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Suchocki T, Czech B, Dunislawska A, Slawinska A, Derebecka N, Wesoly J, Siwek M, Szyda J. SNP prioritization in targeted sequencing data associated with humoral immune responses in chicken. Poult Sci 2021; 100:101433. [PMID: 34551372 PMCID: PMC8458985 DOI: 10.1016/j.psj.2021.101433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/13/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022] Open
Abstract
Our study aimed to identify single nucleotide polymorphisms (SNPs) with a significant impact on the innate immunity represented by antibody response against lipopolysaccharide (LPS) and lipoteichoid acid (LTA) and the adaptive immune response represented toward keyhole limpet hemocyanin (KLH) using the SNP prioritization method. Data set consisted of 288 F2 experimental individuals, created by crossing Green-legged Partridgelike and White Leghorn. The analyzed SNPs were located within 24 short genomic regions of GGA1, GGA2, GGA3, GGA4, GGA9, GGA10, GGA14, GGA18, and GGZ, pre-targeted based on literature references and database information. For the specific antibody response toward KLH at d 0 the most highly prioritized SNP for additive and dominance effects were located on GGA2 in the 3’UTR of MYD88. For the response at d 7, the most highly prioritized SNP pointed at the 3’UTR of MYD88, but potential causal additive variants were located within ADIPOQ and one in PROCR. The highest priority for additive and dominance effects in the antibody response toward lipoteichoic acid at d 0 was attributed to the same SNP, located on GGA2 in the 3’UTR region of MYD88. Two SNPs among the top-10 for additive effect were located in the exon of NOCT. SNPs selected for their additive effect on antibody response toward lipopolysaccharide at d 0 marked 3 genes – NOCT, MYD88, and SNX8, while SNPs selected for their dominance effect marked – NOCT, ADIPOQ, and MYD88. The top-10 variants identified in our study were located in different functional parts of the genome. In the context of causality three groups can be distinguished: variants located in exons of protein coding genes (ADIPOQ, NOCT, PROCR, SNX8), variants within exons of non-coding transcripts, and variants located in genes’ UTR regions. Variants from the first group influence protein structure and variants from both latter groups’ exhibit regulatory roles on DNA (UTR) or RNA (lncRNA).
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Affiliation(s)
- Tomasz Suchocki
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland; National Research Institute of Animal Production, Balice, Poland
| | - Bartosz Czech
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Dunislawska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz 85-084, Poland
| | - Anna Slawinska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz 85-084, Poland
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Maria Siwek
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Bydgoszcz 85-084, Poland.
| | - Joanna Szyda
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland; National Research Institute of Animal Production, Balice, Poland
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Polewko-Klim A, Lesiński W, Golińska AK, Mnich K, Siwek M, Rudnicki WR. Sensitivity analysis based on the random forest machine learning algorithm identifies candidate genes for regulation of innate and adaptive immune response of chicken. Poult Sci 2020; 99:6341-6354. [PMID: 33248550 PMCID: PMC7704721 DOI: 10.1016/j.psj.2020.08.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 11/25/2022] Open
Abstract
Two categories of immune responses—innate and adaptive immunity—have both polygenic backgrounds and a significant environmental component. The goal of the reported study was to define candidate genes and mutations for the immune traits of interest in chickens using machine learning–based sensitivity analysis for single-nucleotide polymorphisms (SNPs) located in candidate genes defined in quantitative trait loci regions. Here the adaptive immunity is represented by the specific antibody response toward keyhole limpet hemocyanin (KLH), whereas the innate immunity was represented by natural antibodies toward lipopolysaccharide (LPS) and lipoteichoic acid (LTA). The analysis consisted of 3 basic steps: an identification of candidate SNPs via feature selection, an optimisation of the feature set using recursive feature elimination, and finally a gene-level sensitivity analysis for final selection of models. The predictive model based on 5 genes (MAPK8IP3 CRLF3, UNC13D, ILR9, and PRCKB) explains 14.9% of variance for KLH adaptive response. The models obtained for LTA and LPS use more genes and have lower predictive power, explaining respectively 7.8 and 4.5% of total variance. In comparison, the linear models built on genes identified by a standard statistical analysis explain 1.5, 0.5, and 0.3% of variance for KLH, LTA, and LPS response, respectively. The present study shows that machine learning methods applied to systems with a complex interaction network can discover phenotype-genotype associations with much higher sensitivity than traditional statistical models. It adds contribution to evidence suggesting a role of MAPK8IP3 in the adaptive immune response. It also indicates that CRLF3 is involved in this process as well. Both findings need additional verification.
