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Schiavo G, Bovo S, Ribani A, Moscatelli G, Bonacini M, Prandi M, Mancin E, Mantovani R, Dall'Olio S, Fontanesi L. Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region. J Dairy Sci 2021; 105:2408-2425. [PMID: 34955250 DOI: 10.3168/jds.2021-20915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (FPED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.
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Affiliation(s)
- Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Giulia Moscatelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy.
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Komiya R, Ogawa S, Aonuma T, Satoh M. Performance of using opposing homozygotes for paternity testing in Japanese Black cattle. J Anim Breed Genet 2021; 139:113-124. [PMID: 34499371 DOI: 10.1111/jbg.12649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide single nucleotide polymorphism (SNP) markers in Japanese Black cattle enable genomic prediction and verifying parent-offspring relationships. We assessed the performance of opposing homozygotes (OH) for paternity testing in Japanese Black cattle, using SNP genotype information of 50 sires and 3,420 fattened animals, 1,945 of which were fathered by the 50 genotyped sires. The number of OH was counted for each sire-progeny pair in 28,764 SNPs with minor allele frequencies of ≥0.05 in this population. Across all pairs of animals, the number of OH tended to increase as the pedigree-based coefficient of relationship decreased. With a threshold of 288 (1% of SNPs) for paternity testing, most sire-progeny pairs were detected as true relationships. The frequency of Mendelian inconsistencies was 2.4%, reflecting the high accuracy of pedigree information in Japanese Black cattle population. The results indicate the utility of OH for paternity testing in Japanese Black cattle.
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Affiliation(s)
- Ryota Komiya
- Faculty of Agriculture, Tohoku University, Sendai, Japan
| | - Shinichiro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tatsuya Aonuma
- Miyagi Prefectural Livestock Experiment Station, Osaki, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Fang Y, Hao X, Xu Z, Sun H, Zhao Q, Cao R, Zhang Z, Ma P, Sun Y, Qi Z, Wei Q, Wang Q, Pan Y. Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data. Front Genet 2021; 12:629966. [PMID: 33995477 PMCID: PMC8116706 DOI: 10.3389/fgene.2021.629966] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Laiwu pigs, distinguished by their high intramuscular fat of 7-9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1-5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.
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Affiliation(s)
- Yifei Fang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Hao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Cao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | | | | | - Qishan Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
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Raschia M, Nani J, Carignano H, Amadio A, Maizon D, Poli M. Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Nwogwugwu CP, Kim Y, Chung YJ, Jang SB, Roh SH, Kim S, Lee JH, Choi TJ, Lee SH. Effect of errors in pedigree on the accuracy of estimated breeding value for carcass traits in Korean Hanwoo cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:1057-1067. [PMID: 32054237 PMCID: PMC7322652 DOI: 10.5713/ajas.19.0021] [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: 01/09/2019] [Accepted: 09/02/2019] [Indexed: 11/27/2022]
Abstract
OBJECTIVE This study evaluated the effect of pedigree errors (PEs) on the accuracy of estimated breeding value (EBV) and genetic gain for carcass traits in Korean Hanwoo cattle. METHODS The raw data set was based on the pedigree records of Korean Hanwoo cattle. The animals' information was obtained using Hanwoo registration records from Korean animal improvement association database. The record comprised of 46,704 animals, where the number of the sires used was 1,298 and the dams were 38,366 animals. The traits considered were carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS). Errors were introduced in the pedigree dataset through randomly assigning sires to all progenies. The error rates substituted were 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, and 80%, respectively. A simulation was performed to produce a population of 1,650 animals from the pedigree data. A restricted maximum likelihood based animal model was applied to estimate the EBV, accuracy of the EBV, expected genetic gain, variance components, and heritability (h2) estimates for carcass traits. Correlation of the simulated data under PEs was also estimated using Pearson's method. RESULTS The results showed that the carcass traits per slaughter year were not consistent. The average CWT, EMA, BFT, and MS were 342.60 kg, 78.76 cm2, 8.63 mm, and 3.31, respectively. When errors were introduced in the pedigree, the accuracy of EBV, genetic gain and h2 of carcass traits was reduced in this study. In addition, the correlation of the simulation was slightly affected under PEs. CONCLUSION This study reveals the effect of PEs on the accuracy of EBV and genetic parameters for carcass traits, which provides valuable information for further study in Korean Hanwoo cattle.
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Affiliation(s)
| | - Yeongkuk Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Yun Ji Chung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Sung Bong Jang
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Seung Hee Roh
- Hanwoo Improvement Center, National Agricultural Cooperative Federation, Seosan 31948, Korea
| | - Sidong Kim
- National Institute of Animal Science, Cheonan 31000, Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Tae Jeong Choi
- National Institute of Animal Science, Cheonan 31000, Korea
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
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Zanella R, Lago LV, da Silva AN, Pértille F, de Carvalho NS, do Carmo Panetto JC, Zanella GC, Facioli FL, da Silva MVGB. Genetic Characterization of Indubrasil Cattle Breed Population. Vet Sci 2018; 5:vetsci5040098. [PMID: 30513897 PMCID: PMC6313910 DOI: 10.3390/vetsci5040098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/19/2018] [Accepted: 11/29/2018] [Indexed: 11/27/2022] Open
Abstract
The Indubrasil breed was developed in the Brazilian region called Triângulo Mineiro as a result of a cross between zebu cattle. Initially, it was used as a terminal cross and currently it represents approximately 4.45% of all the Brazilian zebu cattle. Studies were conducted to estimate genetic parameters in the Indubrasil using pedigree information, however, until now, no study has been developed using large-scale genomic markers in this breed. Pedigree information are widely used to investigate population parameters; however, they can neglect some estimates when compared to the use of genomic markers. Therefore, the objective of this study was to investigate the population structure and the genetic diversity of Indubrasil cattle using a high-density Single Nucleotide Polymorphism (SNP) panel (Illumina BovineHD BeadChip 700k). Levels of genomic homozygosity were evaluated using three different approaches: Runs of homozygosity (FROH), % of homozygosis (FSNP), and inbreeding coefficient (Fx). Further, Runs of Homozygosity (ROH) segments conserved among the animals were investigated to identify possible regions associated with the breed characteristics. Our results indicate that even the Indubrasil breed having a small effective population size, the levels of homozygosity (FROH = 0.046) are still small. This was possibly caused by the cross conducted among different breeds for its development. It suggests no immediate risks associated with loss of genetic variation. This information might be used in breeding programs, for the breed conservation and for the expansion of the Indubrasil breed.
