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Van Tassell CP, Rosen BD, Woodward-Greene MJ, Silverstein JT, Huson HJ, Sölkner J, Boettcher P, Rothschild MF, Mészáros G, Nakimbugwe HN, Gondwe TN, Muchadeyi FC, Nandolo W, Mulindwa HA, Banda LJ, Kaumbata W, Getachew T, Haile A, Soudre A, Ouédraogo D, Rischkowsky BA, Mwai AO, Dzomba EF, Nash O, Abegaz S, Masiga CW, Wurzinger M, Sayre BL, Stella A, Tosser-Klopp G, Sonstegard TS. The African Goat Improvement Network: a scientific group empowering smallholder farmers. Front Genet 2023; 14:1183240. [PMID: 37712066 PMCID: PMC10497955 DOI: 10.3389/fgene.2023.1183240] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/27/2023] [Indexed: 09/16/2023] Open
Abstract
The African Goat Improvement Network (AGIN) is a collaborative group of scientists focused on genetic improvement of goats in small holder communities across the African continent. The group emerged from a series of workshops focused on enhancing goat productivity and sustainability. Discussions began in 2011 at the inaugural workshop held in Nairobi, Kenya. The goals of this diverse group were to: improve indigenous goat production in Africa; characterize existing goat populations and to facilitate germplasm preservation where appropriate; and to genomic approaches to better understand adaptation. The long-term goal was to develop cost-effective strategies to apply genomics to improve productivity of small holder farmers without sacrificing adaptation. Genome-wide information on genetic variation enabled genetic diversity studies, facilitated improved germplasm preservation decisions, and provided information necessary to initiate large scale genetic improvement programs. These improvements were partially implemented through a series of community-based breeding programs that engaged and empowered local small farmers, especially women, to promote sustainability of the production system. As with many international collaborative efforts, the AGIN work serves as a platform for human capacity development. This paper chronicles the evolution of the collaborative approach leading to the current AGIN organization and describes how it builds capacity for sustained research and development long after the initial program funds are gone. It is unique in its effectiveness for simultaneous, multi-level capacity building for researchers, students, farmers and communities, and local and regional government officials. The positive impact of AGIN capacity building has been felt by participants from developing, as well as developed country partners.
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Affiliation(s)
- Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, MD, United States
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, MD, United States
| | - M. Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, MD, United States
- National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, United States
| | - Jeffrey T. Silverstein
- Office of National Programs, USDA Agricultural Research Service, Beltsville, MD, United States
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Boettcher
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gábor Mészáros
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Timothy N. Gondwe
- Department of Animal Science, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Farai C. Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Wilson Nandolo
- Department of Animal Science, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | | | - Liveness J. Banda
- Department of Animal Science, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Wilson Kaumbata
- Department of Animal Science, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Tesfaye Getachew
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Albert Soudre
- Unité de Formation et de Recherches - Sciences et Technologies, Université Norbert ZONGO, Koudougou, Burkina Faso
| | | | | | | | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Oyekanmi Nash
- National Biotechnology Development Agency, Abuja, Nigeria
| | - Solomon Abegaz
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | | | - Maria Wurzinger
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Brian L. Sayre
- Department of Biology, Virginia State University, Petersburg, VA, United States
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology (IBBA), Milano, Italy
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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei. Genes (Basel) 2023; 14:genes14040839. [PMID: 37107597 PMCID: PMC10137967 DOI: 10.3390/genes14040839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
- Correspondence:
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Fabrizio Capoccioni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Luca Buttazzoni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Massimo Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, 72016 Brindisi, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
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Costa TC, Mendes TA, Fontes MM, Lopes MM, Du M, Serão NV, Sanglard LM, Bertolini F, Rothschild MF, Silva FF, Gionbelli MP, Duarte M. Transcriptome changes in newborn goats’ skeletal muscle as a result of maternal feed restriction at different stages of gestation. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104503] [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: 10/21/2022]
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Zurbrigg K, Bertolini F, Walugembe M, van Dreumel T, Alves D, Friendship R, O'Sullivan TL, Rothschild MF. A genome-wide analysis of cardiac lesions of pigs that die during transport: Is heart failure of in-transit-loss pigs associated with a heritable cardiomyopathy? Can J Vet Res 2021; 85:119-126. [PMID: 33883819 PMCID: PMC7995549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/25/2020] [Indexed: 06/12/2023]
Abstract
While heart failure is a primary cause of death for many in-transit-loss (ITL) pigs, the underlying cause of these deaths is not known. Cardiomyopathies are considered a common cause of heart failure in humans and often have a genetic component. The objective of this study was to determine if genes associated with cardiomyopathies could be identified in ITL pigs. Samples from the hearts of pigs that died during transport to an abattoir in Ontario, Canada were collected and genotyped along with samples from pigs that did not die during transport (ILT hearts: n = 149; non-ITL/control hearts: n = 387). Genome-wide analyses were carried out on each of the determined phenotypes (gross cardiac lesions) using a medium density single nucleotide polymorphism (SNP) chip and 500 kb windows/regions for analysis, with 250 kb regions of overlap. The distribution derived by a multidimensional scaling (MDS) analysis of all phenotypes demonstrated a lack of complete separation between phenotypes of affected and unaffected animals, which made diagnosis difficult. Although genetic differences were small, a few genes associated with dilated cardiomyopathy (DCM) and arrhythmogenic right ventricular cardiomyopathy (ARVM) were identified. In addition, multiple genes associated with cardiac arrhythmias and ventricular hypertrophy were identified that can possibly result in heart failure. The results of this preliminary study did not provide convincing evidence that a single, heritable cardiomyopathy is the cause of heart failure in ITL pigs.
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Affiliation(s)
- Katherine Zurbrigg
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - Francesca Bertolini
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - Muhammed Walugembe
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - Toni van Dreumel
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - David Alves
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - Robert Friendship
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - Terri L O'Sullivan
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
| | - Max F Rothschild
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA (Bertolini, Walugembe, Rothschild); National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark (Bertolini); Veterinary Pathology Consultant, Ontario (van Dreumel), Veterinary Epidemiology Consultant, Elora, Ontario (Alves)
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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Utzeri VJ, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. A comparative whole genome sequencing analysis identified a candidate locus for lack of operculum in cultivated gilthead seabream (Sparus aurata). Anim Genet 2021; 52:365-370. [PMID: 33609290 DOI: 10.1111/age.13049] [Citation(s) in RCA: 2] [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] [Accepted: 02/01/2021] [Indexed: 01/29/2023]
Abstract
The gilthead seabream (Sparus aurata, Sparidae family) is commonly used for aquaculture. Despite its great economic value, several problems in its cultivation remain. One of the major concerns is the high frequency of morphological abnormalities occurring during the early developmental stages. Partial and/or total lack of operculum is the most frequent anomaly affecting the fish cranial region. The existence of genetic factors that can at least partially determine this defect has been hypothesized. In this work, two DNA pools of highly related fry, one composed of normal-looking (control) fish and the other lacking an operculum (case), were constructed and whole-genome resequencing data produced from the two were compared. The analysis revealed a 1 Mb region on chromosome 2 with higher heterozygosity in the lack of operculum DNA pool than in the control DNA pool, consistent with the enrichment, in the first DNA pool, of one or more haplotypes causing or predisposing to the defect together with other normal haplotypes. A window-based FST analysis between the two DNA pools indicated that the same region had the highest divergence score. This region contained 2921 SNVs, 10 of which, with predicted high impacts (three splice donor and seven stop-gained variants), were detected in novel genes that are homologous to calcium-sensing receptor-like genes, probably involved in bone development. Other studies are needed to clarify the genetic mechanisms involved in predisposing fry to this deformity and then to identify associated markers that could be used in breeding programs to reduce the frequency of this defect in the broodstock.
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Affiliation(s)
- F Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - F Capoccioni
- Centro di ricerca 'Zootecnia e Acquacoltura', Consiglio per la Ricerca in Agricoltura e L'Analisi dell'Economia Agraria, Via Salaria 31, Monterotondo, Roma, 00015, Italy
| | - L Buttazzoni
- Centro di ricerca 'Zootecnia e Acquacoltura', Consiglio per la Ricerca in Agricoltura e L'Analisi dell'Economia Agraria, Via Salaria 31, Monterotondo, Roma, 00015, Italy
| | - V J Utzeri
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, Brindisi, 72016, Italy
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
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Wang Y, Jia X, Hsieh JCF, Monson MS, Zhang J, Shu D, Nie Q, Persia ME, Rothschild MF, Lamont SJ. Transcriptome Response of Liver and Muscle in Heat-Stressed Laying Hens. Genes (Basel) 2021; 12:genes12020255. [PMID: 33578825 PMCID: PMC7916550 DOI: 10.3390/genes12020255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Exposure to high ambient temperature has detrimental effects on poultry welfare and production. Although changes in gene expression due to heat exposure have been well described for broiler chickens, knowledge of the effects of heat on laying hens is still relatively limited. In this study, we profiled the transcriptome for pectoralis major muscle (n = 24) and liver (n = 24), during a 4-week cyclic heating experiment performed on layers in the early phase of egg production. Both heat-control and time-based contrasts were analyzed to determine differentially expressed genes (DEGs). Heat exposure induced different changes in gene expression for the two tissues, and we also observed changes in gene expression over time in the control animals suggesting that metabolic changes occurred during the transition from onset of lay to peak egg production. A total of 73 DEGs in liver were shared between the 3 h heat-control contrast, and the 4-week versus 3 h time contrast in the control group, suggesting a core set of genes that is responsible for maintenance of metabolic homeostasis regardless of the physiologic stressor (heat or commencing egg production). The identified DEGs improve our understanding of the layer’s response to stressors and may serve as targets for genetic selection in the future to improve resilience.
