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Lipkin E, Smith J, Soller M, Burt DW, Fulton JE. Sex Differences in Response to Marek's Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome. Genes (Basel) 2022; 14:genes14010020. [PMID: 36672761 PMCID: PMC9859034 DOI: 10.3390/genes14010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Marek's Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome (GGZ) a particularly attractive target to study the chicken MD response. Previously, we used a Hy-Line F6 population from a full-sib advanced intercross line to map MD QTL regions (QTLRs) on all chicken autosomes. Here, we mapped MD QTLRs on GGZ in the previously utilized F6 population with individual genotypes and phenotypes, and in eight elite commercial egg production lines with daughter-tested sires and selective DNA pooling (SDP). Four MD QTLRs were found from each analysis. Some of these QTLRs overlap regions from previous reports. All QTLRs were tested by individuals from the same eight lines used in the SDP and genotyped with markers located within and around the QTLRs. All QTLRs were confirmed. The results exemplify the complexity of MD resistance in chickens and the complex distribution of p-values and Linkage Disequilibrium (LD) pattern and their effect on localization of the causative elements. Considering the fragments and interdigitated LD blocks while using LD to aid localization of causative elements, one must look beyond the non-significant markers, for possible distant markers and blocks in high LD with the significant block. The QTLRs found here may explain at least part of the gender differences in MD tolerance, and provide targets for mitigating the effects of MD.
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Affiliation(s)
- Ehud Lipkin
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
- Correspondence: (E.L.); (J.S.)
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
- Correspondence: (E.L.); (J.S.)
| | - Morris Soller
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - David W. Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Janet E. Fulton
- Hy-Line International, P.O. Box 310, 2583 240th St., Dallas Center, IA 50063, USA
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Smith J, Lipkin E, Soller M, Fulton JE, Burt DW. Mapping QTL Associated with Resistance to Avian Oncogenic Marek's Disease Virus (MDV) Reveals Major Candidate Genes and Variants. Genes (Basel) 2020; 11:genes11091019. [PMID: 32872585 PMCID: PMC7564597 DOI: 10.3390/genes11091019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 01/13/2023] Open
Abstract
Marek’s disease (MD) represents a significant global economic and animal welfare issue. Marek’s disease virus (MDV) is a highly contagious oncogenic and highly immune-suppressive α-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impact on animal health and on the poultry industry. Genetic selection provides an alternative and complementary method to vaccination. However, even after years of study, the genetic mechanisms underlying resistance to MDV remain poorly understood. The Major Histocompatability Complex (MHC) is known to play a role in disease resistance, along with a handful of other non-MHC genes. In this study, one of the largest to date, we used a multi-facetted approach to identify quantitative trait locus regions (QTLR) influencing resistance to MDV, including an F6 population from a full-sib advanced intercross line (FSIL) between two elite commercial layer lines differing in resistance to MDV, RNA-seq information from virus challenged chicks, and genome wide association study (GWAS) from multiple commercial lines. Candidate genomic elements residing in the QTLR were further tested for association with offspring mortality in the face of MDV challenge in eight pure lines of elite egg-layer birds. Thirty-eight QTLR were found on 19 chicken chromosomes. Candidate genes, microRNAs, long non-coding RNAs and potentially functional mutations were identified in these regions. Association tests were carried out in 26 of the QTLR, using eight pure lines of elite egg-layer birds. Numerous candidate genomic elements were strongly associated with MD resistance. Genomic regions significantly associated with resistance to MDV were mapped and candidate genes identified. Various QTLR elements were shown to have a strong genetic association with resistance. These results provide a large number of significant targets for mitigating the effects of MDV infection on both poultry health and the economy, whether by means of selective breeding, improved vaccine design, or gene-editing technologies.
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Affiliation(s)
- Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Ehud Lipkin
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Morris Soller
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Janet E Fulton
- Hy-Line International, P.O. Box 310, 2583 240th St., Dallas Center, IA 50063, USA
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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Soller M, Abu-Toamih Atamni HJ, Binenbaum I, Chatziioannou A, Iraqi FA. Designing a QTL Mapping Study for Implementation in the Realized Collaborative Cross Genetic Reference Population. ACTA ACUST UNITED AC 2020; 9:e66. [PMID: 31756057 DOI: 10.1002/cpmo.66] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Collaborative Cross (CC) mouse resource is a next-generation mouse genetic reference population (GRP) designed for high-resolution mapping of quantitative trait loci (QTL) of large effect affecting complex traits during health and disease. The CC resource consists of a set of 72 recombinant inbred lines (RILs) generated by reciprocal crossing of five classical and three wild-derived mouse founder strains. Complex traits are controlled by variations within multiple genes and environmental factors, and their mutual interactions. These traits are observed at multiple levels of the animals' systems, including metabolism, body weight, immune profile, and susceptibility or resistance to the development and progress of infectious or chronic diseases. Herein, we present general guidelines for design of QTL mapping experiments using the CC resource-along with full step-by-step protocols and methods that were implemented in our lab for the phenotypic and genotypic characterization of the different CC lines-for mapping the genes underlying host response to infectious and chronic diseases. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: CC lines for whole body mass index (BMI) Basic Protocol 2: A detailed assessment of the power to detect effect sizes based on the number of lines used, and the number of replicates per line Basic Protocol 3: Obtaining power for QTL with given target effect by interpolating in Table 1 of Keele et al. (2019).
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Affiliation(s)
- Morris Soller
- Department of Genetics, Silverman Institute for Life Sciences, Hebrew University, Jerusalem, Israel
| | - Hanifa J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Ilona Binenbaum
- Department of Biology, University of Patras, Patras, Greece.,Institute of Biology, Medicinal Chemistry & Biotechnology, NHRF, Athens, Greece
| | | | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
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Haas R, Horev G, Lipkin E, Kesten I, Portnoy M, Buhnik-Rosenblau K, Soller M, Kashi Y. Mapping Ethanol Tolerance in Budding Yeast Reveals High Genetic Variation in a Wild Isolate. Front Genet 2019; 10:998. [PMID: 31824552 PMCID: PMC6879558 DOI: 10.3389/fgene.2019.00998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/18/2019] [Indexed: 01/08/2023] Open
Abstract
Ethanol tolerance, a polygenic trait of the yeast Saccharomyces cerevisiae, is the primary factor determining industrial bioethanol productivity. Until now, genomic elements affecting ethanol tolerance have been mapped only at low resolution, hindering their identification. Here, we explore the genetic architecture of ethanol tolerance, in the F6 generation of an Advanced Intercrossed Line (AIL) mapping population between two phylogenetically distinct, but phenotypically similar, S. cerevisiae strains (a common laboratory strain and a wild strain isolated from nature). Under ethanol stress, 51 quantitative trait loci (QTLs) affecting growth and 96 QTLs affecting survival, most of them novel, were identified, with high resolution, in some cases to single genes, using a High-Resolution Mapping Package of methodologies that provided high power and high resolution. We confirmed our results experimentally by showing the effects of the novel mapped genes: MOG1, MGS1, and YJR154W. The mapped QTLs explained 34% of phenotypic variation for growth and 72% for survival. High statistical power provided by our analysis allowed detection of many loci with small, but mappable effects, uncovering a novel “quasi-infinitesimal” genetic architecture. These results are striking demonstration of tremendous amounts of hidden genetic variation exposed in crosses between phylogenetically separated strains with similar phenotypes; as opposed to the more common design where strains with distinct phenotypes are crossed. Our findings suggest that ethanol tolerance is under natural evolutionary fitness-selection for an optimum phenotype that would tend to eliminate alleles of large effect. The study provides a platform for development of superior ethanol-tolerant strains using genome editing or selection.