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Affiliation(s)
- Ricardo Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
- Docente do programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Luísa V Lago
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Arthur N da Silva
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Fábio Pértille
- Laboratório de Biotecnologia Animal, Departamento de Ciência Animal e Pastagens, Universidade de São Paulo/Escola Superior de Agricultura Luiz de Queiroz, Av. Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil.
| | - Nathã S de Carvalho
- Mestrando do Curso de Zootecnia, Universidade Federal do Rio Grande do Sul/Faculdade de Agronomia, Av. Bento Gonçalves, 7712, 91540-000 Porto Alegre, RS, Brazil.
| | | | - Giovana C Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Fernanda L Facioli
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
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VIJH RAMESHKUMAR, SHARMA UPASNA, GAUR UMA, GOKHALE SURESHB. DNA profiling and paternity verification in Murrah buffaloes. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i11.85036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The accuracy of selection for sire’s merit depends upon the number of daughters born to the sire and also the correctness of performance records. The accuracy of records depends on confirmed paternity of the daughters. In this paper, we report paternity confirmation of a large progeny testing program in buffaloes. The work was undertaken in collaboration with BAIF, Pune under National Agricultural Innovation Project. Murrah bulls (12) were selected and around 120,000 buffaloes were inseminated at farmers’ doorsteps. The area of operation was 52 districts of Uttar Pradesh. We targeted 1,000 female calves to be born to each of the 12 sires. The experiment was an effort to develop a reference population for identification of quantitative trait loci for various economic traits in buffaloes using halfsib design. Owing to financial constraints, we targeted 10,000 daughters born to these 12 sires. The DNA was isolated from these daughters. The DNA of sires was also isolated. Since there was no parentage verification kit commercially available for buffaloes, we developed a multiplex PCR reaction consisting of 11 microsatellite markers to confirm the paternity. The correctness of the paternity was established using microsatellite DNA markers and comparison of daughters’ genotype with genotype of sires. The paper reports paternity testing of large reference family. We also developed a software ‘Confirm Paternity’ for comparing the genotypes of daughters with the respective sire. We report paternity correctness of 90.48% in buffaloes under field conditions.
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Zhang T, Guo L, Shi M, Xu L, Chen Y, Zhang L, Gao H, Li J, Gao X. Selection and effectiveness of informative SNPs for paternity in Chinese Simmental cattle based on a high-density SNP array. Gene 2018; 673:211-216. [PMID: 29933017 DOI: 10.1016/j.gene.2018.06.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022]
Abstract
Incorrect paternity assignment in cattle can significantly influence the accuracy of genetic evaluation. Recent advances in high-throughput technology have facilitated the identification of single nucleotide polymorphism (SNP) markers and their applications for filiation and individual identification. We genotyped 1074 bulls from a reference population of Chinese Simmental cattle for genomic selection using a BovineSNP770K BeadChip. Among them, a total of 136 bulls were randomly selected to design a suitable low-density SNP panel for paternity testing in Simmental cattle. Our results showed that 50 SNPs were determined to be the most informative markers in parental testing, with an accuracy of 99.89% for CPE (cumulative probability of exclusion) in the unknown female parent case. The 50 highly informative SNP markers were distributed across 25 chromosomes, and the mean intermarker distance per chromosome was 26.72 Mb. The average minor allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) values were 0.3748, 0.4998, and 0.4818, respectively. Finally, the 50 identified SNPs were used to estimate paternity for the remaining 938 of 1074 bulls from 23 farms. Our results revealed that 76.75% of the 938 bulls were assigned parentage to the pedigree sires with 95% confidence, and the rate of pedigree record mistakes ranged from 9.52%-39.29% in different herds. Our study is the first attempt to provide valuable insights into the extraction of informative markers through the application of high-density SNP chips for paternity testing in Chinese Simmental cattle.
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Affiliation(s)
- Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Liping Guo
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Mingyan Shi
- College of Life Science, Luoyang Normal University, Jiqing Road, 471934 Luoyang, PR China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Long-Term Impact of Optimum Contribution Selection Strategies on Local Livestock Breeds with Historical Introgression Using the Example of German Angler Cattle. G3-GENES GENOMES GENETICS 2017; 7:4009-4018. [PMID: 29089375 PMCID: PMC5714497 DOI: 10.1534/g3.117.300272] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The long-term performance of different selection strategies was evaluated via simulation using the example of a local cattle breed, German Angler cattle. Different optimum contribution selection (OCS) approaches to maximize genetic gain were compared to a reference scenario without selection and truncation selection. The kinships and migrant contribution (MC) were estimated from genomic data. Truncation selection achieved the highest genetic gain but decreased diversity considerably at native alleles. It also caused the highest increase in MCs. Traditional OCS, which only constrains kinship, achieved almost the same genetic gain but also caused a small increase of MC and remarkably reduced the diversity of native alleles. When MC was required not to increase and the increase of kinship at native alleles was restricted, the MC levels and the diversity at native alleles were well managed, and the genetic gain was only slightly reduced. However, genetic progress was substantially lower in the scenario that aimed to recover the original genetic background. Truncation selection and traditional OCS selection both reduce the genetic originality of breeds with historical introgression. The inclusion of MC and kinship at native alleles as additional constraints in OCS showed great potential for conservation. Recovery of the original genetic background is possible but requires many generations of selection and reduces the genetic progress in performance traits. Hence, constraining MCs at their current values can be recommended to avoid further reduction of genetic originality.