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Affiliation(s)
- Yan Wang
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Xinzheng Jia
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - John C. F. Hsieh
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
| | - Melissa S. Monson
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
| | - Jibin Zhang
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
- Toni Stephenson Lymphoma Center, City of Hope, Duarte, CA 91010, USA
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
| | - Michael E. Persia
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, USA;
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
| | - Susan J. Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (Y.W.); (X.J.); (J.C.F.H.); (M.S.M.); (J.Z.); (M.F.R.)
- Correspondence: ; Tel.: +1-515-294-4100
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Donnini EK, Walugembe M, Rothschild MF, Jergens AE, Allenspach K. An initial genome-wide investigation of protein-losing enteropathy in Gordon setters: Exploratory observations. Can J Vet Res 2021; 85:51-60. [PMID: 33390653 PMCID: PMC7747665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/14/2020] [Indexed: 06/12/2023]
Abstract
The objective of this preliminary study was to identify genomic regions that may predispose Gordon setters from the United Kingdom to familial protein-losing enteropathy (PLE) at a young age. A total of 106 related Gordon setters was used, including 6 affected dogs from an affected litter, 6 case controls from the same litter, 10 related/affected dogs, and 84 related/unaffected dogs. Genomic DNA was collected from each Gordon setter and extracted from buccal mucosal swabs. Genotyping of affected and unaffected dogs was carried out using the Canine Illumina HD SNP array and data generated were analyzed with PLINK software, using fixation index (Fst) and runs of homozygosity (ROH) methods. Pairwise Fst analyses between the affected and unaffected Gordon setter dogs identified various regions of differentiation on chromosomes 10, 18, 21, and 23 that contained several important genes. These regions revealed 5 candidate genes, including RARB, TTC7A, SOCS5, PIGF, and RHOD, that are associated with human inflammatory bowel disease (IBD) and could potentially be associated with PLE in Gordon setters. Run of homozygosity (ROH) analyses revealed additional unique regions on chromosomes 15 and 17. These regions contained genes SYT1, UCN, and FNDC that could also be potential candidates for PLE in Gordon setters. The biological functions of the identified genes provided initial insights into the pathophysiology of PLE. Further large-scale studies are warranted to investigate the possible causality of these genomic regions and any possible genetic markers that could be used in predicting susceptibility to PLE syndrome.
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Affiliation(s)
- Elle K Donnini
- Department of Veterinary Clinical Sciences (Donnini, Jergens, Allenspach), College of Veterinary Medicine, 1809 South Riverside Drive, Iowa State University, Ames, Iowa 50010, USA; Department of Animal Science (Walugembe, Rothschild), College of Agriculture and Life Sciences, 2255 H. Kildee Hall, Iowa State University, Ames, Iowa 20011, USA
| | - Muhammed Walugembe
- Department of Veterinary Clinical Sciences (Donnini, Jergens, Allenspach), College of Veterinary Medicine, 1809 South Riverside Drive, Iowa State University, Ames, Iowa 50010, USA; Department of Animal Science (Walugembe, Rothschild), College of Agriculture and Life Sciences, 2255 H. Kildee Hall, Iowa State University, Ames, Iowa 20011, USA
| | - Max F Rothschild
- Department of Veterinary Clinical Sciences (Donnini, Jergens, Allenspach), College of Veterinary Medicine, 1809 South Riverside Drive, Iowa State University, Ames, Iowa 50010, USA; Department of Animal Science (Walugembe, Rothschild), College of Agriculture and Life Sciences, 2255 H. Kildee Hall, Iowa State University, Ames, Iowa 20011, USA
| | - Albert E Jergens
- Department of Veterinary Clinical Sciences (Donnini, Jergens, Allenspach), College of Veterinary Medicine, 1809 South Riverside Drive, Iowa State University, Ames, Iowa 50010, USA; Department of Animal Science (Walugembe, Rothschild), College of Agriculture and Life Sciences, 2255 H. Kildee Hall, Iowa State University, Ames, Iowa 20011, USA
| | - Karin Allenspach
- Department of Veterinary Clinical Sciences (Donnini, Jergens, Allenspach), College of Veterinary Medicine, 1809 South Riverside Drive, Iowa State University, Ames, Iowa 50010, USA; Department of Animal Science (Walugembe, Rothschild), College of Agriculture and Life Sciences, 2255 H. Kildee Hall, Iowa State University, Ames, Iowa 20011, USA
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Chinchilla-Vargas J, Kramer L, Lester TD, Lester TD, Backes EA, Anschutz K, Decker JE, Stalder KJ, Rothschild MF, Koltes JE. 94 Genetic basis of blood traits in beef cattle and their relationship to production traits at weaning. J Anim Sci 2020. [DOI: 10.1093/jas/skaa054.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Disease represents one of the main factors that determine profitability in animal production. Previous research has observed significant correlations between blood cell counts and the animal’s health status. We hypothesize that blood cell traits may be an effective indicator of performance in beef cattle. Complete blood counts were recorded from approximately 500 crossbred animals at weaning (Angus background crossed with Hereford, Charolais, Sim-Angus, Brangus) born between 2015 and 2016 and raised on toxic or novel tall fescue on three different farms. The animals were genotyped at an approximate density of 50,000 SNPs and the genotypes were imputed to an approximate density of 200,000 SNPs. Heritability, genetic and phenotypic correlations were estimated for 15 blood and 4 production traits across and within environments. Finally, with the objective of identifying the genetic basis underlying the different blood traits, a genome wide association study (GWAS) was performed for all traits. Heritability estimates ranged from 0.11 to 0.60, and generally weak phenotypic correlations and strong genetic correlations were found, however these parameters varied across environments, pointing to GxE interactions. GWAS identified 90 1 Mb windows that explained 0.5% or more of the estimated genetic variance for at least 1 trait with 21 windows overlapping two or more traits. Further research efforts include identifying underlying candidate genes for traits and comparing toxic and novel fescue effects on blood traits. It appears that blood traits have weak phenotypic correlations but strong genetic correlations among themselves, as evidenced by important overlapping regions of genetic control for similar blood traits. However, blood traits have limited potential as indicator traits for productivity.
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Chinchilla-Vargas J, Kramer LM, Tucker JD, Hubbell DS, Powell JG, Lester TD, Backes EA, Anschutz K, Decker JE, Stalder KJ, Rothschild MF, Koltes JE. Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning. Front Genet 2020; 11:717. [PMID: 32719722 PMCID: PMC7350949 DOI: 10.3389/fgene.2020.00717] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022] Open
Abstract
The objectives of this study were to explore the usefulness of blood-based traits as indicators of health and performance in beef cattle at weaning and identify the genetic basis underlying the different blood parameters obtained from complete blood counts (CBCs). Disease costs represent one of the main factors determining profitability in animal production. Previous research has observed associations between blood cell counts and an animal’s health status in some species. CBC were recorded from approximately 570 Angus based, crossbred beef calves at weaning born between 2015 and 2016 and raised on toxic or novel tall fescue. The calves (N = ∼600) were genotyped at a density of 50k SNPs and the genotypes (N = 1160) were imputed to a density of 270k SNPs. Genetic parameters were estimated for 15 blood and 4 production. Finally, with the objective of identifying the genetic basis underlying the different blood-based traits, genome-wide association studies (GWAS) were performed for all traits. Heritability estimates ranged from 0.11 to 0.60, and generally weak phenotypic correlations and strong genetic correlations were observed among blood-based traits only. Genome-wide association study identified ninety-one 1-Mb windows that accounted for 0.5% or more of the estimated genetic variance for at least 1 trait with 21 windows overlapping across two or more traits (explaining more than 0.5% of estimated genetic variance for two or more traits). Five candidate genes have been identified in the most interesting overlapping regions related to blood-based traits. Overall, this study represents one of the first efforts represented in scientific literature to identify the genetic basis of blood cell traits in beef cattle. The results presented in this study allow us to conclude that: (1) blood-based traits have weak phenotypic correlations but strong genetic correlations among themselves. (2) Blood-based traits have moderate to high heritability. (3) There is evidence of an important overlap of genetic control among similar blood-based traits which will allow for their use in improvement programs in beef cattle.