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Affiliation(s)
- Roni Haas
- Faculty of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Guy Horev
- Lorey I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ehud Lipkin
- Department of Genetics, Silberman Life Sciences Institute, The Hebrew University of Edmond Safra Campus, Jerusalem, Israel
| | - Inbar Kesten
- Faculty of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Maya Portnoy
- Faculty of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | | | - Morris Soller
- Department of Genetics, Silberman Life Sciences Institute, The Hebrew University of Edmond Safra Campus, Jerusalem, Israel
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion, Haifa, Israel
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Affiliation(s)
- M. Soller
- Department of Genetics, The Hebrew University, Jerusalem
| | - Y. Eitan
- Department of Genetics, The Hebrew University, Jerusalem
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Heifetz EM, Rozenboim I, Soller M, Eitan Y. Hormonal levels of estradiol, testosterone, and progesterone at entry into lay of year 1980 vs. 2000 broiler breeder females under fast and slow release from feed restriction. Poult Sci 2018; 97:3728-3735. [PMID: 29860274 DOI: 10.3382/ps/pey213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/29/2018] [Indexed: 11/20/2022] Open
Abstract
In the mid-1960s egg production, fertility, and hatchability of broiler breeder females dropped precipitously. Due to disrupted follicle hierarchies and development of the erratic oviposition and defective eggs (EODES) syndrome. EODES was controlled by restricting feed. In the 1990s, another set of problems arose at entry of broiler breeders into lay and characterized by high mortality followed by lower peak lay and reduction in egg and chick production. These problems are induced by even slight over-feeding, and hence we termed it the "Over Feeding Complex" (OFC). We have speculated that OFC is a quasi-EODES condition, induced by the intense selection for increased breast proportion. To test this, we compared, under fast (FF) and slow (SF) release from feed restriction, body composition and reproductive performance of a broiler breeder from year 1980 (B1980) and kept without selection for performance traits since then, to a line hatched in 2000 (B2000). During the first 16 d of lay, feeding treatment had little effect on egg mass or Laying % for the B1980 birds, while for the B2000 birds, SF treatment resulted in significantly greater egg mass and Laying % compared to FF, showing that the OFC indeed manifested in this experiment. However, contrary to hypothesis, follicle hierarchies were normal for both lines under both feeding treatments. To gain further insight into the OFC syndrome, we here report levels of estradiol, testosterone, and progesterone for these line and treatment groups in the time period leading up to and into lay. A significant line × feeding treatment interaction effect was found for estradiol and testosterone, to a lesser extent for progesterone. For all 3 hormones, for B1980 levels 2 to 3 wk post entry into lay were similar and intermediate under FF and SF, but differed significantly for B2000, being much greater under SF than under FF. Thus, the hormonal effects were parallel and may explain the egg mass and Laying % effects of FF and SF in the 2 genetic types.
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Affiliation(s)
- Eliyahu M Heifetz
- Faculty of Health Sciences, Jerusalem College of Technology, Jerusalem, 9116001 Israel
| | - Israel Rozenboim
- Department of Animal Science, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7612001 Israel
| | - Morris Soller
- Department of Genetics, Silberman Life Sciences Institute, Edmond Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 91904001 Israel
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Shabtay A, Soller M, Sölkner J, Mészáros G, Sonstegard T, Ünal EO, Huson HJ, Utsunomiya YT, Lipkin E. P4014 Global and local admixture analyses of baladi cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement485a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, Bagnato A, Shabtay A. P6003 The use of Kosher phenotyping for mapping QTL affecting susceptibility to bovine respiratory disease. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4149x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, Bagnato A, Shabtay A. The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease. PLoS One 2016; 11:e0153423. [PMID: 27077383 PMCID: PMC4831767 DOI: 10.1371/journal.pone.0153423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/29/2016] [Indexed: 02/06/2023] Open
Abstract
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity.
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Affiliation(s)
- Ehud Lipkin
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Harel Eitam
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Moran Yishay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | | | - Morris Soller
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Ariel Shabtay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
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Valind A, Haikal C, Klasson MEK, Johansson MC, Gullander J, Soller M, Baldetorp B, Gisselsson D. The fetal thymus has a unique genomic copy number profile resulting from physiological T cell receptor gene rearrangement. Sci Rep 2016; 6:23500. [PMID: 27009469 PMCID: PMC4806331 DOI: 10.1038/srep23500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/09/2016] [Indexed: 12/14/2022] Open
Abstract
Somatic mosaicism, the presence of genetically distinct cells within an organism, has been increasingly associated with human morbidity, ranging from being a cause of rare syndromes to a risk factor for common disorders such as malignancy and cardiovascular disease. Previous studies interrogating the normal prevalence of somatic mosaicism have focused on adults. We here present an estimate of the baseline frequency of somatic mosaic copy number variation (CNV) at the time around birth, by sampling eight different organs from a total of five fetuses and newborns. Overall we find a significantly lower frequency of organ specific (i.e. mosaic) CNVs as compared to adults (p = 0.003; Mann-Whitney U-test). The rate of somatic CNV in adults has been estimated to around 2.2 CNV per organ assayed. In contrast, after stringent filtering, we found no organ-private CNVs in fetuses or newborns with exception of the thymus. This organ exhibited a specific genome profile in the form of deletions resulting from polyclonal T-cell receptor rearrangements. This implies that somatic non-immune related CNVs, if present at birth, are typically confined to very small cell populations within organs.