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Weller JI, Ezra E, Ron M. Invited review: A perspective on the future of genomic selection in dairy cattle. J Dairy Sci 2017; 100:8633-8644. [PMID: 28843692 DOI: 10.3168/jds.2017-12879] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022]
Abstract
Genomic evaluation has been successfully implemented in the United States, Canada, Great Britain, Ireland, New Zealand, Australia, France, the Netherlands, Germany, and the Scandinavian countries. Adoption of this technology in the major dairy producing countries has led to significant changes in the worldwide dairy industry. Gradual elimination of the progeny test system has led to a reduction in the number of sires with daughter records and fewer genetic ties between years. As genotyping costs decrease, the number of cows genotyped will continue to increase, and these records will become the basic data used to compute genomic evaluations, most likely via application of "single-step" methodologies. Although genomic selection has been successful in increasing rates of genetic gain, we still know very little about the genetic architecture of quantitative variation. Apparently, a very large number of genes affect nearly all economic traits, in accordance with the infinitesimal model for quantitative traits. Less emphasis in selection goals will be placed on milk production traits, and more on health, reproduction, and efficiency traits and on environmentally friendly production with reduced waste and gas emission. Genetic variance for economic traits is maintained by the increase in frequency of rare alleles, new mutations, and changes in selection goals and management. Thus, it is unlikely that a selection plateau will be reached in the near future.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel.
| | - E Ezra
- Israeli Cattle Breeders Association, Caesarea Industrial Park 3088900, Israel
| | - M Ron
- Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel
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Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow's Capacity To Harvest Energy from Its Feed. mBio 2017; 8:mBio.00703-17. [PMID: 28811339 PMCID: PMC5559629 DOI: 10.1128/mbio.00703-17] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host’s ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants’ genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome. We accomplished this by studying a population of 78 Holstein-Friesian dairy cows, using a combination of rumen microbiota data and other phenotypes from each animal with genotypic data from a subset of 47 animals. We identified 22 operational taxonomic units (OTUs) whose abundances were associated with rumen metabolic traits and host physiological traits and which showed measurable heritability. The abundance patterns of these microbes can explain high proportions of variance in rumen metabolism and many of the host physiological attributes such as its energy-harvesting efficiency. Interestingly, these OTUs shared higher phylogenetic similarity between themselves than expected by chance, suggesting occupation of a specific ecological niche within the rumen ecosystem. The findings presented here suggest that ruminant genetics and physiology are correlated with microbiome structure and that host genetics may shape the microbiome landscape by enriching for phylogenetically related taxa that may occupy a unique niche. Dairy cows are an essential nutritional source for the world’s population; as such, they are extensively farmed throughout our planet and subsequently impact our environment. The microbial communities that reside in the upper digestive tract of these animals in a compartment named the rumen degrade and ferment the plant biomass that the animal ingests. Our recent efforts, as well as those of others, have shown that this microbial community’s composition and functionality are tightly linked to the cow’s capacity to harvest energy from its feed, as well as to other physiological traits. In this study, we identified microbial groups that are heritable and also linked to the cow’s production parameters. This finding could potentially allow us to apply selection programs on specific rumen microbial components that are linked to the animal’s physiology and beneficial to production. Hence, it is a steppingstone toward microbiome manipulation for increasing food availability while lowering environmental impacts such as methane emission.
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Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet 2016; 48:255-271. [PMID: 27910110 DOI: 10.1111/age.12526] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2016] [Indexed: 12/17/2022]
Abstract
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED ). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.
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Affiliation(s)
- E Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - D P Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
| | - M V G B Silva
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | - A L F Lima
- Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - R Irgang
- Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
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Retelling the recent evolution of genetic diversity for Guzerá: Inferences from LD decay, runs of homozygosity and Ne over the generations. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Raoul J, Palhière I, Astruc JM, Elsen JM. Genetic and economic effects of the increase in female paternal filiations by parentage assignment in sheep and goat breeding programs1. J Anim Sci 2016; 94:3663-3683. [DOI: 10.2527/jas.2015-0165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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15
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Zvinorova PI, Halimani TE, Muchadeyi FC, Matika O, Riggio V, Dzama K. Breeding for resistance to gastrointestinal nematodes - the potential in low-input/output small ruminant production systems. Vet Parasitol 2016; 225:19-28. [PMID: 27369571 PMCID: PMC4938797 DOI: 10.1016/j.vetpar.2016.05.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 04/28/2016] [Accepted: 05/12/2016] [Indexed: 02/07/2023]
Abstract
The control of gastrointestinal nematodes (GIN) is mainly based on the use of drugs, grazing management, use of copper oxide wire particles and bioactive forages. Resistance to anthelmintic drugs in small ruminants is documented worldwide. Host genetic resistance to parasites, has been increasingly used as a complementary control strategy, along with the conventional intervention methods mentioned above. Genetic diversity in resistance to GIN has been well studied in experimental and commercial flocks in temperate climates and more developed economies. However, there are very few report outputs from the more extensive low-input/output smallholder systems in developing and emerging countries. Furthermore, results on quantitative trait loci (QTL) associated with nematode resistance from various studies have not always been consistent, mainly due to the different nematodes studied, different host breeds, ages, climates, natural infections versus artificial challenges, infection level at sampling periods, among others. The increasing use of genetic markers (Single Nucleotide Polymorphisms, SNPs) in GWAS or the use of whole genome sequence data and a plethora of analytic methods offer the potential to identify loci or regions associated nematode resistance. Genomic selection as a genome-wide level method overcomes the need to identify candidate genes. Benefits in genomic selection are now being realised in dairy cattle and sheep under commercial settings in the more advanced countries. However, despite the commercial benefits of using these tools, there are practical problems associated with incorporating the use of marker-assisted selection or genomic selection in low-input/output smallholder farming systems breeding schemes. Unlike anthelmintic resistance, there is no empirical evidence suggesting that nematodes will evolve rapidly in response to resistant hosts. The strategy of nematode control has evolved to a more practical manipulation of host-parasite equilibrium in grazing systems by implementation of various strategies, in which improvement of genetic resistance of small ruminant should be included. Therefore, selection for resistant hosts can be considered as one of the sustainable control strategy, although it will be most effective when used to complement other control strategies such as grazing management and improving efficiency of anthelmintics currently.