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Affiliation(s)
- Aneta Polewko-Klim
- Institute of Computer Science, University of Bialystok, Białystok, Poland.
| | - Wojciech Lesiński
- Institute of Computer Science, University of Bialystok, Białystok, Poland
| | | | - Krzysztof Mnich
- Computational Centre, University of Bialystok, Białystok, Poland
| | - Maria Siwek
- Animal Biotechnology and Genetics Department, University of Technology and Life Sciences, Bydgoszcz, Poland
| | - Witold R Rudnicki
- Institute of Computer Science, University of Bialystok, Białystok, Poland; Computational Centre, University of Bialystok, Białystok, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
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Paukszto L, Mikolajczyk A, Szeszko K, Smolinska N, Jastrzebski JP, Kaminski T. Transcription analysis of the response of the porcine adrenal cortex to a single subclinical dose of lipopolysaccharide from Salmonella Enteritidis. Int J Biol Macromol 2019; 141:1228-1245. [PMID: 31520703 DOI: 10.1016/j.ijbiomac.2019.09.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 12/20/2022]
Abstract
Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of inflammatory responses. LPS may also play a significant role in some neurodegenerative, oncological and metabolic disorders. The aim of the current study was to determine the effect of a subclinical low single dose of LPS from Salmonella Enteritidis administrated in vivo on the transcriptome of porcine adrenal cortex cells, especially gene expression levels, long non-coding RNA (lncRNA) profiles, alternative splicing events and RNA editing sites using RNA-seq technology. The subclinical dose of LPS changed the expression of 354 genes, 27 lncRNA loci and other unclassified RNAs. An analysis of alternative splicing events revealed 104 genes with differentially expressed splice junction sites, and the single nucleotide variant calling approach supported the identification of 376 canonical RNA editing candidates and 7249 allele-specific expression variants. The obtained results suggest that the RIG-I-like receptor signaling pathway, may play a more important role than the Toll-like signaling pathway after the administration of a subclinical dose of LPS. Single subclinical dose of LPS can affect the expression profiles of genes coding peptide hormones, steroidogenic enzymes and transcriptional factors, and modulate the endocrine functions of the gland.
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Affiliation(s)
- Lukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland.
| | - Anita Mikolajczyk
- Department of Public Health, Faculty of Health Sciences, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Warszawska 30, 10-082 Olsztyn, Poland.
| | - Karol Szeszko
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Nina Smolinska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland.
| | - Jan P Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Tadeusz Kaminski
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland.
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Zhu B, Li Q, Liu R, Zheng M, Wen J, Zhao G. Genome-Wide Association Study of H/L Traits in Chicken. Animals (Basel) 2019; 9:ani9050260. [PMID: 31117270 PMCID: PMC6562784 DOI: 10.3390/ani9050260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 11/16/2022] Open
Abstract
Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10-6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10-5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.
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Affiliation(s)
- Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
- School of Life Science and Engineering, Foshan University, Foshan 528000, China.
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Knaga S, Siwek M, Tavaniello S, Maiorano G, Witkowski A, Jezewska-Witkowska G, Bednarczyk M, Zieba G. Identification of quantitative trait loci affecting production and biochemical traits in a unique Japanese quail resource population. Poult Sci 2018; 97:2267-2277. [PMID: 29672744 DOI: 10.3382/ps/pey110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/10/2018] [Indexed: 11/20/2022] Open
Abstract
The objective of the current study was to identify QTL associated with body weight, growth rate, egg quality traits, concentration of selected blood plasma, and yolk lipids as well as concentration of selected macro- and microelements, color, pH, basic chemical composition, and drip loss of breast muscle of Japanese quail (Coturnix japonica). Twenty-two meat-type males (line F33) were crossed with twenty-two laying-type females (line S22) to produce a generation of F1 hybrids. The F2 generation was created by mating 44 randomly chosen F1 hybrids, which were full siblings. The birds were individually weighed from the first to eighth week of age. At the age of 19 wk, 2 to 4 eggs were individually collected from each female and an analysis of the egg quality traits was performed. At slaughter, blood and breast muscles were collected from 324 individuals of the resource population. The basic chemical composition, concentration of chosen macro- and microelements, color, pH, and drip loss were determined in the muscle samples. The concentration of chosen lipids was determined in egg yolk and blood plasma. In total, 30 microsatellite markers located on chromosome 1 and 2 were genotyped. QTL mapping including additive and dominance genetic effects revealed 6 loci on chromosome 1 of the Japanese quail affecting the egg number, egg production rate, egg weight, specific gravity, egg shell weight, concentration of Na in breast muscle. In turn, there were 9 loci on chromosome 2 affecting the body weight in the first, fourth, and sixth week of age, growth rate in the second and seventh week of age, specific gravity, concentration of K and Cu in breast muscle, and the levels of triacylglycerols in blood plasma. In this study, QTL with a potential effect on the Na, K, and Cu content in breast muscles in poultry and on specific gravity in the Japanese quail were mapped for the first time.