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Affiliation(s)
- Anders Valind
- Department of Clinical Genetics, Lund University BMC C13, Lund University, SE 221 84, Lund, Sweden
| | - C. Haikal
- Department of Clinical Genetics, Lund University BMC C13, Lund University, SE 221 84, Lund, Sweden
| | - M. E. K. Klasson
- Department of Clinical Genetics, Lund University BMC C13, Lund University, SE 221 84, Lund, Sweden
| | - M. C. Johansson
- Department of Oncology, Lund University University Hospital, SE 221 85, Lund, Sweden
| | - J. Gullander
- Department of Clinical Genetics, Lund University BMC C13, Lund University, SE 221 84, Lund, Sweden
| | - M. Soller
- Department of Clinical Genetics, Skåne Regional and University Laboratories University Hospital, SE 221 85, Lund, Sweden
| | - B. Baldetorp
- Department of Oncology, Lund University University Hospital, SE 221 85, Lund, Sweden
| | - David Gisselsson
- Department of Clinical Genetics, Lund University BMC C13, Lund University, SE 221 84, Lund, Sweden
- Department of Pathology, Skåne Regional and University Laboratories University Hospital, SE 221 85, Lund, Sweden
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Fontanesi L, Scotti E, Dolezal M, Lipkin E, Dall’Olio S, Zambonelli P, Bigi D, Davoli R, Soller M, Russo V. Bovine chromosome 20: milk production QTL and candidate gene analysis in the Italian Holstein-Friesian breed. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2007.1s.133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- L. Fontanesi
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
| | - E. Scotti
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
| | - M. Dolezal
- Department of Sustainable Agricultural Systems, University of Natural Resources and Applied Sciences, Boku-Vienna, Austria
| | - E. Lipkin
- Department of Genetics, The Hebrew University of Jerusalem, Israel
| | - S. Dall’Olio
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
| | - P. Zambonelli
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
| | - D. Bigi
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
| | - R. Davoli
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
| | - M. Soller
- Department of Genetics, The Hebrew University of Jerusalem, Israel
| | - V. Russo
- Dipartimento di Protezione e Valorizzazione Agroalimentare, Università di Bologna, Italy
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Fontanesi L, Scotti E, Pecorari D, Zambonelli P, Bigi D, Dall’Olio S, Davoli R, Lipkin E, Soller M, Russo V. The BovMAS Consortium: investigation of bovine chromosome 14 for quantitative trait loci affecting milk production and quality traits in the Italian Holstein Friesian breed. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2005.2s.16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bagnato A, Schiavini F, Dolezal M, Dubini S, Rossoni A, Maltecca C, Santus E, Medugorac I, Sölkner J, Fontanesi L, Friedman A, Lipkin E, Soller M. The BovMAS Consortium: identification of QTL for milk yield and milk protein percent on chromosome 14 in the Brown Swiss breed. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2005.2s.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Atamni HJAT, Mott R, Soller M, Iraqi FA. High-fat-diet induced development of increased fasting glucose levels and impaired response to intraperitoneal glucose challenge in the collaborative cross mouse genetic reference population. BMC Genet 2016; 17:10. [PMID: 26728312 PMCID: PMC4700737 DOI: 10.1186/s12863-015-0321-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/20/2015] [Indexed: 12/17/2022] Open
Abstract
Background The prevalence of Type 2 Diabetes (T2D) mellitus in the past decades, has reached epidemic proportions. Several lines of evidence support the role of genetic variation in the pathogenesis of T2D and insulin resistance. Elucidating these factors could contribute to developing new medical treatments and tools to identify those most at risk. The aim of this study was to characterize the phenotypic response of the Collaborative Cross (CC) mouse genetic resource population to high-fat diet (HFD) induced T2D-like disease to evluate its suitability for this purpose. Results We studied 683 mice of 21 different lines of the CC population. Of these, 265 mice (149 males and 116 females) were challenged by HFD (42 % fat); and 384 mice (239 males and145 females) of 17 of the 21 lines were reared as control group on standard Chow diet (18 % fat). Briefly, 8 week old mice were maintained on HFD until 20 weeks of age, and subsequently assessed by intraperitoneal glucose tolerance test (IPGTT). Biweekly body weight (BW), body length (BL), waist circumstance (WC), and body mass index (BMI) were measured. On statistical analysis, trait measurements taken at 20 weeks of age showed significant sex by diet interaction across the different lines and traits. Consequently, males and females were analyzed, separately. Differences among lines were analyzed by ANOVA and shown to be significant (P <0.05), for BW, WC, BMI, fasting blood glucose, and IPGTT-AUC. We use these data to infer broad sense heritability adjusted for number of mice tested in each line; coefficient of genetic variation; genetic correlations between the same trait in the two sexes, and phenotypic correlations between different traits in the same sex. Conclusions These results are consistent with the hypothesis that host susceptibility to HFD-induced T2D is a complex trait and controlled by multiple genetic factors and sex, and that the CC population can be a powerful tool for genetic dissection of this trait. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0321-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hanifa J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
| | | | | | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
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Ilinca A, Kristoffersson U, Soller M, Lindgren AG. Familial aggregation of stroke amongst young patients in Lund Stroke Register. Eur J Neurol 2015; 23:401-7. [PMID: 26499090 DOI: 10.1111/ene.12881] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND PURPOSE The known monogenic forms of stroke are rare. The aim of this study was to analyze pedigrees of young stroke patients regarding possible monogenic cerebrovascular disease and to evaluate the possibility of genetic stroke in these families. This may contribute to a better understanding of disease mechanism in stroke. METHODS Lund Stroke Register includes consecutive patients with first-ever stroke from a defined geographical area in southern Sweden. Early-onset (≤55 years) stroke patients were systematically screened with regard to family history (FHx), and families with stroke aggregation were compiled. Participants provided information in a questionnaire on occurrence of stroke or transient ischaemic attack (TIA) in their families. Information on cardiovascular risk factors (VRFs) and clinical stroke subtype was collected. FHx for stroke was considered positive when the patient reported either ≥1 first-degree relative with stroke/TIA, or no first-degree relative but ≥3 second- or third-degree relatives with stroke/TIA in a distribution compatible with monogenic inheritance. RESULTS Of 4103 stroke patients registered, 426 (10%) had first-ever stroke at ≤55 years and 338 (79%) of these answered the questionnaire. Of them, 159 (47%) reported a positive FHx. Twenty-eight (18%) of the probands with positive FHx had no known VRFs. Thirty-two families with ≥4 members with stroke were identified. In all these larger families the affected individuals with stroke were present in more than one generation. CONCLUSION Aggregation of stroke in families of early-onset stroke patients is not uncommon. Genetic factors with impact on stroke risk, including monogenic causes, need to be evaluated in future stroke studies.
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Affiliation(s)
- A Ilinca
- Lund University, Department of Clinical Sciences Lund, Neurology, Lund, Sweden.,Department of Internal Medicine, Landskrona Hospital, Landskrona, Sweden
| | - U Kristoffersson
- Department of Clinical Genetics, Lund University and Regional Laboratories, Region Skåne, Sweden
| | - M Soller
- Department of Clinical Genetics, Lund University and Regional Laboratories, Region Skåne, Sweden
| | - A G Lindgren
- Lund University, Department of Clinical Sciences Lund, Neurology, Lund, Sweden.,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden
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Heifetz EM, Soller M. Targeted Recombinant Progeny: a design for ultra-high resolution mapping of Quantitative Trait Loci in crosses between inbred or pure lines. BMC Genet 2015; 16:76. [PMID: 26148479 PMCID: PMC4492090 DOI: 10.1186/s12863-015-0206-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-resolution mapping of the loci (QTN) responsible for genetic variation in quantitative traits is essential for positional cloning of candidate genes, and for effective marker assisted selection. The confidence interval (QTL) flanking the point estimate of QTN-location is proportional to the number of individuals in the mapping population carrying chromosomes recombinant in the given interval. Consequently, many designs for high resolution QTN mapping are based on increasing the proportion of recombinants in the mapping population. The "Targeted Recombinant Progeny" (TRP) design is a new design for high resolution mapping of a target QTN in crosses between pure, or inbred lines. It is a three-generation procedure generating a large number of recombinant individuals within a QTL previously shown to contain a QTN. This is achieved by having individuals that carry chromosomes recombinant across the target QTL interval as parents of a large mapping population; most of whom will therefore carry recombinant chromosomes targeted to the given QTL. The TRP design is particularly useful for high resolution mapping of QTN that differentiate inbred or pure lines, and hence are not amenable to high resolution mapping by genome-wide association tests. RESULTS In the absence of residual polygenic variation, population sizes required for achieving given mapping resolution by the TRP-F2 design relative to a standard F2 design ranged from 0.289 for a QTN with standardized allele substitution effect = 0.2, mapped to an initial QTL of 0.2 Morgan to 0.041 for equivalent QTN mapped to an initial QTL of 0.02 M. In the presence of residual polygenic variation, the relative effectiveness of the TRP design ranges from 1.068 to 0.151 for the same initial QTL intervals and QTN effect. Thus even in the presence of polygenic variation, the TRP can still provide major savings. Simulation showed that mapping by TRP should be based on 30-50 markers spanning the initial interval; and on at least 50 or more G2 families representing this number of recombination points,. CONCLUSIONS The TRP design can be an effective procedure for achieving high and ultra-high mapping resolution of a target QTN previously mapped to a known confidence interval (QTL).