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Affiliation(s)
- P I Zvinorova
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; Department of Para-clinical Veterinary Studies, University of Zimbabwe, P.O. MP167, Mt. Pleasant, Harare, Zimbabwe.
| | - T E Halimani
- Department of Animal Science, University of Zimbabwe, P.O. MP167, Mt. Pleasant, Harare, Zimbabwe.
| | - F C Muchadeyi
- Biotechnology Platform, Agriculture Research Council Private Bag X5, Onderstepoort, 0110, South Africa.
| | - O Matika
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, MidlothianEH25 9RG, UK.
| | - V Riggio
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, MidlothianEH25 9RG, UK.
| | - K Dzama
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
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Szmatoła T, Gurgul A, Ropka-Molik K, Jasielczuk I, Ząbek T, Bugno-Poniewierska M. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Gurgul A, Szmatoła T, Topolski P, Jasielczuk I, Żukowski K, Bugno-Poniewierska M. The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. J Appl Genet 2016; 57:527-530. [DOI: 10.1007/s13353-016-0337-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/24/2015] [Accepted: 01/08/2016] [Indexed: 01/06/2023]
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18
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Riggio V, Portolano B. Genetic selection for reduced somatic cell counts in sheep milk: A review. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Silva MV, dos Santos DJ, Boison SA, Utsunomiya AT, Carmo AS, Sonstegard TS, Cole JB, Van Tassell CP. The development of genomics applied to dairy breeding. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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da Silva EC, McManus CM, de Paiva Guimarães MPSLM, Gouveia AMG, Facó O, Pimentel DM, Caetano AR, Paiva SR. Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil. Genet Mol Biol 2014; 37:54-60. [PMID: 24688291 PMCID: PMC3958326 DOI: 10.1590/s1415-47572014000100010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/03/2013] [Indexed: 11/22/2022] Open
Abstract
Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.
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Affiliation(s)
- Elizabete Cristina da Silva
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Concepta Margaret McManus
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Aurora M G Gouveia
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Daniel M Pimentel
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília, DF, Brazil
| | - Alexandre Rodrigues Caetano
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Samuel Rezende Paiva
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil . ; Embrapa Sede, Secretaria de Relações Internacionais, Brasília, DF, Brazil
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The application of genome-wide SNP genotyping methods in studies on livestock genomes. J Appl Genet 2014; 55:197-208. [PMID: 24566962 DOI: 10.1007/s13353-014-0202-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/14/2014] [Accepted: 02/04/2014] [Indexed: 01/07/2023]
Abstract
Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.
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Rosa A, Sardina M, Mastrangelo S, Tolone M, Portolano B. Parentage verification of Valle del Belice dairy sheep using multiplex microsatellite panel. Small Rumin Res 2013. [DOI: 10.1016/j.smallrumres.2013.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Ferenčaković M, Hamzić E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Sölkner J. Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J Anim Breed Genet 2012; 130:286-93. [PMID: 23855630 DOI: 10.1111/jbg.12012] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/14/2012] [Indexed: 11/27/2022]
Abstract
Using genome-wide SNP data, we calculated genomic inbreeding coefficients (FROH > 1 Mb , FROH > 2 Mb , FROH > 8 Mb and FROH > 16 Mb ) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (FHOM ). We compared these values of inbreeding coefficients with those calculated from pedigrees (FPED ) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (FPED = 0.014, FROH > 8 Mb = 0.019 and FROH > 16 Mb = 0.008); the highest, for Brown Swiss (FPED = 0.048, FROH > 8 Mb = 0.074 and FROH > 16 Mb = 0.037). In contrast, inbreeding estimates based on the genomic coefficients FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3-1.7-fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.
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Affiliation(s)
- M Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Jakhesara SJ, Rank DN, Kansara JD, Parikh RC, Patel VM, Vataliya PH, Solanki JV. Parentage verification in field progeny testing program of Mehsana buffalo. J Anim Sci 2012; 90:4723-8. [PMID: 22851245 DOI: 10.2527/jas.2011-4353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The present study was undertaken to construct a multiplex microsatellite panel for parentage testing in Mehsana buffalo (Bubalus bubalis). The study was based on a total of 212 Mehsana buffalos (100 dams, 100 daughters, and 12 sires). Genomic DNA was extracted from blood and semen samples. A panel of 10 microsatellite markers (CSSM61, ILSTS29, ILSTS17, ILSTS28, CSSM57, CSSM22, ILSTS61, CSSM8, ETH152, and ILSTS11) was amplified in a single multiplex reaction and analyzed by capillary electrophoresis on an automated DNA sequencer. The expected heterozygosity ranged from 0.642 to 0.833 (mean 0.762). The total exclusion probability using 10 microsatellite loci with 1 known parent was 0.993. Seven out of 10 microsatellite loci revealed relatively high polymorphic information content (>0.7). Eighty-one daughters out of 100 daughters qualified by compatibility according to Mendelism. The results suggest that multiplex microsatellite panel is a fast, robust, reliable, and economic tool to verify the parentage as well as to assign the putative sire to daughters under progeny testing with very high accuracy and hence can be used in routine parentage testing.
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Affiliation(s)
- S J Jakhesara
- Dept. of Animal Biotechnology, Veterinary College, Anand Agricultural University, Anand, Gujarat, India-388001.