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Affiliation(s)
| | - Luke M Kramer
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - John D Tucker
- Division of Agriculture, Livestock and Forestry Research Station, Batesville, AR, United States
| | - Donald S Hubbell
- Division of Agriculture, Livestock and Forestry Research Station, Batesville, AR, United States
| | - Jeremy G Powell
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Toby D Lester
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Elizabeth A Backes
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Karen Anschutz
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Jared E Decker
- Division of Animal Science, University of Missouri, Columbia, MO, United States
| | - Kenneth J Stalder
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
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10
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Muchadeyi FC, Ibeagha-Awemu EM, Javaremi AN, Gutierrez Reynoso GA, Mwacharo JM, Rothschild MF, Sölkner J. Editorial: Why Livestock Genomics for Developing Countries Offers Opportunities for Success. Front Genet 2020; 11:626. [PMID: 32676098 PMCID: PMC7333237 DOI: 10.3389/fgene.2020.00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 05/26/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Farai C Muchadeyi
- Agricultural Research Council-Biotechnology Platform, Pretoria, South Africa
| | | | | | | | - Joram M Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
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11
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Cogné B, Latypova X, Senaratne LDS, Martin L, Koboldt DC, Kellaris G, Fievet L, Le Meur G, Caldari D, Debray D, Nizon M, Frengen E, Bowne SJ, Cadena EL, Daiger SP, Bujakowska KM, Pierce EA, Gorin M, Katsanis N, Bézieau S, Petersen-Jones SM, Occelli LM, Lyons LA, Legeai-Mallet L, Sullivan LS, Davis EE, Isidor B, Buckley RM, Aberdein D, Alves PC, Barsh GS, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Häggström J, Harvey RJ, Hasegawa D, Haase B, Helps CR, Hernandez I, Hytönen MK, Kaukonen M, Kaelin CB, Kosho T, Leclerc E, Lear TL, Leeb T, Li RH, Lohi H, Longeri M, Magnuson MA, Malik R, Mane SP, Munday JS, Murphy WJ, Pedersen NC, Rothschild MF, Rusbridge C, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y. Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy. Am J Hum Genet 2020; 106:893-904. [PMID: 32386558 DOI: 10.1016/j.ajhg.2020.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/02/2020] [Indexed: 11/26/2022] Open
Abstract
Kinesin-2 enables ciliary assembly and maintenance as an anterograde intraflagellar transport (IFT) motor. Molecular motor activity is driven by a heterotrimeric complex comprised of KIF3A and KIF3B or KIF3C plus one non-motor subunit, KIFAP3. Using exome sequencing, we identified heterozygous KIF3B variants in two unrelated families with hallmark ciliopathy phenotypes. In the first family, the proband presents with hepatic fibrosis, retinitis pigmentosa, and postaxial polydactyly; he harbors a de novo c.748G>C (p.Glu250Gln) variant affecting the kinesin motor domain encoded by KIF3B. The second family is a six-generation pedigree affected predominantly by retinitis pigmentosa. Affected individuals carry a heterozygous c.1568T>C (p.Leu523Pro) KIF3B variant segregating in an autosomal-dominant pattern. We observed a significant increase in primary cilia length in vitro in the context of either of the two mutations while variant KIF3B proteins retained stability indistinguishable from wild type. Furthermore, we tested the effects of KIF3B mutant mRNA expression in the developing zebrafish retina. In the presence of either missense variant, rhodopsin was sequestered to the photoreceptor rod inner segment layer with a concomitant increase in photoreceptor cilia length. Notably, impaired rhodopsin trafficking is also characteristic of recessive KIF3B models as exemplified by an early-onset, autosomal-recessive, progressive retinal degeneration in Bengal cats; we identified a c.1000G>A (p.Ala334Thr) KIF3B variant by genome-wide association study and whole-genome sequencing. Together, our genetic, cell-based, and in vivo modeling data delineate an autosomal-dominant syndromic retinal ciliopathy in humans and suggest that multiple KIF3B pathomechanisms can impair kinesin-driven ciliary transport in the photoreceptor.
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12
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Barrett NW, Rowland K, Schmidt CJ, Lamont SJ, Rothschild MF, Ashwell CM, Persia ME. Effects of acute and chronic heat stress on the performance, egg quality, body temperature, and blood gas parameters of laying hens. Poult Sci 2020; 98:6684-6692. [PMID: 31573614 PMCID: PMC8914008 DOI: 10.3382/ps/pez541] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [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: 04/30/2019] [Accepted: 09/09/2019] [Indexed: 12/29/2022] Open
Abstract
The goal of this experiment was to measure the physiological response of individual laying hens exposed to heat stress (HS). Performance, egg quality, body temperature (BT), and blood chemistry of laying hens were individually recorded before and after various intervals of daily cyclic HS. In total, 407 18-week-old W-36 parent-line laying hens (Hy-Line International, Dallas Center, IA) were housed individually in battery cages. After an acclimation period, baseline data were collected from 22 to 24-wk before the hens were subjected to a daily cyclic HS consisting of 7 h at 35°C returning to 30°C for the remaining 17 h/D from 24 to 28-wk of age. Eggs were collected and individually weighed daily. Feed intake (FI), egg production (EP), egg weights, egg mass, BW, and feed efficiency (FE) (g egg/kg FI) were calculated over 2-wk time periods. Eggs were collected for quality assessment the day before HS began, the 2nd day of HS, and on a weekly basis throughout the 4-wk HS. Blood was collected and BT measured the day before heat HS was initiated, on the first day of HS, and again at 2 and 4-wk of HS. Blood PCO2 and iCa decreased, and blood pH increased within 4 to 6 h of HS (P ≤ 0.01). Shell weights decreased with acute HS, possibly due to the reduction in blood iCa (P ≤ 0.01). After 4-wk of HS the blood pH returned to pre-HS levels but iCa remained decreased (P ≤ 0.01). Shell weights remained low and Haugh units decreased after 2 and 4-wk of HS (P ≤ 0.01). Feed efficiency was increased and FI, EP, and BW decreased by 2-wk of HS and remained low through 4-wk (P ≤ 0.01). The cyclic HS had a significant effect on the performance, egg quality, and blood chemistry over the 4-wk HS.
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Affiliation(s)
| | - Kaylee Rowland
- Department of Animal Science, Iowa State University, Ames 50011
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames 50011
| | | | - Chris M Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh 27695
| | - Michael E Persia
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg 24061
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13
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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Utzeri VJ, Bovo S, Schiavo G, Caggiano M, Fontanesi L, Rothschild MF. Identification of a major locus determining a pigmentation defect in cultivated gilthead seabream (Sparus aurata). Anim Genet 2020; 51:319-323. [PMID: 31900984 DOI: 10.1111/age.12890] [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] [Accepted: 11/15/2019] [Indexed: 12/30/2022]
Abstract
The gilthead seabream (Sparus aurata) is an important cultivated species in the Mediterranean area. A major problem for the gilthead seabream aquaculture sector derives from the high frequency of phenotypic abnormalities, including discolorations. In this study, we applied a whole-genome resequencing approach to identify a genomic region affecting a pigmentation defect that occurred in a cultivated S. aurata population. Two equimolar DNA pools were constructed using DNA extracted from 30 normally coloured and 21 non-pigmented fish collected among the offspring of the same broodstock nucleus. Whole-genome resequencing reads from the two DNA pools were aligned to the S. aurata draft genome and variant calling was performed. A whole-genome heterozygosity scan from single pool sequencing data highlighted a peak of reduced heterozygosity of approximately 5 Mbp on chromosome 6 in the non-pigmented pool that was not present in the normally coloured pool. The comparison of the non-pigmented with the normally coloured fish using a whole-genome FST analysis detected three main regions within the coordinates previously detected with the heterozygosity analysis. The results support the presence of a major locus affecting this discoloration defect in this fish population. The results of this study have practical applications, including the possibility of eliminating this defect from the breeding stock, with direct economic advantages derived from the reduction of discarded fry. Other studies are needed to identify the candidate gene and the causative mutation, which could add information to understand the complex biology of fish pigmentation.
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Affiliation(s)
- F Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.,Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - F Capoccioni
- Centro di ricerca di Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Rome, 00198, Italy
| | - L Buttazzoni
- Centro di ricerca di Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Rome, 00198, Italy
| | - V J Utzeri
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - M Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, Brindisi, 72016, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA
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14
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Rowland K, Persia ME, Rothschild MF, Schmidt C, Lamont SJ. Venous blood gas and chemistry components are moderately heritable in commercial white egg-laying hens under acute or chronic heat exposure. Poult Sci 2019; 98:3426-3430. [PMID: 31002114 PMCID: PMC6698185 DOI: 10.3382/ps/pez204] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/21/2019] [Indexed: 11/20/2022] Open
Abstract
Heat stress has a large negative impact on poultry around the world in both intensive and small-scale production systems. Better understanding of genetic factors contributing to response to high ambient temperatures would provide a basis to develop strategies for alleviating negative impacts of heat on poultry production. The objective of this work was to characterize the genetic control (heritability estimate and quantitative trait loci (QTL)) of blood chemistry components before and after exposure to acute and chronic high ambient temperature in a commercial egg laying line Hy-Line W-36 female parent line mature hens were exposed to 4 wk of daily cyclic heat exposure. Blood was collected pre-heat, on the first day of heat, and 2 and 4 wk post heat initiation and analyzed immediately using an i-STAT® hand-held blood analyzer. Thirteen blood components were quantified at the 4 time points: pH, pCO2, pO2, HCO3, TCO2, sO2, iCa, Na, K, base excess, glucose, "hematocrit" (estimated from blood electrical conductivity, BEC), and "hemoglobin" (calculated from BEC). Heritabilities were estimated using genomic relationship information obtained from 600k SNP chip data. All 13 parameters exhibited a significant change after 5 h of heat exposure and most did not return to pre-heat levels throughout the duration of the study. Eight parameters (base excess, glucose, hemoglobin, HCO3, hematocrit, K, pCO2, TCO2) had heritability estimates differing from zero at one or more time points (0.21 to 0.45). The traits with significant heritability would be good candidates for use as biomarkers in a selection program if they are correlated with traits of economic importance that are more difficult to measure. QTL were identified for nine of the traits at one or more time point. These nine traits, however, did not have significant heritability estimates suggesting that while some QTL have been identified their effects are generally small.