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Affiliation(s)
| | - Morris Soller
- Department of Genetics, Silverman Life Sciences Institute, Edmund Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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Abstract
I became enamored of genetics at an early age. The desire to participate in the rebuilding of my people in our ancient homeland led to dairy science at Rutgers University, to Animal Breeding Plans by J.L. Lush, and to the realization that I could combine genetics and dairy science in animal breeding. It is to my mother-in-law that I owe the felicitous phrasing of the titular scientific question that has occupied my professional life: If a bull were a cow, how much milk would he give? Following my PhD (in 1956), I joined the Volcani Institute in Israel and, later (in 1972), the Applied Genetics group at the Hebrew University. The Applied Genetics group had an active marker lab, and this and a paper by Spickett & Thoday led me to explore genetic markers for quantitative trait loci mapping and marker-assisted selection. A chance encounter with Jacques Beckmann in 1980 opened my eyes to the potential of DNA-level markers for these purposes, and the rest followed.
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Affiliation(s)
- Morris Soller
- Department of Genetics, The Silberman Life Sciences Institute, Edmund Safra Campus, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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18
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Strillacci MG, Frigo E, Schiavini F, Samoré AB, Canavesi F, Vevey M, Cozzi MC, Soller M, Lipkin E, Bagnato A. Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA. BMC Genet 2014; 15:106. [PMID: 25288516 PMCID: PMC4198737 DOI: 10.1186/s12863-014-0106-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/25/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mastitis is a major disease of dairy cattle occurring in response to environmental exposure to infective agents with a great economic impact on dairy industry. Somatic cell count (SCC) and its log transformation in somatic cell score (SCS) are traits that have been used as indirect measures of resistance to mastitis for decades in selective breeding. A selective DNA pooling (SDP) approach was applied to identify Quantitative Trait Loci (QTL) for SCS in Valdostana Red Pied cattle using the Illumina Bovine HD BeadChip. RESULTS A total of 171 SNPs reached the genome-wide significance for association with SCS. Fifty-two SNPs were annotated within genes, some of those involved in the immune response to mastitis. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found. These regions identified novel genomic regions related to mastitis (1-Mb SNP windows) and confirmed those already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb. CONCLUSIONS The genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Alessandro Bagnato
- Department of Health, Animal Science and Food Safety (VESPA), University of Milan, Via Celoria 10, Milan, 20133, Italy.
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Strillacci MG, Frigo E, Canavesi F, Ungar Y, Schiavini F, Zaniboni L, Reghenzani L, Cozzi MC, Samoré AB, Kashi Y, Shimoni E, Tal-Stein R, Soller M, Lipkin E, Bagnato A. Quantitative trait loci mapping for conjugated linoleic acid, vaccenic acid and ∆9-desaturase in Italian Brown Swiss dairy cattle using selective DNA pooling. Anim Genet 2014; 45:485-99. [DOI: 10.1111/age.12174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 02/04/2023]
Affiliation(s)
- M. G. Strillacci
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - E. Frigo
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - F. Canavesi
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - Y. Ungar
- Israel Institute of Technology (Technion); Department of Biotechnology and Food Engineering; Technion City; Haifa 3200003 Israel
| | - F. Schiavini
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
- Genomic and Bioinformatics Platform; University of Milan; c/o Fondazione Filarete, Viale Ortles 20 Milano 20100 Italy
| | - L. Zaniboni
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - L. Reghenzani
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - M. C. Cozzi
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - A. B. Samoré
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - Y. Kashi
- Israel Institute of Technology (Technion); Department of Biotechnology and Food Engineering; Technion City; Haifa 3200003 Israel
| | - E. Shimoni
- Israel Institute of Technology (Technion); Department of Biotechnology and Food Engineering; Technion City; Haifa 3200003 Israel
| | - R. Tal-Stein
- Department of Genetics; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - M. Soller
- Department of Genetics; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - E. Lipkin
- Department of Genetics; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - A. Bagnato
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
- Genomic and Bioinformatics Platform; University of Milan; c/o Fondazione Filarete, Viale Ortles 20 Milano 20100 Italy
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Eitan Y, Lipkin E, Soller M. Body composition and reproductive performance at entry into lay of anno 1980 versus anno 2000 broiler breeder females under fast and slow release from feed restriction. Poult Sci 2014; 93:1227-35. [DOI: 10.3382/ps.2013-03239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Iraqi FA, Athamni H, Dorman A, Salymah Y, Tomlinson I, Nashif A, Shusterman A, Weiss E, Houri-Haddad Y, Mott R, Soller M. Heritability and coefficient of genetic variation analyses of phenotypic traits provide strong basis for high-resolution QTL mapping in the Collaborative Cross mouse genetic reference population. Mamm Genome 2014; 25:109-19. [PMID: 24445421 DOI: 10.1007/s00335-014-9503-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
Most biological traits of human importance are complex in nature; their manifestation controlled by the cumulative effect of many genetic factors interacting with one another and with the individual's life history. Because of this, mouse genetic reference populations (GRPs) consisting of collections of inbred lines or recombinant inbred lines (RIL) derived from crosses between inbred lines are of particular value in analysis of complex traits, since massive amounts of data can be accumulated on the individual lines. However, existing mouse GRPs are derived from inbred lines that share a common history, resulting in limited genetic diversity, and reduced mapping precision due to long-range gametic disequilibrium. To overcome these limitations, the Collaborative Cross (CC) a genetically highly diverse collection of mouse RIL was established. The CC, now in advanced stages of development, will eventually consist of about 500 RIL derived from reciprocal crosses of eight divergent founder strains of mice, including three wild subspecies. Previous studies have shown that the CC indeed contains enormous diversity at the DNA level, that founder haplotypes are inherited in expected frequency, and that long-range gametic disequilibrium is not present. We here present data, primarily from our own laboratory, documenting extensive genetic variation among CC lines as expressed in broad-sense heritability (H(2)) and by the well-known "coefficient of genetic variation," demonstrating the ability of the CC resource to provide unprecedented mapping precision leading to identification of strong candidate genes.