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Russo V, Fontanesi L, Dolezal M, Lipkin E, Scotti E, Zambonelli P, Dall'Olio S, Bigi D, Davoli R, Canavesi F, Medugorac I, Föster M, Sölkner J, Schiavini F, Bagnato A, Soller M. A whole genome scan for QTL affecting milk protein percentage in Italian Holstein cattle, applying selective milk DNA pooling and multiple marker mapping in a daughter design. Anim Genet 2012; 43 Suppl 1:72-86. [DOI: 10.1111/j.1365-2052.2012.02353.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- V. Russo
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | - L. Fontanesi
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | | | | | - E. Scotti
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | - P. Zambonelli
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | - S. Dall'Olio
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | - D. Bigi
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | - R. Davoli
- Department of Agro-Food Science and Technology; Sezione di Allevamenti Zootecnici; University of Bologna; Viale Fanin 46; 40127; Bologna; Italy
| | | | - I. Medugorac
- Faculty of Veterinary Medicine; Institute for Animal Breeding; The Ludwig-Maximilians-University Munich; Veterinaerstr. 13; 80539; Munich; Germany
| | - M. Föster
- Faculty of Veterinary Medicine; Institute for Animal Breeding; The Ludwig-Maximilians-University Munich; Veterinaerstr. 13; 80539; Munich; Germany
| | - J. Sölkner
- Division of Livestock Sciences; Department of Sustainable Agricultural Systems; University of Natural Resources and Applied Sciences (BOKU); Vienna; Austria
| | - F. Schiavini
- Department of VSA; Faculty of Veterinary Medicine; University of Milano; Milano; Italy
| | - A. Bagnato
- Department of VSA; Faculty of Veterinary Medicine; University of Milano; Milano; Italy
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Calus MPL, Mulder HA, Bastiaansen JWM. Identification of Mendelian inconsistencies between SNP and pedigree information of sibs. Genet Sel Evol 2011; 43:34. [PMID: 21988752 PMCID: PMC3377921 DOI: 10.1186/1297-9686-43-34] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 10/11/2011] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement. METHODS Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals. RESULTS Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals.Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT. CONCLUSIONS Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs.
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Affiliation(s)
- Mario PL Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 8200 AB Lelystad, The Netherlands
| | - Han A Mulder
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 8200 AB Lelystad, The Netherlands
| | - John WM Bastiaansen
- Animal Breeding and Genomics Centre, Wageningen University, 6709 PG Wageningen, The Netherlands
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Kugonza D, Kiwuwa G, Mpairwe D, Jianlin H, Nabasirye M, Okeyo A, Hanotte O. Accuracy of pastoralists’ memory-based kinship assignment of Ankole cattle: a microsatellite DNA analysis. J Anim Breed Genet 2011; 129:30-40. [DOI: 10.1111/j.1439-0388.2011.00937.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Kios D, van Marle-Köster E, Visser C. Application of DNA markers in parentage verification of Boran cattle in Kenya. Trop Anim Health Prod 2011; 44:471-6. [DOI: 10.1007/s11250-011-9921-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2011] [Indexed: 11/29/2022]
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29
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Silva A, Azevedo A, Verneque R, Gasparini K, Peixoto M, da Silva M, Lopes P, Guimarães S, Machado M. Quantitative trait loci affecting milk production traits on bovine chromosome 6 in zebuine Gyr breed. J Dairy Sci 2011; 94:971-80. [DOI: 10.3168/jds.2009-2970] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 10/21/2010] [Indexed: 11/19/2022]
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30
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Ozkan E, Soysal MI, Ozder M, Koban E, Sahin O, Togan İ. Evaluation of parentage testing in the Turkish Holstein population based on 12 microsatellite loci. Livest Sci 2009. [DOI: 10.1016/j.livsci.2009.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Tian F, Sun D, Zhang Y. Establishment of paternity testing system using microsatellite markers in Chinese Holstein. J Genet Genomics 2009; 35:279-84. [PMID: 18499071 DOI: 10.1016/s1673-8527(08)60040-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 12/01/2007] [Accepted: 12/02/2007] [Indexed: 11/18/2022]
Abstract
To estimate the efficiency of microsatellite markers in paternity testing among Chinese Holstein, 30 microsatellite loci were used to differentiate 330 Chinese Holstein genotypes, according to the calculation of the allele frequency, number of alleles, effective number of alleles, genetic heterozygosity, polymorphic information content (PIC), and the exclusion probability in this cattle population. The results demonstrated that the exclusion probability ranged from 0.620 in locus BM1818 to 0.265 in locus INRA005 with the average of 0.472 and 11 microsatellite markers exceeding 0.5. The combined exclusion probability of nine microsatellite markers was over 0.99. The result showed that paternity testing of Chinese Holstein was basically resolved using the nine microsatellite markers selected.
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Affiliation(s)
- Fei Tian
- College of Animal Science and Technology and Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
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Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TPL, Sonstegard TS, Van Tassell CP. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 2009; 4:e5350. [PMID: 19390634 PMCID: PMC2669730 DOI: 10.1371/journal.pone.0005350] [Citation(s) in RCA: 654] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 03/23/2009] [Indexed: 11/18/2022] Open
Abstract
The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.
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Affiliation(s)
- Lakshmi K Matukumalli
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, United States of America
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33
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Sun W, Chen H, Lei C, Lei X, Zhang Y. Study on population genetic characteristics of Qinchuan cows using microsatellite markers. J Genet Genomics 2009; 34:17-25. [PMID: 17469774 DOI: 10.1016/s1673-8527(07)60003-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 06/25/2006] [Indexed: 11/20/2022]
Abstract
To evaluate the genetic polymorphisms and to search for available molecular markers for Qinchuan cattle, 90 Qinchuan cows were genotyped with 12 microsatellite markers. A total of 247 alleles were detected, with the number of alleles ranging from 13 (INRA005) to 33 (HEL13), giving a mean number of 21 alleles per locus. The total and mean effective allele number were 142.6229 and 11.8852, respectively. Mean sampling variance of the allele frequency was 2.6036 x 10(-4). Allele size ranges of the 12 microsatellite loci were different. The observed heterozygosity and expected heterozygosity were from 0.7842 (INRA005) to 0.9775 (BM315) and 0.7952 (BM315) to 0.9446 (HEL13), respectively. Mean observed heterozygosity and mean expected heterozygosity were 0.9117 and 0.9047, respectively. Polymorphism information content values were from 0.7653 (INRA005) to 0.9420 (HEL13), and mean polymorphism information content of the 12 microsatellite loci was 0.8965. All the 12 microsatellite loci were highly polymorphic, which showed that there were rich genetic polymorphisms at these detected microsatellite loci in Qinchuan cows. At the 12 microsatellite loci, the mean fixation index was -0.0076, reflecting that the degree of heterozygote defect at these loci was not high and deviations from Hardy-Weinberg equilibrium were not significant.