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Affiliation(s)
- Kaylee Rowland
- Department of Animal Science, Iowa State University, Ames, IA 50011
| | - Michael E Persia
- Virginia Tech, Department of Animal and Poultry Sciences, Blacksburg, VA 24061
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011
| | - Carl Schmidt
- University of Delaware, Animal and Food Sciences, Newark, DE 19716
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011
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15
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Dolebo AT, Khayatzadeh N, Melesse A, Wragg D, Rekik M, Haile A, Rischkowsky B, Rothschild MF, Mwacharo JM. Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries). Mamm Genome 2019; 30:339-352. [PMID: 31758253 PMCID: PMC6884434 DOI: 10.1007/s00335-019-09820-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 09/04/2019] [Accepted: 11/12/2019] [Indexed: 02/05/2023]
Abstract
Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.
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Affiliation(s)
- Asrat Tera Dolebo
- Southern Agricultural Research Institute (SARI), P.O. Box 06, Hawassa, Ethiopia
- Department of Animal and Range Sciences, Hawassa University, P.O Box 5, Hawassa, Ethiopia
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences (BOKU), Gregor-Mendel-Strasse, 1180, Vienna, Austria
| | - Aberra Melesse
- Department of Animal and Range Sciences, Hawassa University, P.O Box 5, Hawassa, Ethiopia
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, UK
| | - Mourad Rekik
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Barbara Rischkowsky
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia.
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16
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Talenti A, Bertolini F, Williams J, Moaeen-Ud-Din M, Frattini S, Coizet B, Pagnacco G, Reecy J, Rothschild MF, Crepaldi P. Genomic Analysis Suggests KITLG is Responsible for a Roan Pattern in two Pakistani Goat Breeds. J Hered 2019; 109:315-319. [PMID: 29099936 DOI: 10.1093/jhered/esx093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/25/2017] [Indexed: 11/12/2022] Open
Abstract
The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been carried out to find the gene(s) that control(s) roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goat breeds that did not have the same coat color pattern (Group B). Runs of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6, and 12 were considered unique among the group A versus group B comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats.
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Affiliation(s)
- Andrea Talenti
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | | | - Jamie Williams
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Muhammad Moaeen-Ud-Din
- Laboratories of Animal Breeding & Genetics, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Stefano Frattini
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Coizet
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Giulio Pagnacco
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Paola Crepaldi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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17
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Bertolini F, Chinchilla-Vargas J, Khadse JR, Juneja A, Deshpande PD, Bhave K, Potdar V, Kakramkar PM, Karlekar AR, Pande AB, Fernando RL, Rothschild MF. Marker discovery and associations with β-carotene content in Indian dairy cattle and buffalo breeds. J Dairy Sci 2019; 102:10039-10055. [PMID: 31477308 PMCID: PMC7753891 DOI: 10.3168/jds.2019-16361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/24/2019] [Accepted: 06/30/2019] [Indexed: 01/17/2023]
Abstract
Vitamin A is essential for human health, but current intake levels in many developing countries such as India are too low due to malnutrition. According to the World Health Organization, an estimated 250 million preschool children are vitamin A deficient globally. This number excludes pregnant women and nursing mothers, who are particularly vulnerable. Efforts to improve access to vitamin A are key because supplementation can reduce mortality rates in young children in developing countries by around 23%. Three key genes, BCMO1, BCO2, and SCARB1, have been shown to be associated with the amount of β-carotene (BC) in milk. Whole-genome sequencing reads from the coordinates of these 3 genes in 202 non-Indian cattle (141 Bos taurus, 61 Bos indicus) and 35 non-Indian buffalo (Bubalus bubalis) animals from several breeds were collected from data repositories. The number of SNP detected in the coding regions of these 3 genes ranged from 16 to 26 in the 3 species, with 5 overlapping SNP between B. taurus and B. indicus. All these SNP together with 2 SNP in the upstream part of the gene but already present in dbSNP (https://www.ncbi.nlm.nih.gov/projects/SNP/) were used to build a custom Sequenom array. Blood for DNA and milk samples for BC were obtained from 2,291 Indian cows of 5 different breeds (Gir, Holstein cross, Jersey Cross, Tharparkar, and Sahiwal) and 2,242 Indian buffaloes (Jafarabadi, Murrah, Pandharpuri, and Surti breeds). The DNA was extracted and genotyped with the Sequenom array. For each individual breed and the combined breeds, SNP with an association that had a P-value <0.3 in the first round of linear analysis were included in a second step of regression analyses to determine allele substitution effects to increase the content of BC in milk. Additionally, an F-test for all SNP within gene was performed with the objective of determining if overall the gene had a significant effect on the content of BC in milk. The analyses were repeated using a Bayesian approach to compare and validate the previous frequentist results. Multiple significant SNP were found using both methodologies with allele substitution effects ranging from 6.21 (3.13) to 9.10 (5.43) μg of BC per 100 mL of milk. Total gene effects exceeded the mean BC value for all breeds with both analysis approaches. The custom panel designed for genes related to BC production demonstrated applicability in genotyping of cattle and buffalo in India and may be used for cattle or buffalo from other developing countries. Moreover, the recommendation of selection for significant specific alleles of some gene markers provides a route to effectively increase the BC content in milk in the Indian cattle and buffalo populations.
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Affiliation(s)
- F Bertolini
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, 806 Stange Road, Ames 50011; National Institute of Aquatic Resources, Technical University of Denmark, Kemitoryet 2800, KGs. Lyngby, Denmark
| | - J Chinchilla-Vargas
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, 806 Stange Road, Ames 50011
| | - J R Khadse
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - A Juneja
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - P D Deshpande
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - K Bhave
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - V Potdar
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - P M Kakramkar
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - A R Karlekar
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - A B Pande
- Bharatiya Agro Industries Foundation, Development Research Foundation, Bhavan, Dr. Manibhai Desai Nagar Warje, Pune 411058, India
| | - Rohan L Fernando
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, 806 Stange Road, Ames 50011
| | - M F Rothschild
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, 806 Stange Road, Ames 50011.
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18
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Stock JD, Supakorn C, Calderon Diaz JA, Rothschild MF, Stalder KJ. 19 Overview of the National Pork Board replacement gilt feet and leg evaluation trial. J Anim Sci 2019. [DOI: 10.1093/jas/skz122.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Replacement gilt feet and leg conformation traits are subjectively evaluated at early ages (150 d) in order to select acceptable replacements. The objectives of this study were to: 1) evaluate replacement gilt feet and leg conformation (FLC) using subjective and objective measurement methods, 2) estimate objective joint angle changes over two parities, and 3) evaluate the effect of three diets differing in standardized ileal digestible (SID) lysine concentrations on FLC traits using the objective evaluation method. Crossbred Large White × Landrace gilts (n = 641) were used. Gilts were moved to GDU at 77 days-of-age and randomly allotted to three ad libitum fed dietary treatments providing similar ME but differing in SID lysine concentrations (low, medium, and high) during the grow-finisher period. All animals received common gestation and lactation diets. Feet and leg conformation traits were evaluated at 100 d, 200 d, 1st litter (392 ± 25 d) and 2nd litter (548 ± 49 d) weaning events. Subjective evaluation was done on a scale from 1 to 5. Data were analyzed using mixed linear model methods. The majority of gilts received the intermediate score (i.e. 3) when joint angles were subjectively evaluated. No differences (P ≥ 0.05) were observed for knee, front pastern and hock objective joint angles between subjective scores assigned. Differences in subjectively evaluated rear pastern (P < 0.05) were observed, where objective joint angles associated with scores of ≤ 2 and 3 were lower than score of ≥ 4. There was no interaction between dietary treatment and objective evaluation time-period for any FLC traits studied (P > 0.05). Females with greater knee, hock, front and rear pastern objective joint angles at 100 d of age, continued to have greater joint angles (0.2 ± 0.04 degrees; P < 0.001) later in life. Front and rear pastern joint angles decreased (P < 0.001) and hock joint angles increased from 100 d to end of study (P < 0.001).