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Affiliation(s)
- Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel,
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Shusterman A, Salyma Y, Nashef A, Soller M, Wilensky A, Mott R, Weiss EI, Houri-Haddad Y, Iraqi FA. Genotype is an important determinant factor of host susceptibility to periodontitis in the Collaborative Cross and inbred mouse populations. BMC Genet 2013; 14:68. [PMID: 23937452 PMCID: PMC3751202 DOI: 10.1186/1471-2156-14-68] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 08/02/2013] [Indexed: 01/09/2023] Open
Abstract
Background Periodontal infection (Periodontitis) is a chronic inflammatory disease, which results in the breakdown of the supporting tissues of the teeth. Previous epidemiological studies have suggested that resistance to chronic periodontitis is controlled to some extent by genetic factors of the host. The aim of this study was to determine the phenotypic response of inbred and Collaborative Cross (CC) mouse populations to periodontal bacterial challenge, using an experimental periodontitis model. In this model, mice are co-infected with Porphyromonas gingivalis and Fusobacterium nucleatum, bacterial strains associated with human periodontal disease. Six weeks following the infection, the maxillary jaws were harvested and analyzed for alveolar bone loss relative to uninfected controls, using computerized microtomography (microCT). Initially, four commercial inbred mouse strains were examined to calibrate the procedure and test for gender effects. Subsequently, we applied the same protocol to 23 lines (at inbreeding generations 10–18) from the newly developed mouse genetic reference population, the Collaborative Cross (CC) to determine heritability and genetic variation of control bone volume prior to infection (CBV, naïve bone volume around the teeth of uninfected mice), and residual bone volume (RBV, bone volume after infection) and loss of bone volume (LBV, the difference between CBV and RBV) following infection. Results BALB/CJ mice were highly susceptible (P<0.05) whereas DBA/2J, C57BL/6J and A/J mice were resistant. Six lines of the tested CC population were susceptible, whereas the remaining lines were resistant to alveolar bone loss. Gender effects on bone volume were tested across the four inbred and 23 CC lines, and found not to be significant. Based on ANOVA analyses, broad-sense heritabilities were statistically significant and equal to 0.4 for CBV and 0.2 for LBV. Conclusions The moderate heritability values indicate that the variation in host susceptibility to the disease is controlled to an appreciable extent by genetic factors. These results strongly support the possibility of using the Collaborative Cross, as well as developing dedicated F2 (resistant x susceptible inbred strains) resource populations, for future dissection of genetic factors in periodontitis.
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Affiliation(s)
- Ariel Shusterman
- Department of Prosthodontics, Faculty of Dental Medicine, Hadassah Medical Centers and The Hebrew University, Jerusalem, Israel
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23
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Fulton JE, Soller M, Lund AR, Arango J, Lipkin E. Variation in the ovocalyxin-32 gene in commercial egg-laying chickens and its relationship with egg production and egg quality traits. Anim Genet 2012; 43 Suppl 1:102-13. [PMID: 22742508 DOI: 10.1111/j.1365-2052.2012.02384.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Avian eggshell quality is an important trait for commercial egg production, as the eggshell is the primary packaging material and antimicrobial barrier for the internal food resource. Strong eggshells are essential to ensure that eggs can reach their final destination without damage. Ovocalyxin-32 (OCX32) is a matrix protein found within the outer layers of the eggshell and in the cuticle. Numerous reports in the literature have identified association between variants in the gene encoding this protein, OCX32, and various eggshell quality traits. Thus, OCX32 is a candidate gene for selection for eggshell traits in commercial poultry populations. Sequencing of exons 2-6 of the OCX32 gene in eight elite brown and white eggshell commercial egg-laying lines revealed 28 SNPs and one SNP/indel. Eighteen of these SNPs were predicted to alter the amino acid sequence of the protein. Clusters of SNPs in complete linkage disequilibrium were found in both exons 2 and 6. A total of 19 different versions or protein-sequence haplotypes of the OCX32 protein were inferred, revealing considerable variation within commercial lines. Genotypes for 13 of the SNPs were determined for 330-1819 individuals per line. Trait association studies revealed a significant effect of OCX32 on shell color in white egg lines and line-specific significant effects on albumen height, early egg weight, puncture score, and yolk weight. Three of the lines showed a significant change in OCX32 frequency over time, indicating selection pressure for certain variants of this gene during the breeding program.
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Affiliation(s)
- J E Fulton
- Hy-Line International, PO Box 310, Dallas Center, IA 50063, USA.
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24
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Orenge CO, Munga L, Kimwele CN, Kemp S, Korol A, Gibson JP, Hanotte O, Soller M. Trypanotolerance in N'Dama x Boran crosses under natural trypanosome challenge: effect of test-year environment, gender, and breed composition. BMC Genet 2012; 13:87. [PMID: 23075408 PMCID: PMC3519672 DOI: 10.1186/1471-2156-13-87] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 10/11/2012] [Indexed: 11/23/2022] Open
Abstract
Background Trypanosomosis, a protozoal disease affecting livestock, transmitted by Glossina (tsetse) flies is a major constraint to agricultural production in Sub-Saharan Africa. It is accepted that utilization of the native trypanotolerance exhibited in some of the African cattle breeds to improve trypanotolerance of more productive but susceptible breeds, will offer a cost effective and sustainable solution to the problem. The success of this approach is based on the premise that quantitative trait loci previously identified under relatively controlled situations confer useful trypanotolerance under natural field situations. As part of a study to authenticate this hypothesis, a population of 192 cattle, consisting of six batches of N’Dama and Kenya-Boran backcross animals [(N’Dama x Kenya-Boran) x Kenya-Boran] born over the period 2002 to 2006 was constructed. Some of the batches also included pure Kenya-Boran cattle, or N’Dama x Kenya- Boran F1 animals. Each batch was exposed as yearlings to natural field trypanosomosis challenge over a period of about one year; the entire challenge period extending from December 2003 to June 2007. Performance of the animals was evaluated by weekly or biweekly measurements of body weight, packed blood cell volume (PCV), parasitemia score, and number of trypanocide treatments. From these basic data, 49 phenotypes were constructed reflecting dynamics of body weight, packed cell volume (PCV) and parasitemia under challenge. Results Females were distinctly more trypanotolerant than males. F1, backcross and pure Kenya- Boran animals ranked in that order with respect to trypanotolerance. Overall batch effects were highly significant (p<0.001) for most traits, and were generally more significant than the gender or genetic type effects. The superior trypanotolerance of the F1 animals was expressed in all three components of animal defense strategies against pathogens: Avoidance resistance, and tolerance. Conclusions The results show that trypanotolerance derived from the N’Dama is expressed under field conditions; and that the trait is primarily additive in nature, being expressed in heterozygous condition and in a three-quarters Boran genetic background. The results further, underscore the complexity of the trait in the field manifesting all three host disease-control strategies, and show the importance of gender and local environmental conditions in determining response to challenge.
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Affiliation(s)
- Caleb O Orenge
- South Eastern University College (A constituent college of the University of Nairobi), P,O, Box 170-90200, Kitui, Kenya.