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Affiliation(s)
- Weibin Sun
- College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
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34
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Gomez-Raya L. Inferring unknown genotypes of sires at codominant deoxyribonucleic acid markers in half-sib families. J Anim Sci 2009; 87:1872-82. [PMID: 19251934 DOI: 10.2527/jas.2008-1425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deoxyribonucleic acid from sires is usually not available from experiments aimed at QTL mapping for traits of the dam in cow-calf operations and free range sheep populations. In this study, methods to reconstruct sire genotypes using genotype information from large half-sib progeny were developed. The methods are based on 1) all offspring genotypes are compatible with more than 1 genotype for the sire, but 1 of the genotypes is more likely than the others when comparing the proportion of the different genotypes among offspring with its expected values assuming Mendelian inheritance, or 2) all offspring genotypes are compatible with just 1 possible genotype for the sire in the pedigree. A Monte Carlo simulation experiment was carried out to test the methods with 1 million replicates. A 99.7% correct sire genotype reconstruction was obtained with 30 offspring and a DNA marker with 3 or more alleles segregating at similar frequencies. Methods to test for incorrect paternity in half-sib offspring without DNA from the sire were also developed. A maximum likelihood method was developed to test for departure of Mendelian segregation due to a contaminating sire whose offspring are fully compatible with the genotype of the pedigree sire. A large number of offspring was needed to detect offspring from a contaminating sire (1,000 progeny for a power of 0.99 and proportion of true paternity of the pedigree of 0.80). Multi-marker methods were also developed for detection of paternity misidentification. Probabilities of detection of wrong paternity for a contaminating sire not sharing any alleles with the sire in the pedigree were 0.95 and 0.99 when using 5 and 10 markers in 30 half-sib offspring, respectively. The methods to infer the sire genotypes were tested with 49 progeny of a Merino ram whose genotype was inferred for 7 microsatellites. Methods to infer genotype of the sire are feasible, but QTL mapping experiments without DNA from the sires are more costly due to the need of genotyping markers in progeny for which the sire in the pedigree is homozygous.
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Affiliation(s)
- L Gomez-Raya
- Department of Animal Biotechnology, University of Nevada, Reno 89557, USA.
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35
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Dechow C, Norman H, Zwald N, Cowan C, Meland O. Relationship Between Individual Herd-Heritability Estimates and Sire Misidentification Rate. J Dairy Sci 2008; 91:1640-7. [DOI: 10.3168/jds.2007-0534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Carneiro T, Gonçalves E, Schneider M, Silva A. Diversidade genética e eficiência de DNA microssatélites para o controle genealógico da raça Nelore. ARQ BRAS MED VET ZOO 2007. [DOI: 10.1590/s0102-09352007000500024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Foram estimados na raça Nelore a variabilidade genética e os valores de determinação de paternidade usando-se 11 marcadores microssatélites do painel ISAG/FAO. Estes foram organizados em quatro conjuntos de amplificação para genotipagem semi-automática por fluorescência. Todos os marcadores apresentaram-se altamente polimórficos, com média de 8,2 alelos por loco. A heterozigosidade observada, com média de 0,48, foi menor que a esperada em 10 locos. Foram observadas deficiências de heterozigotos em nove locos, o que resultou no desequilíbrio de Hardy-Weinberg para a população estudada. O conteúdo polimórfico informativo foi superior a 0,5 em 10 locos. O poder de discriminação foi >0,999 e as probabilidades de exclusão de paternidade quando são conhecidos os genótipos de um bezerro, sua mãe e um pai alegado, ou quando um ou outro genótipo parental não está disponível, para o conjunto de marcadores foram >0,999 e >0,989, respectivamente. O conjunto de 11 marcadores constitui método eficiente para a determinação de paternidade na raça Nelore.
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37
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Lirón JP, Ripoli MV, Peral-García P, Giovambattista G. Implication of Population Structure in the Resolution of Cattle Stealing Cases. J Forensic Sci 2007; 52:1077-81. [PMID: 17680792 DOI: 10.1111/j.1556-4029.2007.00521.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Estimation of population subdivision using genetic markers shows that genetic differentiation in livestock and pet breeds is significantly higher than in human populations. Nevertheless, the influence of population substructure and sample size on match probability has not been extensively analyzed in domestic species. To evaluate the magnitude of the subpopulation effect on estimation of match probabilities in bovine robbery cases, we calculated and compared the match probabilities obtained from cattle breed databases using both real, adjudicated cases from the Buenos Aires Province (Argentina), as well as simulated data. While the Balding and Nichols' correction, when applied to the population database used in the case, produce a more conservative value favorable to the defendant, the match probabilities calculated using the simple product estimator produce a value favorable to the prosecution. We suggest an alternative procedure that can be used. The method consists of choosing the highest value from all match probabilities calculated from the database of each breed. This approach represents an intermediate and more accurate estimation of match probability, although it still produces a slight conservative value favorable to the defense.
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Affiliation(s)
- Juan P Lirón
- Centro de Investigaciones en Genética Básica y Aplicada, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
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38
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DNA microsatellites to ascertain pedigree-recorded information in a selecting nucleus of Murciano-Granadina dairy goats. Small Rumin Res 2006. [DOI: 10.1016/j.smallrumres.2005.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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39
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Sanders K, Bennewitz J, Kalm E. Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population. J Dairy Sci 2006; 89:315-21. [PMID: 16357295 DOI: 10.3168/jds.s0022-0302(06)72096-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the present study, molecular genetic markers were used to help estimate the degree of wrong sire information in the German Angeln dairy cattle population. Sixteen polymorphic microsatellite markers were genotyped on 5 different paternal half-sib families with a total of 805 daughters. For the genotyping process, blood samples of the daughters and semen samples of the sires were used. Allelic frequencies and exclusion probabilities were estimated. The simultaneous effect of wrong (WSI) and missing sire information (MSI) on the reliability of estimated breeding values and on the genetic gain was investigated using deterministic simulations. For these simulations, different values for the number of daughters per sire, heritability, WSI, and MSI were chosen. The estimated proportion of the WSI was 7% in the German Angeln dairy cattle population. The combined impact of WSI and MSI on the genetic gain was relatively large, especially in the case of small progeny size per sire and low heritability. The impact of WSI was more harmful than MSI on response to selection.
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Affiliation(s)
- K Sanders
- Institut für Tierzucht und Tierhaltung der Christian-Albrechts-Universität zu Kiel, D-24098 Kiel, Germany.