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Affiliation(s)
| | - China Supakorn
- Teagasc Moorepark Grassland Research and Innovation Centre
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19
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Chinchilla-Vargas J, Kramer LM, Tucker JD, Hubbell DS, Powell JG, Lester TD, Backes EA, Anschutz K, Stalder KJ, Rothschild MF, Koltes JE. PSIII-12 Peripheral blood parameters as proxies of performance in beef cattle: Heritability and genetic correlations between peripheral blood parameters and performance phenotypes. J Anim Sci 2019. [DOI: 10.1093/jas/skz122.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Disease incidence and feed costs are two main drivers in cattle production operations. Frequently environmental stressors such as fescue toxicosis have negative effects on livestock performance and health. Low-cost methods to measure these types of health and stress response phenotypes are needed to capture their impact on production traits. Previous research has correlated white blood cell parameters to disease resistance in beef cattle. Based on this, blood parameters at weaning may be candidates that could be a proxy for selection and identification of high-performance animals in commercial settings. To identify candidate blood parameters, blood samples were collected at weaning on approximately 500 crossbred animals (Angus background crossed with Hereford, Charolais, Sim-Angus, Brangus) born between 2015 and 2016 and raised on toxic fescue. The animals were also genotyped at an approximate density of 50,000 SNPs. Complete blood counts (CBC) were obtained the blood samples and heritabilities for 15 peripheral blood parameters were estimated. For the CBC traits that were measured, heritabilities ranged from low to moderate (0.02 to 0.35). Based on current findings, a substantial genetic component for some CBC parameters exists and selection could be effective at improving these traits. Further research will estimate genetic correlations between peripheral blood parameters, weaning weight and average daily gain (ADG) with the intention of identifying correlated traits to be used in commercial selection programs.
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Rowland K, Ashwell CM, Persia ME, Rothschild MF, Schmidt C, Lamont SJ. Genetic analysis of production, physiological, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data. Genet Sel Evol 2019; 51:31. [PMID: 31238874 PMCID: PMC6593552 DOI: 10.1186/s12711-019-0474-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/06/2018] [Accepted: 06/13/2019] [Indexed: 12/02/2022] Open
Abstract
Background Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In this study, we recorded several production traits, feed intake, body weight, digestibility, and egg quality of 400 commercial white egg-laying hens before and during a 4-week heat treatment. For the phenotypes that had estimated heritabilities (using 600k SNP chip data) higher than 0, SNP associations were tested using the same 600k genotype data. Results Seventeen phenotypes had heritability estimates higher than 0, including measurements at various time points for feed intake, feed efficiency, body weight, albumen weight, egg quality expressed in Haugh units, egg mass, and also for change in egg mass from prior to heat exposure to various time points during the 4-week heat treatment. Quantitative trait loci (QTL) were identified for 10 of these 17 phenotypes. Some of the phenotypes shared QTL including Haugh units before heat exposure and after 4 weeks of heat treatment. Conclusions Estimated heritabilities differed from 0 for 17 traits, which indicates that they are under genetic control and that there is potential for improving these traits through selective breeding. The association of different QTL with the same phenotypes before heat exposure and during heat treatment indicates that genomic control of traits under heat stress is distinct from that under thermoneutral conditions. This study contributes to the knowledge on the genomic control of response to heat stress in laying hens. Electronic supplementary material The online version of this article (10.1186/s12711-019-0474-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaylee Rowland
- Department of Animal Science, Iowa State University, Ames, USA
| | - Chris M Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, USA
| | - Michael E Persia
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, USA
| | | | - Carl Schmidt
- University of Delaware, Animal and Food Sciences, Newark, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, USA.
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21
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Elbeltagy AR, Bertolini F, Fleming DS, Van Goor A, Ashwell CM, Schmidt CJ, Kugonza DR, Lamont SJ, Rothschild MF. Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes. Front Genet 2019; 10:376. [PMID: 31139205 PMCID: PMC6518202 DOI: 10.3389/fgene.2019.00376] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 05/19/2018] [Accepted: 04/09/2019] [Indexed: 01/09/2023] Open
Abstract
Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations' ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda-Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda-Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.
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Affiliation(s)
- Ahmed R Elbeltagy
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Damarius S Fleming
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Angelica Van Goor
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Institute of Food Production and Sustainability, National Institute of Food and Agriculture, United States Department of Agriculture, Washington, DC, United States
| | - Chris M Ashwell
- Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | - Donald R Kugonza
- Department of Agricultural Production, Makerere University, Kampala, Uganda
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
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22
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Walugembe M, Bertolini F, Dematawewa CMB, Reis MP, Elbeltagy AR, Schmidt CJ, Lamont SJ, Rothschild MF. Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions. Front Genet 2019; 9:737. [PMID: 30693019 PMCID: PMC6339939 DOI: 10.3389/fgene.2018.00737] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 04/13/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022] Open
Abstract
Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal's immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of São Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix Axiom®600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments.
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Affiliation(s)
- Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | - Matheus P Reis
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil
| | - Ahmed R Elbeltagy
- Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt
| | - Carl J Schmidt
- Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
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23
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Zurbrigg K, van Dreumel T, Rothschild MF, Alves D, Friendship RM, O'Sullivan TL. Rapid Communication: A comparison of cardiac lesions and heart weights from market pigs that did and did not die during transport to one Ontario abattoir. Transl Anim Sci 2018; 3:149-154. [PMID: 32704787 PMCID: PMC7200518 DOI: 10.1093/tas/txy124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/20/2018] [Indexed: 11/15/2022] Open
Abstract
In-transit losses of market hogs represent a small proportion of all market-weight pigs shipped in a year. This suggests that individual pig factors may be a significant cause of in-transit losses along with more traditionally considered environmental and transport factors. An investigation was performed to determine whether cardiac pathology and heart weights were associated with pigs that did or did not die during transport to an abattoir. The hearts from 70 pigs that died in-transit to one Ontario abattoir and 388 pigs that arrived alive were collected and examined. Hearts from pigs that died during transport demonstrated greater frequencies of cardiac lesions (P < 0.05). These included hypertrophy of ventricle walls (Left: 97% vs. 64%; Right: 86% vs. 57%), dilation of ventricle chambers (Left: 79% vs. 0.5%; Right: 100% vs. 5%), and dilation of the pulmonary artery and aorta (59% vs. 1.5%). Total heart weight to body weight ratios were increased (3.6 vs. 3.3 g/kg) and left ventricle plus septum weight over right ventricle weight ratio was decreased in pigs that died during transport over non–in-transit loss pigs (2.5 vs. 2.8; P < 0.05). This may indicate reduced cardiac function in hogs that died during transport. Pigs with reduced cardiac function would have exercise intolerance and be more susceptible to death during transport due to the increased cardiac workload required during sorting, loading, and transport of the pigs to the abattoir. Further research to quantify cardiac function in pigs with cardiac lesions or abnormal heart weight ratios is warranted.
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Affiliation(s)
- Kathy Zurbrigg
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | | | - David Alves
- Veterinary Epidemiology Consultant, Elora, ON, Canada
| | - Robert M Friendship
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Terri L O'Sullivan
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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24
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Bertolini F, Servin B, Talenti A, Rochat E, Kim ES, Oget C, Palhière I, Crisà A, Catillo G, Steri R, Amills M, Colli L, Marras G, Milanesi M, Nicolazzi E, Rosen BD, Van Tassell CP, Guldbrandtsen B, Sonstegard TS, Tosser-Klopp G, Stella A, Rothschild MF, Joost S, Crepaldi P. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genet Sel Evol 2018; 50:57. [PMID: 30449276 PMCID: PMC6240954 DOI: 10.1186/s12711-018-0421-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [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: 11/10/2017] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Claire Oget
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Isabelle Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Gennaro Catillo
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Roberto Steri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
| | | | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | | | - Gwenola Tosser-Klopp
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Stella
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - the AdaptMap consortium
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Recombinetics Inc, St Paul, 55104 MN USA
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
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Bertolini F, Cardoso TF, Marras G, Nicolazzi EL, Rothschild MF, Amills M. Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats. Genet Sel Evol 2018; 50:59. [PMID: 30449279 PMCID: PMC6241033 DOI: 10.1186/s12711-018-0424-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [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: 11/22/2017] [Accepted: 10/15/2018] [Indexed: 01/15/2023] Open
Abstract
Background Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats. Results The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH (< 3 Mb) are the most frequent ones. Our data also indicate that ~ 60% of the breeds display low FROH coefficients (< 0.10), while ~ 30 and ~ 10% of the goat populations show moderate (0.10 < FROH < 0.20) or high (> 0.20) FROH values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection. Conclusions Patterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; FROH < 0.15) are similar in goats from different geographic areas. The increased homozygosity in local breeds is the consequence of their small population size and geographic isolation as well as of founder effects and recent inbreeding. The existence of three ROH hotspots that co-localize with signatures of selection demonstrates that selection has also played an important role in increasing the homozygosity of specific regions in the goat genome. Finally, most of the goat breeds analysed in this work display low levels of homozygosity, which is favourable for their genetic management and viability. Electronic supplementary material The online version of this article (10.1186/s12711-018-0424-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. .,National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark.