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25
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Orenge CO, Munga L, Kimwele CN, Kemp S, Korol A, Gibson JP, Hanotte O, Soller M. Trypanotolerance in N'Dama x Boran crosses under natural trypanosome challenge: effect of test-year environment, gender, and breed composition. BMC Genet 2012. [PMID: 23075408 DOI: 10.1186/1471-2156-13-87.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosomosis, a protozoal disease affecting livestock, transmitted by Glossina (tsetse) flies is a major constraint to agricultural production in Sub-Saharan Africa. It is accepted that utilization of the native trypanotolerance exhibited in some of the African cattle breeds to improve trypanotolerance of more productive but susceptible breeds, will offer a cost effective and sustainable solution to the problem. The success of this approach is based on the premise that quantitative trait loci previously identified under relatively controlled situations confer useful trypanotolerance under natural field situations. As part of a study to authenticate this hypothesis, a population of 192 cattle, consisting of six batches of N'Dama and Kenya-Boran backcross animals [(N'Dama x Kenya-Boran) x Kenya-Boran] born over the period 2002 to 2006 was constructed. Some of the batches also included pure Kenya-Boran cattle, or N'Dama x Kenya- Boran F1 animals. Each batch was exposed as yearlings to natural field trypanosomosis challenge over a period of about one year; the entire challenge period extending from December 2003 to June 2007. Performance of the animals was evaluated by weekly or biweekly measurements of body weight, packed blood cell volume (PCV), parasitemia score, and number of trypanocide treatments. From these basic data, 49 phenotypes were constructed reflecting dynamics of body weight, packed cell volume (PCV) and parasitemia under challenge. RESULTS Females were distinctly more trypanotolerant than males. F1, backcross and pure Kenya- Boran animals ranked in that order with respect to trypanotolerance. Overall batch effects were highly significant (p<0.001) for most traits, and were generally more significant than the gender or genetic type effects. The superior trypanotolerance of the F1 animals was expressed in all three components of animal defense strategies against pathogens: Avoidance resistance, and tolerance. CONCLUSIONS The results show that trypanotolerance derived from the N'Dama is expressed under field conditions; and that the trait is primarily additive in nature, being expressed in heterozygous condition and in a three-quarters Boran genetic background. The results further, underscore the complexity of the trait in the field manifesting all three host disease-control strategies, and show the importance of gender and local environmental conditions in determining response to challenge.
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Affiliation(s)
- Caleb O Orenge
- South Eastern University College (A constituent college of the University of Nairobi), P,O, Box 170-90200, Kitui, Kenya.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Huang W, Nadeem A, Zhang B, Babar M, Soller M, Khatib H. Characterization and comparison of the leukocyte transcriptomes of three cattle breeds. PLoS One 2012; 7:e30244. [PMID: 22291923 PMCID: PMC3264571 DOI: 10.1371/journal.pone.0030244] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/15/2011] [Indexed: 11/24/2022] Open
Abstract
In this study, mRNA-Seq was used to characterize and compare the leukocyte transcriptomes from two taurine breeds (Holstein and Jersey), and one indicine breed (Cholistani). At the genomic level, we identified breed-specific base changes in protein coding regions. Among 7,793,425 coding bases, only 165 differed between Holstein and Jersey, and 3,383 (0.04%) differed between Holstein and Cholistani, 817 (25%) of which resulted in amino acid changes in 627 genes. At the transcriptional level, we assembled transcripts and estimated their abundances including those from more than 3,000 unannotated intergeneic regions. Differential gene expression analysis showed a high similarity between Holstein and Jersey, and a much greater difference between the taurine breeds and the indicine breed. We identified gene ontology pathways that were systematically altered, including the electron transport chain and immune response pathways that may contribute to different levels of heat tolerance and disease resistance in taurine and indicine breeds. At the post-transcriptional level, sequencing mRNA allowed us to identify a number of genes undergoing differential alternative splicing among different breeds. This study provided a high-resolution survey of the variation between bovine transcriptomes at different levels and may provide important biological insights into the phenotypic differentiation among cattle breeds.
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Affiliation(s)
- Wen Huang
- Department of Dairy Science, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Bao Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Masroor Babar
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Morris Soller
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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Orenge C, Munga L, Kimwele C, Kemp S, Korol A, Gibson J, Hanotte O, Soller M. Expression of trypanotolerance in N'Dama x Boran crosses under field challenge in relation to N'Dama genome content. BMC Proc 2011; 5 Suppl 4:S23. [PMID: 21645303 PMCID: PMC3108218 DOI: 10.1186/1753-6561-5-s4-s23] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Animal trypanosomosis in sub-Saharan Africa is a major obstacle to livestock based agriculture. Control relies on drugs with increasing incidence of multiple-drug resistance. A previous mapping experiment in an F2 population derived from the indigenous trypanotolerant N’Dama cattle crossed to susceptible (Kenya)-Boran cattle under controlled challenge, uncovered a number of trypanotolerance QTL (T-QTL). The present study was to determine expression of N’Dama trypanotolerance in a backcross to the Boran under conditions of field challenge, and whether chromosomal regions associated with trypanotolerance in the F2 experiment showed similar effects in the BC population. Methods 192 backcross animals to the Boran were produced in six batches from June 2001 to December 2006. At one year of age animals were moved to the field and exposed to natural challenge over about one year in Southwest Kenya (Narok). The animals were individually recorded weekly for body weight, packed cell volume, parasitaemia score, and drug treatments, and were genotyped using 35 microsatellite markers spanning 5 chromosomes found in the F2 study to harbour T-QTL. Results The F1 were most trypanotolerant, Boran least, and BC intermediate. Females showed distinctly higher trypanotolerance than males. There was a positive correlation in the BC population between trypanotolerance and number of N’Dama origin marker alleles. QTL mapping revealed T-QTL distributed among all five targeted chromosomes, corresponding in part to the results obtained in the F2 experiment. Conclusions N’Dama origin trypanotolerance is expressed in a BC population under field conditions in proportion to N’Dama origin marker alleles. Consequently, marker assisted selection in such populations may be a means of increasing trypanotolerance, while retaining the desirable productive qualities of the recurrent parent.
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Affiliation(s)
- Caleb Orenge
- Department of Genetics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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Tal-Stein R, Fontanesi L, Dolezal M, Scotti E, Bagnato A, Russo V, Canavesi F, Friedmann A, Soller M, Lipkin E. A genome scan for quantitative trait loci affecting milk somatic cell score in Israeli and Italian Holstein cows by means of selective DNA pooling with single- and multiple-marker mapping. J Dairy Sci 2010; 93:4913-27. [PMID: 20855026 DOI: 10.3168/jds.2010-3254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/25/2010] [Indexed: 11/19/2022]
Abstract
Mastitis is an important and common dairy cattle disease affecting milk yield, quality, and consumer safety as well as cheese yields and quality. Animal welfare and residues of the antibiotics used to treat mastitis cause public concern. Considerable genetic variation may allow selection for increased resistance to mastitis. Because of high genetic correlation to milk somatic cell score (SCS), SCS can serve as a surrogate trait for mastitis resistance. The present study intended to identify quantitative trait loci (QTL) affecting SCS in Israeli and Italian Holstein dairy cattle (IsH and ItH, respectively), using selective DNA pooling with single and multiple marker mapping. Milk samples of 4,788 daughters of 6 IsH and 7 ItH sires were used to construct sire-family high- and low-tail pools, which were genotyped at 123 (IsH) and 133 (ItH) microsatellite markers. Shadow correction was used to obtain pool allele frequency estimates. Frequency difference between the tails and empirical standard error of D, SE(D), were used to obtain P-values. All markers significant by single marker mapping were also significant by multiple marker mapping, but not vice versa. Combining both populations, 22 QTL on 21 chromosomes were identified; all corresponded to previous reports in the literature. Confidence intervals were set by chi-squared drop method. Heterozygosity of QTL was estimated at 44.2%. Allele substitution effects ranged from 1,782 to 4,930 cells/mL in estimated breeding value somatic cell count units. Most (80%) of the observed variation in estimated breeding value somatic cell score could be explained by the QTL identified under the stringent criteria. The results found here can be used as a basis for further genome-wide association studies for the same trait.