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Affiliation(s)
- S Knaga
- Institute of Biological Bases of Animal Production, University of Life Sciences, Akademicka 13,20-950 Lublin, Poland
| | - M Siwek
- Department of Animal Biochemistry and Biotechnology, UTP University of Sciences and Technology, Bydgoszcz 85-064, Poland
| | - S Tavaniello
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso 86100, Italy
| | - G Maiorano
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso 86100, Italy
| | - A Witkowski
- Institute of Biological Bases of Animal Production, University of Life Sciences, Akademicka 13,20-950 Lublin, Poland
| | - G Jezewska-Witkowska
- Institute of Biological Bases of Animal Production, University of Life Sciences, Akademicka 13,20-950 Lublin, Poland
| | - M Bednarczyk
- Department of Animal Biochemistry and Biotechnology, UTP University of Sciences and Technology, Bydgoszcz 85-064, Poland
| | - G Zieba
- Institute of Biological Bases of Animal Production, University of Life Sciences, Akademicka 13,20-950 Lublin, Poland
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Zheng F, Yu X, Huang J, Dai Y. Circular RNA expression profiles of peripheral blood mononuclear cells in rheumatoid arthritis patients, based on microarray chip technology. Mol Med Rep 2017; 16:8029-8036. [PMID: 28983619 PMCID: PMC5779885 DOI: 10.3892/mmr.2017.7638] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/07/2017] [Indexed: 12/15/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic synovial inflammation and finally leads to variable degrees of bone and cartilage erosion. The diagnosis of RA is not an accurate indicator, but a series of scores and the mechanisms underlying it remain only partially understood. The present study explored whether circular RNAs (circRNAs) contribute to the RA pathophysiological mechanism. Total RNA from peripheral blood mononuclear cells of 10 RA patients and 10 healthy controls were extracted and circRNA expression profiling was followed by microarray analysis. In addition, circRNA interactions with microRNAs were performed and microRNA response elements were listed to identify differentially expressed binding site targets in RA. Reverse transcription-quantitative polymerase chain reaction amplification (RT-qPCR) was used to verify the differential expression of circRNAs. A total of 584 circRNAs were differentially expressed in RA patients vs. healthy controls, by circRNA microarray, including 255 circRNAs which were significantly upregulated and 329 downregulated among the RA samples. RT-qPCR validation demonstrated that the expression levels of hsa_circRNA_104194, hsa_circRNA_104593, hsa_circRNA_103334, hsa_circRNA_101407 and hsa_circRNA_102594 were consistent with the results from the microarray analysis. The current study presented differentially expressed circRNAs and their corresponding microRNA binding sites in RA. circRNAs may exhibit a role in the regulation of expression of symbol genes that influence the occurrence and development of RA.
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Affiliation(s)
- Fengping Zheng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Xiangqi Yu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Jiahuang Huang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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Psifidi A, Banos G, Matika O, Desta TT, Bettridge J, Hume DA, Dessie T, Christley R, Wigley P, Hanotte O, Kaiser P. Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes. Genet Sel Evol 2016; 48:74. [PMID: 27687164 PMCID: PMC5041578 DOI: 10.1186/s12711-016-0252-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/15/2016] [Indexed: 12/24/2022] Open
Abstract
Background The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are hampered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability. In this study, we investigated the genetic architecture of antibody response to four major infectious diseases [infectious bursal disease (IBDV), Marek’s disease (MDV), fowl typhoid (SG), fowl cholera (PM)] and resistance to Eimeria and cestode parasitism, along with two production traits [body weight and body condition score (BCS)] in two distinct indigenous Ethiopian chicken ecotypes. We conducted variance component analyses, genome-wide association studies, and pathway and selective sweep analyses. Results The large majority of birds was found to have antibody titres for all pathogens and were infected with both parasites, suggesting almost universal exposure. We derived significant moderate to high heritabilities for IBDV, MDV and PM antibody titres, cestodes infestation, body weight and BCS. We identified single nucleotide polymorphisms (SNPs) with genome-wide significance for each trait. Based on these associations, we identified for each trait, pathways, networks and functional gene clusters that include plausible candidate genes. Selective sweep analyses revealed a locus on chromosome 18 associated with viral antibody titres and resistance to Eimeria parasitism that is within a positive selection signal. We found no significant genetic correlations between production, immune and disease traits, implying that selection for altered antibody response and/or disease resistance will not affect production. Conclusions We confirmed the presence of genetic variability and identified SNPs significantly associated with immune, disease and production traits in indigenous village chickens. Results underpin the feasibility of concomitant genetic improvement for enhanced antibody response, resistance to parasitism and productivity within and across indigenous chicken ecotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0252-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Scotland's Rural College, Easter Bush, Edinburgh, Midlothian, EH25 9RG, UK
| | - Oswald Matika
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Takele T Desta
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Judy Bettridge
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Tadelle Dessie
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Rob Christley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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