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40
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Cervini M, Henrique-Silva F, Mortari N, Matheucci Jr E. Genetic variability of 10 microsatellite markers in the characterization of Brazilian Nellore cattle (Bos indicus). Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000300015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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41
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Mezzadra CA, Melucci LM, Corva PM, López Valiente S, Rípoli MV, Lirón P, Giovambattista G. Effects of cytoplasmic inheritance on preweaning traits of Hereford cattle. Genet Mol Biol 2005. [DOI: 10.1590/s1415-47572005000300003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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42
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Weller JI, Feldmesser E, Golik M, Tager-Cohen I, Domochovsky R, Alus O, Ezra E, Ron M. Factors affecting incorrect paternity assignment in the Israeli Holstein population. J Dairy Sci 2004; 87:2627-40. [PMID: 15328288 DOI: 10.3168/jds.s0022-0302(04)73389-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A total of 6040 Israeli Holstein cows from 181 Kibbutz herds listed as progeny of 11 sires were genotyped for 104 microsatellites. Seventeen markers were deleted due to a frequency of erroneous genotypes >1%, leaving 160,470 valid genotypes. Conflicts between the putative sire and daughter in at least 2 markers and for at least 10% of the markers genotyped per cow were required to reject paternity. Cows that did not meet the requirements for paternity confirmation or rejection were deleted from further analysis. The frequency of rejected paternity was 11.7%. The effects of recorded sire, birth year, geographical region, herd, and inseminator on the frequency of paternity rejection were analyzed with linear and nonlinear models. Only the effects of inseminator and recorded sire were significant in all models tested that included these effects. The main causes of incorrect paternity recording appear to be inseminator recording mistakes, and possibly mistakes with respect to semen labeling at the AI institutes. Incorrect paternity recording due to multiple inseminations by different sires could explain, at most, 20% of the paternity mistakes. Instituting a system of quality control, especially at the level of the inseminator, should reduce paternity errors to no more than 8%, and increase genetic progress by at least 1%.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences ARO, The Volcani Center, Bet Dagan 50250, Israel.
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43
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Ron M, Feldmesser E, Golik M, Tager-Cohen I, Kliger D, Reiss V, Domochovsky R, Alus O, Seroussi E, Ezra E, Weller JI. A Complete Genome Scan of the Israeli Holstein Population for Quantitative Trait Loci by a Daughter Design. J Dairy Sci 2004; 87:476-90. [PMID: 14762091 DOI: 10.3168/jds.s0022-0302(04)73187-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Eleven Israeli Holstein families including 5221 cows were analyzed by a daughter design for eight economic traits: milk, fat and protein production, fat and protein percentage, somatic cell score (SCS), herd-life, and female fertility. The cows were genotyped for 73 microsatellites with maximum spacing between markers of 53 cM. There were 86,304 informative genotypes. Preliminary analysis was by ANOVA of each trait, with the marker effect nested within sire. Significance was determined by controlling the false discovery rate at 0.4, after excluding markers with genome-wide significance for at least a single trait, and traits without any significant effects at this level. Thus, four markers on chromosomes 6 and 14 and female fertility were excluded. There remained 40 significant marker-trait combinations, and it is expected that 24 of these are true effects. To perform interval mapping for the families with significant contrasts, 21 additional markers were genotyped on chromosomes 2, 7, and 27. The bootstrap confidence intervals for gene effect did not include zero for protein percent on chromosome 2 and fat yield, protein yield, and SCS on chromosome 7. Quantitative trait locus heterozygosity was 33%, which is consistent with the hypothesis that only two alleles are segregating with unequal allele frequency.
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Affiliation(s)
- M Ron
- Institute of Animal Sciences, ARO, The Volcani Center, Bet Dagan 50250, Israel
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44
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Ron M, Domochovsky R, Golik M, Seroussi E, Ezra E, Shturman C, Weller JI. Analysis of vaginal swabs for paternity testing and marker-assisted selection in cattle. J Dairy Sci 2003; 86:1818-20. [PMID: 12778592 DOI: 10.3168/jds.s0022-0302(03)73767-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Blood is the standard source for DNA analysis, but requires venipuncture of cows by veterinarian and tedious and costly DNA extraction. A procedure was developed for sampling of vaginal cells from cows, establishing a cell lysis protocol using robotics, and applying fluorescent analysis of genetic markers. Two insemination technicians collected vaginal cells from 254 elite Israeli Holstein cows located in 152 herds using commercial Catch-All sample collection brushes. Cells were lysed in a 400-microliters solution, and 5 microliters was used as template for polymerase chain reaction (PCR). Sensitivity of the PCR was enhanced using only 1 microliter of lysed cells. Eight markers of the International Society of Animal Genetics paternity panel were amplified in four separate PCR. ILSTS039, a marker for a quantitative trait loci on BTA14, was amplified in a separate reaction. Genotypes from one to nine genetic markers were obtained for 253 out of 254 samples, and 244 cows had genotypes for at least three markers (96%). Cows that did not inherit either paternal allele for at least two loci were considered not to be daughters of the sire listed. Fifteen cows met this criterion, for a paternity misidentification rate of 6.25%. The frequency of allele 225 of ILSTS039, which was associated with increased milk fat content, was 11.1% in the bull-dam population, similar to the 12% found in the cow population in Israel. The use of vaginal cells for genetic analysis is accurate, as demonstrated by replicated analysis and by comparison to individual and population analysis based on DNA derived from blood.
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Affiliation(s)
- M Ron
- Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
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45
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García D, Carleos C, Parra D, Cañón J. Sib-parentage testing using molecular markers when parents are unknown. Anim Genet 2002; 33:364-71. [PMID: 12354145 DOI: 10.1046/j.1365-2052.2002.00882.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The formulae for computing the so-called Sib Index using codominant alleles for (1) full-sib and (2) half-sib parentage are given. Hypothesis testing is based on the distribution of conditional likelihood ratio or Bayes' factor. Thresholds for rejecting the null hypothesis and P-values were obtained in function of the number of alleles and their frequency distributions. Simulations showed that a relatively low number of marker systems (e.g. 20) are enough to accept the hypothesis of sib parentage with a reasonable power for usual significance levels, but that a higher number would be necessary if full-sib against half-sib parentage is the contrast to be carried out. The effect of sampling variation on the allele frequencies on power calculations is also analysed.