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Affiliation(s)
- R Tal-Stein
- Department of Genetics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Wolff K, Brun W, Kvale G, Ehrencrona H, Soller M, Nordin K. How to handle genetic information: a comparison of attitudes among patients and the general population. Public Health Genomics 2010; 13:396-405. [PMID: 20606381 DOI: 10.1159/000313458] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/13/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND So far there are no studies comparing the attitudes of patients with hereditary conditions to the attitudes of the general public on how to handle genetic risk information which mutation carriers refuse to disclose to relevant family members. The purpose of the present study was to investigate whether such patients and members of the general public want to be informed about the existence of hereditary conditions within their family, and under which conditions they want healthcare providers to breach confidentiality. METHODS It was hypothesized that the desire to be informed would be influenced by characteristics of both the disease and the individual. Systematically varying 3 disease characteristics (fatality, penetrance and treatment availability) yielded 8 versions of a questionnaire, which was administered to general population samples in Norway and Sweden (N = 3,207) and to patient samples in both countries (N = 822). Individual differences in uncertainty avoidance, coping style and consideration for future consequences were also assessed. RESULTS AND CONCLUSION A majority of both patients and the general public want to be informed about the existence of hereditary conditions within their family. However, patients are more positive towards being informed, both with and without the relative's consent, than the general public. The main predictor of the desire to be informed was uncertainty avoidance in both samples.
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Affiliation(s)
- K Wolff
- Department of Psychosocial Science, University of Bergen, Bergen, Norway.
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Nganga JK, Soller M, Iraqi FA. High resolution mapping of trypanosomosis resistance loci Tir2 and Tir3 using F12 advanced intercross lines with major locus Tir1 fixed for the susceptible allele. BMC Genomics 2010; 11:394. [PMID: 20569426 PMCID: PMC2898758 DOI: 10.1186/1471-2164-11-394] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 06/22/2010] [Indexed: 11/29/2022] Open
Abstract
Background Trypanosomosis is the most economically important disease constraint to livestock productivity in Africa. A number of trypanotolerant cattle breeds are found in West Africa, and identification of the genes conferring trypanotolerance could lead to effective means of genetic selection for trypanotolerance. In this context, high resolution mapping in mouse models are a promising approach to identifying the genes associated with trypanotolerance. In previous studies, using F2 C57BL/6J × A/J and C57BL/6J × BALB/cJ mouse resource populations, trypanotolerance QTL were mapped within a large genomic intervals of 20-40 cM to chromosomes MMU17, 5 and 1, and denoted Tir1, Tir2 and Tir3 respectively. Subsequently, using F6 C57BL/6J × A/J and C57BL/6J × BALB/cJ F6 advanced intercross lines (AIL), Tir1 was fine mapped to a confidence interval (CI) of less than 1 cM, while Tir2 and Tir3, were mapped within 5-12 cM. Tir1 represents the major trypanotolerance QTL. Results In order to improve map resolutions of Tir2 and Tir3, an F12 C57BL/6J × A/J AIL population fixed for the susceptible alleles at Tir1 QTL was generated. An F12 C57BL/6J × A/J AIL population, fixed for the resistant alleles at Tir1 QTL was also generated to provide an additional estimate of the gene effect of Tir1. The AIL populations homozygous for the resistant and susceptible Tir1 alleles and the parental controls were challenged with T. congolense and followed for survival times over 180 days. Mice from the two survival extremes of the F12 AIL population fixed for the susceptible alleles at Tir1 were genotyped with a dense panel of microsatellite markers spanning the Tir2 and Tir3 genomic regions and QTL mapping was performed. Tir2 was fine mapped to less than 1 cM CI while Tir3 was mapped to three intervals named Tir3a, Tir3b and Tir3c with 95% confidence intervals (CI) of 6, 7.2 and 2.2 cM, respectively. Conclusions The mapped QTL regions encompass genes that are vital to innate immune response and can be potential candidate genes for the underlying QTL.
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Affiliation(s)
- Joseph K Nganga
- International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
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Affiliation(s)
- H Khatib
- Department of Genetics, Alexander Silberman Life Sciences Institute, Hebrew University of Jerusalem, Israel
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Khatib H, Soller M. Mononucleotide repeat polymorphism at the CMYCA locus in chicken. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00061.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Khatib H, Genislav E, Soller M. Chicken microsatellites at the HUJERELA and HUJ106 loci. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00454.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hallerman EM, Nave A, Kashi Y, Holzer Z, Soller M, Beckmann JS. Restriction fragment length polymorphisms in dairy and beef cattle at the growth hormone and prolactin loci. Anim Genet 2009; 18:213-22. [PMID: 2889409 DOI: 10.1111/j.1365-2052.1987.tb00761.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two bovine populations, a Holstein-Friesian dairy stock and a synthetic (Baladi X Hereford X Simmental X Charolais) beef stock, were screened for restriction fragment length polymorphisms (RFLPs) at the growth hormone and prolactin genes. Most RFLPs at the growth hormone gene are apparently the consequence of an insertion/deletion event which was localized to a region downstream of the structural gene. The restriction map for the genomic region including the growth hormone gene was extended. Two HindIII RFLPs at the growth hormone locus, as well as several RFLPs at the prolactin gene, seemed to be the consequence of a series of point mutations. The results are discussed in terms of the possibility that minor genomic variability underlies quantitative genetic variation.
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Affiliation(s)
- E M Hallerman
- Department of Genetics, Hebrew University of Jerusalem, Israel
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Abstract
The present status of the bovine gene map as well as some of the methods and strategies important for future efforts in completing the gene map of cattle are reviewed.
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Affiliation(s)
- R Fries
- Department of Animal Science, Federal Institute of Technology, Zurich, Switzerland
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Shalom A, Mosig MO, Barendse W, Friedmann A, Soller M. Dinucleotide repeat polymorphism at the bovine HUJ246, HUJII77, HUJ223, HUJVI74 and HUJI75 loci. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00455.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The genes encoding bovine prolactin and rhodopsin were assigned to syntenic groups on the basis of hybridization of DNA from a panel of bovine-hamster hybrid somatic cell lines with cloned prolactin and rhodopsin gene probes. Prolactin was found to be syntenic with previously mapped glyoxalase, BoLA and 21-hydroxylase genes, establishing a syntenic conservation with human chromosome 6. The presence of bovine rhodopsin sequences among the various hybrid cell lines was not concordant with any gene previously assigned to one of the 23 defined autosomal syntenic groups. Thus, rhodopsin marks a new bovine syntenic group, U24, leaving only five cattle autosomes unmarked by at least one biochemical or molecular marker.