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900, Lodi, Italy
| | | | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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Colli L, Milanesi M, Talenti A, Bertolini F, Chen M, Crisà A, Daly KG, Del Corvo M, Guldbrandtsen B, Lenstra JA, Rosen BD, Vajana E, Catillo G, Joost S, Nicolazzi EL, Rochat E, Rothschild MF, Servin B, Sonstegard TS, Steri R, Van Tassell CP, Ajmone-Marsan P, Crepaldi P, Stella A. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes. Genet Sel Evol 2018; 50:58. [PMID: 30449284 PMCID: PMC6240949 DOI: 10.1186/s12711-018-0422-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [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: 02/02/2018] [Accepted: 10/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. RESULTS A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. CONCLUSIONS After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.
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Affiliation(s)
- Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy. .,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy.
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,School of Veterinary Medicine, Department of Support, Production and Animal Health, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, USA.,National Institute of Aquatic Resources, Technical University of Denmark, DTU, Lyngby, Denmark
| | - Minhui Chen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark.,Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alessandra Crisà
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Kevin Gerard Daly
- Population Genetics Lab, Smurfit Institute of Genetics, Trinity College of Dublin, Dublin, Ireland
| | - Marcello Del Corvo
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Elia Vajana
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Roberto Steri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Lodi, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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Kim KS, Seibert JT, Edea Z, Graves KL, Kim ES, Keating AF, Baumgard LH, Ross JW, Rothschild MF. Characterization of the acute heat stress response in gilts: III. Genome-wide association studies of thermotolerance traits in pigs. J Anim Sci 2018; 96:2074-2085. [PMID: 29669012 DOI: 10.1093/jas/sky131] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 04/12/2018] [Indexed: 01/09/2023] Open
Abstract
Heat stress is one of the limiting factors negatively affecting pig production, health, and fertility. Characterizing genomic regions responsible for variation in HS tolerance would be useful in identifying important genetic factor(s) regulating physiological responses to HS. In the present study, we performed genome-wide association analyses for respiration rate (RR), rectal temperature (TR), and skin temperature (TS) during HS in 214 crossbred gilts genotyped for 68,549 single nucleotide polymorphisms (SNP) using the Porcine SNP 70K BeadChip. Considering the top 0.1% smoothed phenotypic variances explained by SNP windows, we detected 26, 26, 21, and 14 genes that reside within SNPs explaining the largest proportion of variance (top 25 SNP windows) and associated with change in RR (ΔRR) from thermoneutral (TN) conditions to HS environment, as well as the change in prepubertal TR (ΔTR), change in postpubertal ΔTR, and change in TS (ΔTS), respectively. The region between 28.85 Mb and 29.10 Mb on chromosome 16 explained about 0.05% of the observed variation for ΔRR. The growth hormone receptor (GHR) gene resides in this region and is associated with the HS response. The other important candidate genes associated with ΔRR (PAIP1, NNT, and TEAD4), ΔTR (LIMS2, TTR, and TEAD4), and ΔTS (ERBB4, FKBP1B, NFATC2, and ATP9A) have reported roles in the cellular stress response. The SNP explaining the largest proportion of variance and located within and in the vicinity of genes were related to apoptosis or cellular stress and are potential candidates that underlie the physiological response to HS in pigs.
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Affiliation(s)
- Kwan-Suk Kim
- Department of Animal Science, Iowa State University, Ames, IA.,Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Jacob T Seibert
- Department of Animal Science, Iowa State University, Ames, IA
| | - Zewde Edea
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Kody L Graves
- Department of Animal Science, Iowa State University, Ames, IA
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, Ames, IA.,Recombinetics, St. Paul, MN
| | | | | | - Jason W Ross
- Department of Animal Science, Iowa State University, Ames, IA
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Edea Z, Dadi H, Dessie T, Uzzaman MR, Rothschild MF, Kim ES, Sonstegard TS, Kim KS. Genome-wide scan reveals divergent selection among taurine and zebu cattle populations from different regions. Anim Genet 2018; 49:550-563. [PMID: 30246258 DOI: 10.1111/age.12724] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 01/02/2023]
Abstract
In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (FST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (FST ≥ 0.53), representing the top 1% smoothed FST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.
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Affiliation(s)
- Z Edea
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea
| | - H Dadi
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia
| | - T Dessie
- International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - M R Uzzaman
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea.,Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, S. Korea
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - E-S Kim
- Recombinetics, Inc., Saint Paul, MN, 55104, USA
| | | | - K-S Kim
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea
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29
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Stock JD, Calderón Díaz JA, Rothschild MF, Mote BE, Stalder KJ. Objective evaluation of female feet and leg joint conformation at time of selection and post first parity in swine1. J Anim Sci 2018; 96:3549-3557. [PMID: 29893887 PMCID: PMC6127821 DOI: 10.1093/jas/sky227] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/08/2018] [Indexed: 11/14/2022] Open
Abstract
Feet and legs of replacement females were objectively evaluated at selection, i.e., approximately 150 d of age (n = 319) and post first parity, i.e., any time after weaning of first litter and before second parturition (n = 277) to 1) compare feet and leg joint angle ranges between selection and post first parity; 2) identify feet and leg joint angle differences between selection and first 3 wk of second gestation; 3) identify feet and leg joint angle differences between farms and gestation days during second gestation; and 4) obtain genetic variance components for conformation angles for the two time points measured. Angles for carpal joint (knee), metacarpophalangeal joint (front pastern), metatarsophalangeal joint (rear pastern), tarsal joint (hock), and rear stance were measured using image analysis software. Between selection and post first parity, significant differences were observed for all joints measured (P < 0.05). Knee, front and rear pastern angles were less (more flexion), and hock angles were greater (less flexion) as age progressed (P < 0.05), while the rear stance pattern was less (feet further under center) at selection than post first parity (only including measures during first 3 wk of second gestation). Only using post first parity leg conformation information, farm was a significant source of variation for front and rear pasterns and rear stance angle measurements (P < 0.05). Knee angle was less (more flexion; P < 0.05) as gestation age progressed. Heritability estimates were low to moderate (0.04-0.35) for all traits measured across time points. Genetic correlations between the same joints at different time points were high (>0.8) between the front leg joints and low (<0.2) between the rear leg joints. High genetic correlations between time points indicate that the trait can be considered the same at either time point, and low genetic correlations indicate that the trait at different time points should be considered as two separate traits. Minimal change in the front leg suggests conformation traits that remain between selection and post first parity, while larger changes in rear leg indicate that rear leg conformation traits should be evaluated at multiple time periods.
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Affiliation(s)
- Joseph D Stock
- Department of Animal Science, Iowa State University, Ames, IA
| | - Julia A Calderón Díaz
- Pig Development Department, Teagasc Moorepark Grassland Research and Innovation Centre, Pig Development, Fermoy, Co. Cork, Ireland
| | | | - Benny E Mote
- Department of Animal Science, University of Nebraska - Lincoln, Lincoln, NE
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30
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Monson MS, Van Goor AG, Ashwell CM, Persia ME, Rothschild MF, Schmidt CJ, Lamont SJ. Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two distinct chicken lines. BMC Genomics 2018; 19:643. [PMID: 30165812 PMCID: PMC6117931 DOI: 10.1186/s12864-018-5033-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 03/07/2018] [Accepted: 08/22/2018] [Indexed: 02/07/2023] Open
Abstract
Background Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Identifying genes and pathways that are affected by high temperatures, especially heat-induced changes in immune responses, could provide targets to improve disease resistance in chickens. This study utilized RNA-sequencing (RNA-seq) to investigate transcriptome responses in the bursa of Fabricius, a primary immune tissue, after exposure to acute heat stress and/or subcutaneous immune stimulation with lipopolysaccharide (LPS) in a 2 × 2 factorial design: Thermoneutral + Saline, Heat + Saline, Thermoneutral + LPS and Heat + LPS. All treatments were investigated in two chicken lines: a relatively heat- and disease-resistant Fayoumi line and a more susceptible broiler line. Results Differential expression analysis determined that Heat + Saline had limited impact on gene expression (N = 1 or 63 genes) in broiler or Fayoumi bursa. However, Thermoneutral + LPS and Heat + LPS generated many expression changes in Fayoumi bursa (N = 368 and 804 genes). Thermoneutral + LPS was predicted to increase immune-related cell signaling and cell migration, while Heat + LPS would activate mortality-related functions and decrease expression in WNT signaling pathways. Further inter-treatment comparisons in the Fayoumi line revealed that heat stress prevented many of the expression changes caused by LPS. Although fewer significant expression changes were observed in the broiler bursa after exposure to Thermoneutral + LPS (N = 59 genes) or to Heat + LPS (N = 146 genes), both treatments were predicted to increase cell migration. Direct comparison between lines (broiler to Fayoumi) confirmed that each line had distinct responses to treatment. Conclusions Transcriptome analysis identified genes and pathways involved in bursal responses to heat stress and LPS and elucidated that these effects were greatest in the combined treatment. The interaction between heat and LPS was line dependent, with suppressive expression changes primarily in the Fayoumi line. Potential target genes, especially those involved in cell migration and immune signaling, can inform future research on heat stress in poultry and could prove useful for improving disease resistance. Electronic supplementary material The online version of this article (10.1186/s12864-018-5033-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melissa S Monson
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | | | - Michael E Persia
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, USA.
