. Characterizing and Eliminating the Inbreeding Load. Vet Sci 2023; 11:8. [PMID: 38250914 PMCID: PMC10819885 DOI: 10.3390/vetsci11010008] [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: 10/29/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding-purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding-purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.
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Affiliation(s)
- István Nagy
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary;
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Pakpahan S, Widayanti R, Artama WT. Selection signatures and formation of the Samosir goat breed through the cultures of the Batak Toba Tribe in Samosir Island, Indonesia. Vet World 2022; 15:1044-1050. [PMID: 35698517 PMCID: PMC9178575 DOI: 10.14202/vetworld.2022.1044-1050] [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: 12/29/2021] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: The Samosir goat has a high cultural value and is a source of germplasm in Indonesia. This study aimed to reveal the history and selection signatures of the Samosir goat. Materials and Methods: A total of 25 goats were divided into seven subpopulations of Indonesian goat breeds. Deoxyribonucleic acid (DNA) from blood samples was isolated with the use of the gSYNC™ DNA Mini Kit (Geneaid, Taipei, Taiwan). Cytb gene amplification was performed by the polymerase chain reaction (PCR) method, and the PCR products were sequenced. A phylogenetic tree was constructed by the neighbor-joining method using MEGA 11 software. A questionnaire was used to collect information related to the history and breeding practices of the Samosir goat on Samosir Island. Results: Samosir goats are divided into four groups based on their coat color: Completely white, white with brown spots, white with black spots, and white with brown and black spots. The body form of the Samosir goat is similar to that of the Kacang goat. The space below a traditional Toba Batak house is used as a goat pen. The genetic difference between the Samosir goat and the Kacang goat based on the Cytb gene was approximately 0.1%. Conclusion: Phylogenetic analysis between Samosir goats and other indigenous Indonesian goats revealed that Samosir goats form a single clade, with a very close genetic distance from other local goats, such as the Kacang goat. The Toba Batak culture on Samosir Island has significantly influenced the selection and formation of the Samosir goat breed.
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Affiliation(s)
- Suhendra Pakpahan
- Museum Zoologicum Bogoriense, Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Wayan T. Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Wang Z, Zhou B, Zhang T, Yan X, Yu Y, Li J, Mei B, Wang Z, Zhang Y, Wang R, Lv Q, Liu Z, Zhao Y, Du C, Su R. Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis. Front Vet Sci 2021; 8:665872. [PMID: 34239910 PMCID: PMC8258104 DOI: 10.3389/fvets.2021.665872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs. Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs. Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD. Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.
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Affiliation(s)
- Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bohan Zhou
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Tao Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Inner Mongolia Bigvet Co., Ltd., Hohhot, China
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongsheng Yu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinquan Li
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China.,Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agriculture University, Hohhot, China
| | - Bujun Mei
- Department of Agriculture, Hetao College, Hetao University, Bayannaoer, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Liu
- Inner Mongolia Bigvet Co., Ltd., Hohhot, China
| | | | - Chen Du
- Reproductive Medicine Center, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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