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Affiliation(s)
- E M Hallerman
- Department of Genetics, Hebrew University of Jerusalem, Israel
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Khatib H, Genislav E, Soller M. Chicken microsatellites at the HUJERELA and HUJ106 loci. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00062.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Shalom A, Mosig MO, Barendse W, Friedmann A, Soller M. Dinucleotide repeat polymorphism at the bovine HUJ246, HUJII77, HUJ223, HUJVI74 and HUJI75 loci. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00063.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kashi Y, Nave A, Gruenbaum Y, Soller M, Beckmann JS. A minisatellite from bovine which produces highly polymorphic DNA fingerprint patterns in mammals and chickens. Anim Genet 2009; 23:570. [PMID: 1492711 DOI: 10.1111/j.1365-2052.1992.tb00184.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Y Kashi
- Department of Genetics, Alexander Silberman Life Sciences Institute, Hebrew University, Jerusalem, Israel
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Affiliation(s)
- H Khatib
- Department of Genetics, Alexander Silberman Life Sciences Institute, Hebrew University of Jerusalem, Israel
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Shalom A, Soller M, Friedmann A. Dinucleotide repeat polymorphism at the bovine HUJ614 locus. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1993.tb00325.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rincón G, Islas-Trejo A, Casellas J, Ronin Y, Soller M, Lipkin E, Medrano JF. Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4. J Dairy Sci 2009; 92:758-64. [PMID: 19164688 DOI: 10.3168/jds.2008-1395] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r(2) values of 0.10 and 0.46, respectively; outside the blocks, r(2) values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.
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Affiliation(s)
- G Rincón
- Department of Animal Science, University of California, Davis 95616, USA
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Heifetz EM, Fulton JE, O'Sullivan NP, Arthur JA, Cheng H, Wang J, Soller M, Dekkers JCM. Mapping QTL affecting resistance to Marek's disease in an F6 advanced intercross population of commercial layer chickens. BMC Genomics 2009; 10:20. [PMID: 19144166 PMCID: PMC2651900 DOI: 10.1186/1471-2164-10-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 01/14/2009] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Marek's disease (MD) is a T-cell lymphoma of chickens caused by the Marek's disease virus (MDV), an oncogenic avian herpesvirus. MD is a major cause of economic loss to the poultry industry and the most serious and persistent infectious disease concern. A full-sib intercross population, consisting of five independent families was generated by crossing and repeated intercrossing of two partially inbred commercial White Leghorn layer lines known to differ in genetic resistance to MD. At the F6 generation, a total of 1615 chicks were produced (98 to 248 per family) and phenotyped for MD resistance measured as survival time in days after challenge with a very virulent plus (vv+) strain of MDV. RESULTS QTL affecting MD resistance were identified by selective DNA pooling using a panel of 15 SNPs and 217 microsatellite markers. Since MHC blood type (BT) is known to affect MD resistance, a total of 18 independent pool pairs were constructed according to family x BT combination, with some combinations represented twice for technical reasons. Twenty-one QTL regions (QTLR) affecting post-challenge survival time were identified, distributed among 11 chromosomes (GGA1, 2, 3, 4, 5, 8, 9, 15, 18, 26 and Z), with about two-thirds of the MD resistance alleles derived from the more MD resistant parental line. Eight of the QTLR associated with MD resistance, were previously identified in a backcross (BC) mapping study with the same parental lines. Of these, 7 originated from the more resistant line, and one from the less resistant line. CONCLUSION There was considerable evidence suggesting that MD resistance alleles tend to be recessive. The width of the QTLR for these QTL appeared to be reduced about two-fold in the F6 as compared to that found in the previous BC study. These results provide a firm basis for high-resolution linkage disequilibrium mapping and positional cloning of the resistance genes.
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Affiliation(s)
- Eliyahu M Heifetz
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
- Department of Molecular Biology, Ariel University, Ariel 44837, Israel
| | | | | | | | - Hans Cheng
- USDA-ARS-ADOL, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jing Wang
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
- Pioneer Hi-Bred International Inc., Johnston, IA 50131, USA
| | - Morris Soller
- Department of Genetics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Jack CM Dekkers
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
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Lipkin E, Tal-Stein R, Friedmann A, Soller M. Effect of quantitative trait loci for milk protein percentage on milk protein yield and milk yield in Israeli Holstein dairy cattle. J Dairy Sci 2008; 91:1614-27. [PMID: 18349254 DOI: 10.3168/jds.2007-0655] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although numerous quantitative trait loci (QTL) mapping studies involving milk protein percent (PP), milk yield (MY), and protein yield (PY) have been carried out, there has not been any systematic evaluation of the effects of individual QTL on these 3 interrelated traits. Consequently, the aim of the present study was to investigate the effects on MY and PY of QTL for PP previously mapped in various laboratories. The study, based on selective DNA pooling of milk samples, included 10 Israeli Holstein artificial insemination bulls, each the sire of 1,800 or more milk-recorded daughters. For each sire-trait combination across the 10 sires, milk samples of the highest and lowest daughters with respect to estimated breeding values for PP, PY, and MY were collected for pooling. A total of 134 dinucleotide microsatellites distributed over 25 bovine autosomes were used. An empirical standard error for marker-QTL linkage testing was calculated based on the variation among split samples within the same tail. Threshold comparison-wise error rate P-values were set to control proportion of false positives at P = 0.10 level for declaring significant effects at the marker-trait level. Estimates of the number of true null hypotheses for each trait were obtained from the histogram of marker comparison-wise error rate P-values. Based on these estimates, effective power of the experiment at the marker-trait level was estimated as 0.75, 0.41, and 0.73 for PP, PY, and MY. The proportion of heterozygosity at the QTL was estimated as 0.46, 0.39, and 0.40, respectively. After correcting for incomplete power and proportion of false positives, it was estimated that 38.7 and 37.5% of the markers affecting PP and MY, respectively, also affected PY. Of the markers affecting PY, 68.9 and 76.5%, respectively, also affected PP and MY. Apparently, none of the significant markers affected PY exclusively, and only 6.5 and 16.0%, respectively, affected PP or MY exclusively. Thus, almost all significant markers, and by inference almost all QTL, had effects on at least 2 of the 3 traits.
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Affiliation(s)
- E Lipkin
- Department of Genetics, Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Lipkin E, Bagnato A, Soller M. Expected Effects on Protein Yield of Marker-Assisted Selection at Quantitative Trait Loci Affecting Milk Yield and Milk Protein Percentage. J Dairy Sci 2008; 91:2857-63. [DOI: 10.3168/jds.2008-1011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Dolezal M, Schwarzenbacher H, Soller M, Sölkner J, Visscher P. Multiple-Marker Mapping for Selective DNA Pooling Within Large Families. J Dairy Sci 2008; 91:2864-73. [DOI: 10.3168/jds.2007-0397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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