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31
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Peiravan A, Bertolini F, Rothschild MF, Simpson KW, Jergens AE, Allenspach K, Werling D. Genome-wide association studies of inflammatory bowel disease in German shepherd dogs. PLoS One 2018; 13:e0200685. [PMID: 30028859 PMCID: PMC6054420 DOI: 10.1371/journal.pone.0200685] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
Canine Inflammatory Bowel Disease (IBD) is considered a multifactorial disease caused by complex interactions between the intestinal immune system, intestinal microbiota and environmental factors in genetically susceptible individuals. Although IBD can affect any breed, German shepherd dogs (GSD) in the UK are at increased risk of developing the disease. Based on previous evidence, the aim of the present study was to identify single nucleotide polymorphisms (SNPs), which may confer genetic susceptibility or resistance to IBD using a genome-wide association study (GWAS). Genomic DNA was extracted from EDTA blood or saliva samples of 96 cases and 98 controls. Genotyping of cases and controls was performed on the Canine Illumina HD SNP array and data generated was analyzed using PLINK. Several SNPs and regions on chromosomes 7,9,11 and 13 were detected to be associated with IBD using different SNP-by-SNP association methods and FST windows approach. Searching one Mb up-and down-stream of the most significant SNPs, as identified by single SNP analysis as well as 200Kb before and after the start and the end position of the associated regions identified by FST windows approach, we identified 63 genes. Using a combination of pathways analysis and a list of genes that have been reported to be involved in human IBD, we identified 16 candidate genes potentially associated with IBD in GSD.
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Affiliation(s)
- Atiyeh Peiravan
- Department of Pathology and Pathogen Biology, Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Kenneth W. Simpson
- College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Albert E. Jergens
- College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Karin Allenspach
- College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Dirk Werling
- Department of Pathology and Pathogen Biology, Royal Veterinary College, University of London, North Mymms, United Kingdom
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32
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Zurbrigg K, van Dreumel T, Rothschild MF, Alves D, Friendship R, O'Sullivan TL. Cardiac weights and weight ratios as indicators of cardiac lesions in pigs: A study of pig hearts from an Ontario abattoir. Can J Vet Res 2018; 82:198-202. [PMID: 30026644 PMCID: PMC6040014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/10/2017] [Indexed: 06/08/2023]
Abstract
Clinically healthy pigs used in research are assumed to have normal cardiac structure and function. Subclinical cardiac abnormalities may adversely affect the responses being measured in these experiments. The gross and histologic lesions observed in hearts collected from a Canadian abattoir between 2012 and 2015 indicated an unexpectedly high prevalence of cardiac abnormalities: 75% (297/396) of the hearts examined had such lesions. The ratios of total heart weight to body weight and of right ventricle weight to body weight were significantly greater for the hearts with lesions than for the hearts with no lesions, which suggests that cardiac remodeling, particularly hypertrophy, had occurred. The large percentage of hearts with cardiac remodeling from asymptomatic market pigs demonstrates an increased probability that subclinical cardiac abnormalities may exist in research pigs, especially those accessed through commercial channels. Researchers should be aware of this likelihood if subclinical cardiac abnormalities could adversely affect their experimental findings.
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Affiliation(s)
- Kathy Zurbrigg
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011, USA (Rothschild)
| | - Tony van Dreumel
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011, USA (Rothschild)
| | - Max F Rothschild
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011, USA (Rothschild)
| | - David Alves
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011, USA (Rothschild)
| | - Robert Friendship
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011, USA (Rothschild)
| | - Terri L O'Sullivan
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 (Zurbrigg, Friendship, O'Sullivan); Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011, USA (Rothschild)
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33
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Zurbrigg K, van Dreumel T, Rothschild MF, Alves D, Friendship R, O'Sullivan TL. Rapid Communication: Postmortem lesions and heart weights of in-transit-loss market pigs in Ontario. J Anim Sci 2018; 95:5532-5536. [PMID: 29293772 DOI: 10.2527/jas2017.2089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In-transit losses (ITL) of market-weight pigs are defined as pigs that die or pigs that become nonambulatory during loading and shipping from the farm to the abattoir. The low proportion of ITL in market pigs implies that individual pig factors may influence ITL, in addition to commonly considered environmental or transport factors. Postmortem examinations of in-transit-loss pigs ( = 85) from 1 Ontario, Canada, abattoir indicated the cause of death to be acute heart failure as a result of cardiac lesions that developed prior to transport. The presence of preexisting cardiac lesions may explain why no or only a few pigs die in a trailer even when the entire load is exposed to extreme temperatures and other common transport risk factors.
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34
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Chinchilla-Vargas J, Kerns K, Rothschild MF. Lunar and climatic effects on boar ejaculate traits. Anim Reprod Sci 2018; 193:117-125. [DOI: 10.1016/j.anireprosci.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
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35
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Chinchilla-Vargas J, Jahnke MM, Dohlman TM, Rothschild MF, Gunn PJ. Climatic factors affecting quantity and quality grade of in vivo derived embryos of cattle. Anim Reprod Sci 2018; 192:53-60. [DOI: 10.1016/j.anireprosci.2018.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/03/2018] [Accepted: 02/16/2018] [Indexed: 10/18/2022]
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36
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Bertolini F, Yang T, Huang Y, Harding JCS, Plastow GS, Rothschild MF. Genomic investigation of porcine periweaning failure to thrive syndrome (PFTS). Vet Rec 2018; 183:95. [PMID: 29695451 DOI: 10.1136/vr.104825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/14/2017] [Revised: 03/09/2018] [Accepted: 04/04/2018] [Indexed: 01/28/2023]
Abstract
Porcine periweaning failure to thrive syndrome (PFTS) can be defined by anorexia, lethargy, progressive debilitation and compulsive behaviours that occur in seemingly healthy pigs within two to threeweeks of weaning in the absence of any known infectious, nutritional, management or environmental factors. A genetic component has been hypothesised for this syndrome. In the present study, 119 commercial pigs (80 cases and 39 controls) were genotyped with the porcine 80K single nucleotide polymorphism-chip and were analysed with logistic regression and two Fixation Index-based approaches. The analyses revealed several regions on chromosomes 1, 3, 6 and 11 with moderate divergence between cases and controls, particularly three haplotypes on SSC3 and 11. The gene-based analyses of the candidate regions revealed the presence of genes that have been reported to be associated with phenotypes like PFST including depression (PDE10A) and intestinal villous atrophy (CUL4A). It is important to increase the effort of collecting more samples to improve the power of these analyses.
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Affiliation(s)
| | - Tianfu Yang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Yanyun Huang
- Prairie Diagnostic Services Inc, Saskatoon, Saskatchewan, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
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Chinchilla Vargas J, Kerns K, Rothschild MF. 396 Climatic and Lunar Effects on Boar Ejaculate Traits. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - K Kerns
- International Boar Semen, Eldora, IA
- Division of Animal Science, University of Missouri, Columbia, MO
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA
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Rothschild MF. Following one's scientific compass. J Anim Breed Genet 2018; 135:3-4. [PMID: 29345070 DOI: 10.1111/jbg.12310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
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39
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Mwacharo JM, Kim ES, Elbeltagy AR, Aboul-Naga AM, Rischkowsky BA, Rothschild MF. Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts. Sci Rep 2017; 7:17647. [PMID: 29247174 PMCID: PMC5732286 DOI: 10.1038/s41598-017-17775-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 09/06/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023] Open
Abstract
African indigenous sheep are classified as fat-tail, thin-tail and fat-rump hair sheep. The fat-tail are well adapted to dryland environments, but little is known on their genome profiles. We analyzed patterns of genomic variation by genotyping, with the Ovine SNP50K microarray, 394 individuals from five populations of fat-tail sheep from a desert environment in Egypt. Comparative inferences with other East African and western Asia fat-tail and European sheep, reveal at least two phylogeographically distinct genepools of fat-tail sheep in Africa that differ from the European genepool, suggesting separate evolutionary and breeding history. We identified 24 candidate selection sweep regions, spanning 172 potentially novel and known genes, which are enriched with genes underpinning dryland adaptation physiology. In particular, we found selection sweeps spanning genes and/or pathways associated with metabolism; response to stress, ultraviolet radiation, oxidative stress and DNA damage repair; activation of immune response; regulation of reproduction, organ function and development, body size and morphology, skin and hair pigmentation, and keratinization. Our findings provide insights on the complexity of genome architecture regarding dryland stress adaptation in the fat-tail sheep and showcase the indigenous stocks as appropriate genotypes for adaptation planning to sustain livestock production and human livelihoods, under future climates.
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Affiliation(s)
- Joram M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia.