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Affiliation(s)
- D García
- Laboratorio de Genética, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
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46
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Visscher PM, Woolliams JA, Smith D, Williams JL. Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection. J Dairy Sci 2002; 85:2368-75. [PMID: 12362470 DOI: 10.3168/jds.s0022-0302(02)74317-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The proportion of cows in the UK dairy herd whose sires were misidentified was estimated using DNA markers. Genetic marker genotypes were determined on 568 cows (from 168 milk samples and 400 hair samples) and 96 putative sires (from semen samples). The estimated pedigree error rate from the hair samples was 8.8%, and from the milk samples, 13.1%, giving an overall estimate of the error rate of 10%. This level of pedigree errors will have a relatively large impact on the efficiency of progeny testing and the accuracy of cow predicted breeding values. We predict a loss of response to selection of approximately 2 to 3% given this error rate.
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Affiliation(s)
- P M Visscher
- University of Edinburgh, Institute of Cell, Animal and Population Biology, West Mains Road, Edinburgh EH9 3JT, UK.
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47
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Baron EE, Martinez ML, Verneque RS, Coutinho LL. Parentage testing and effect of misidentification on the estimation of breeding value in Gir cattle. Genet Mol Biol 2002. [DOI: 10.1590/s1415-47572002000400006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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48
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Banos G, Wiggans GR, Powell RL. Impact of paternity errors in cow identification on genetic evaluations and international comparisons. J Dairy Sci 2001; 84:2523-9. [PMID: 11768094 DOI: 10.3168/jds.s0022-0302(01)74703-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The impact of paternity identification errors on US genetic evaluations and international comparisons of Holstein dairy bulls for milk, fat, and protein yields was investigated. Sire identification was replaced for 11% of Holstein cows that were sired by AI bulls and had records in the US database for national genetic evaluations; US evaluations were computed based on those modified pedigrees and compared with official national evaluations. Estimated breeding values from the data with introduced paternity errors were biased, especially for later generations. Estimated genetic trends decreased by 11 to 15%. Estimates of standard deviations of sire transmitting ability also decreased by 8 to 9%. International multitrait across-country comparisons of bulls were computed based on national evaluations from the United States, Canada, New Zealand, and The Netherlands. Estimates of genetic correlations between the United States and other countries decreased by 0.04 to 0.06 when US evaluations were based on modified pedigree. The resulting bias toward selection of domestic bulls and the inability to identify truly superior animals that are available internationally could decrease potential selection differentials by 0.07 to 0.09 standard deviation units on the US scale, which corresponds to sire breeding values of approximately 50 kg for milk, 3 kg for fat, and 1.7 kg for protein. Losses for the other countries were lower and ranged from 0.02 to 0.05 standard deviation units, because a correlation of less than unity with the United States decreased the impact of US cow paternity errors on the scales of other countries. Although paternity verification is desirable and technically feasible, commercial implementation would require low testing costs.
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Affiliation(s)
- G Banos
- Interbull Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala.
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49
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Ron M, Kliger D, Feldmesser E, Seroussi E, Ezra E, Weller JI. Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design. Genetics 2001; 159:727-35. [PMID: 11606547 PMCID: PMC1461848 DOI: 10.1093/genetics/159.2.727] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nine Israeli Holstein sire families with 2978 daughters were analyzed for quantitative trait loci effects on chromosome 6 for five milk production traits by a daughter design. All animals were genotyped for 2 markers. The three families with significant effects were genotyped for up to 10 additional markers spanning positions 0-122 cM of BTA6. Two sires were segregating for a locus affecting protein and fat percentage near position 55 cM with an estimated substitution effect of 0.18% protein, which is equivalent to one phenotypic standard deviation. This locus was localized to a confidence interval of 4 cM. One of these sires was also heterozygous for a locus affecting milk, fat, and protein production near the centromere. The hypothesis of two segregating loci was verified by multiple regression analysis. A third sire was heterozygous for a locus affecting milk and protein percentage near the telomeric end of the chromosome. Possible candidates for the major quantitative gene near position 55 cM were determined by comparative mapping. IBSP and SSP1 were used as anchors for the orthologous region on human chromosome 4. Twelve genes were detected within a 2-Mbp sequence. None of these genes have been previously associated with lactogenesis.
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Affiliation(s)
- M Ron
- Institute of Animal Sciences, ARO, The Volcani Center, Bet Dagan 50250, Israel
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50
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Roughsedge T, Brotherstone S, Visscher PM. Bias and Power in the Estimation of a Maternal Family Variance Component in the Presence of Incomplete and Incorrect Pedigree Information. J Dairy Sci 2001; 84:944-50. [PMID: 11352171 DOI: 10.3168/jds.s0022-0302(01)74552-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several studies over the last 15 yr have estimated the magnitude of cytoplasmic inheritance of production and type traits in dairy cattle. Pedigree information can be used to assign maternal lineages, and the between-maternal lineage variance is then assumed to be an estimate of cytoplasmic inheritance. Two potential sources of bias and reduction of the power of estimation of cytoplasmic inheritance using such a method are 1) incomplete and 2) incorrect pedigree information being used in the assignment of maternal lineages. The theoretical bias introduced by these two sources of error is investigated and the results of a simulation study varying the number of families, the percentage of pedigree errors, and the level of incomplete lineage assignment are presented. Pedigree errors were found to have the biggest impact. A pedigree error rate of 8% per generation would result in a 75% reduction in the estimable magnitude of a 5% true component of variance after nine generations. The effect that these mechanisms have on the power of estimation are discussed and investigated by simulation. It was concluded that using historical pedigree, with incomplete and incorrect maternal family information, to assign maternal lineage would cause a downward bias in the magnitude of the cytoplasmic effect estimated. In the future, it will be possible to overcome pedigree problems by using molecular information to directly assign cytoplasmic lineage groups.
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Affiliation(s)
- T Roughsedge
- Institute of Ecology and Resource Management, University of Edinburgh.
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