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
| | - Ahmed R Elbeltagy
- Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture, Nadi Elsaid Street, Dokki, Cairo, Egypt
| | - Adel M Aboul-Naga
- Animal Production Research Institute (APRI), Agriculture Research Centre (ARC), Ministry of Agriculture, Nadi Elsaid Street, Dokki, Cairo, Egypt
| | - Barbara A Rischkowsky
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
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Sánchez JP, Ragab M, Quintanilla R, Rothschild MF, Piles M. Genetic parameters and expected responses to selection for components of feed efficiency in a Duroc pig line. Genet Sel Evol 2017; 49:86. [PMID: 29191169 PMCID: PMC5710070 DOI: 10.1186/s12711-017-0362-x] [Citation(s) in RCA: 11] [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: 05/15/2017] [Accepted: 11/21/2017] [Indexed: 11/24/2022] Open
Abstract
Background Improving feed efficiency (\documentclass[12pt]{minimal}
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\begin{document}$${\text{FE}}$$\end{document}FE) is a key factor for any pig breeding company. Although this can be achieved by selection on an index of multi-trait best linear unbiased prediction of breeding values with optimal economic weights, considering deviations of feed intake from actual needs (\documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI) should be of value for further research on biological aspects of \documentclass[12pt]{minimal}
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\begin{document}$${\text{FE}}$$\end{document}FE. Here, we present a random regression model that extends the classical definition of \documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI by including animal-specific needs in the model. Using this model, we explore the genetic determinism of several \documentclass[12pt]{minimal}
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\begin{document}$${\text{FE}}$$\end{document}FE components: use of feed for growth (\documentclass[12pt]{minimal}
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\begin{document}$${\text{WG}}$$\end{document}WG), use of feed for backfat deposition (\documentclass[12pt]{minimal}
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\begin{document}$${\text{FG}}$$\end{document}FG), use of feed for maintenance (\documentclass[12pt]{minimal}
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\begin{document}$${\text{MW}}$$\end{document}MW), and unspecific efficiency in the use of feed (\documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI). Expected response to alternative selection indexes involving different components is also studied. Results Based on goodness-of-fit to the available feed intake (\documentclass[12pt]{minimal}
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\begin{document}$${\text{FI}}$$\end{document}FI) data, the model that assumes individual (genetic and permanent) variation in the use of feed for maintenance, \documentclass[12pt]{minimal}
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\begin{document}$${\text{WG}}$$\end{document}WG and \documentclass[12pt]{minimal}
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\begin{document}$${\text{FG}}$$\end{document}FG showed the best performance. Joint individual variation in feed allocation to maintenance, growth and backfat deposition comprised 37% of the individual variation of \documentclass[12pt]{minimal}
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\begin{document}$${\text{FI}}$$\end{document}FI. The estimated heritabilities of \documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI using the model that accounts for animal-specific needs and the traditional \documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI model were 0.12 and 0.18, respectively. The estimated heritabilities for the regression coefficients were 0.44, 0.39 and 0.55 for \documentclass[12pt]{minimal}
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\begin{document}$${\text{MW}}$$\end{document}MW, \documentclass[12pt]{minimal}
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\begin{document}$${\text{WG}}$$\end{document}WG and \documentclass[12pt]{minimal}
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\begin{document}$${\text{FG}}$$\end{document}FG, respectively. Estimates of genetic correlations of \documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI were positive with amount of feed used for \documentclass[12pt]{minimal}
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\begin{document}$${\text{WG}}$$\end{document}WG and \documentclass[12pt]{minimal}
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\begin{document}$${\text{FG}}$$\end{document}FG but negative for \documentclass[12pt]{minimal}
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\begin{document}$${\text{MW}}$$\end{document}MW. Expected response in overall efficiency, reducing \documentclass[12pt]{minimal}
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\begin{document}$${\text{FI}}$$\end{document}FI without altering performance, was 2.5% higher when the model assumed animal-specific needs than when the traditional definition of \documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI was considered. Conclusions Expected response in overall efficiency, by reducing \documentclass[12pt]{minimal}
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\begin{document}$${\text{FI}}$$\end{document}FI without altering performance, is slightly better with a model that assumes animal-specific needs instead of batch-specific needs to correct \documentclass[12pt]{minimal}
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\begin{document}$${\text{FI}}$$\end{document}FI. The relatively small difference between the traditional \documentclass[12pt]{minimal}
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\begin{document}$${\text{RFI}}$$\end{document}RFI model and our model is due to random intercepts (unspecific use of feed) accounting for the majority of variability in \documentclass[12pt]{minimal}
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\begin{document}$${\text{FI}}$$\end{document}FI. Overall, a model that accounts for animal-specific needs for \documentclass[12pt]{minimal}
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\begin{document}$${\text{MW}}$$\end{document}MW, \documentclass[12pt]{minimal}
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\begin{document}$${\text{WG}}$$\end{document}WG and \documentclass[12pt]{minimal}
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\begin{document}$${\text{FG}}$$\end{document}FG is statistically superior and allows for the possibility to act differentially on \documentclass[12pt]{minimal}
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\begin{document}$${\text{FE}}$$\end{document}FE components.
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Affiliation(s)
- Juan P Sánchez
- Genetica i Millora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain.
| | - Mohamed Ragab
- Genetica i Millora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain.,Poultry Production Department, Kafr El-Sheikh University, Kafr El-Sheikh, 33516, Egypt
| | - Raquel Quintanilla
- Genetica i Millora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Miriam Piles
- Genetica i Millora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain
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Renaville B, Glenn KL, Mote BE, Fan B, Stalder KJ, Rothschild MF. SREBP pathway genes as candidate markers in country ham production. Italian Journal of Animal Science 2017. [DOI: 10.4081/ijas.2010.e7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Kimberly L. Glenn
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Benny E. Mote
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Bin Fan
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Kenneth J. Stalder
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Max F. Rothschild
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
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Thekkoot DM, Young JM, Rothschild MF, Dekkers JCM. Genomewide association analysis of sow lactation performance traits in lines of Yorkshire pigs divergently selected for residual feed intake during grow-finish phase. J Anim Sci 2017; 94:2317-31. [PMID: 27285909 DOI: 10.2527/jas.2015-0258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lactation is an economically and biologically important phase in the life cycle of sows. Short generation intervals in nucleus herds and low heritability of traits associated with lactation along with challenges associated with collecting accurate lactation performance phenotypes emphasize the importance of using genomic tools to examine the underlying genetics of these traits. We report the first genomewide association study (GWAS) on traits associated with lactation and efficiency in 2 lines of Yorkshire pigs that were divergently selected for residual feed intake during grow-finish phase. A total of 862 farrowing records from 2 parities were analyzed using a Bayesian whole genome variable selection model (Bayes B) to locate 1-Mb regions that were most strongly associated with each trait. The GWAS was conducted separately for parity 1 and 2 records. Marker-based heritabilities ranged from 0.03 to 0.39 for parity 1 traits and from 0.06 to 0.40 for parity 2 traits. For all traits studied, around 90% of genetic variance came from a large number of genomic regions with small effects, whereas genomic regions with large effects were found to be different for the same trait measured in parity 1 and 2. The highest percentage of genetic variance explained by a 1-Mb window for each trait ranged from 0.4% for feed intake during lactation to 4.2% for back fat measured at farrowing in parity 1 sows and from 0.2% for lactation feed intake to 5.4% for protein mass loss during lactation in parity 2 sows. A total of thirteen 1-Mb nonoverlapping windows were found to explain more than 1.5% of genetic variance for either a single trait or across multiple traits. These 1-Mb windows were on chromosomes 2, 3, 6, 7, 8, 11, 14, 15, 17, and 18. The major positional candidate genes within 1 Mb upstream and downstream of these windows were , (SSC2), (SSC6) (SSC7), (SSC8), (SSC11), (SSC14), (SSC17). Further validation studies on larger populations are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with sow lactation performance.
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Thekkoot DM, Kemp RA, Rothschild MF, Plastow GS, Dekkers JCM. Estimation of genetic parameters for traits associated with reproduction, lactation, and efficiency in sows. J Anim Sci 2017; 94:4516-4529. [PMID: 27898935 DOI: 10.2527/jas.2015-0255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increased milk production due to high litter size, coupled with low feed intake, results in excessive mobilization of sow body reserves during lactation, which can have detrimental effects on future reproductive performance. A possibility to prevent this is to improve sow lactation performance genetically, along with other traits of interest. The aim of this study was to estimate breed-specific genetic parameters (by parity, between parities, and across parities) for traits associated with lactation and reproduction in Yorkshire and Landrace sows. Performance data were available for 2,107 sows with 1 to 3 parities (3,424 farrowings total). Sow back fat, loin depth and BW at farrowing, sow feed intake (SFI), and body weight loss (BWL) during lactation showed moderate heritabilities (0.21 to 0.37) in both breeds, whereas back fat loss (BFL), loin depth loss (LDL), and litter weight gain (LWG) showed low heritabilities (0.12 to 0.18). Among the efficiency traits, sow lactation efficiency showed extremely low heritability (near zero) in Yorkshire sows but a slightly higher (0.05) estimate in Landrace sows, whereas sow residual feed intake (SRFI) and energy balance traits showed moderate heritabilities in both breeds. Genetic correlations indicated that SFI during lactation had strong negative genetic correlations with body resource mobilization traits (BWL, BFL, and LDL; -0.35 to -0.70), and tissue mobilization traits in turn had strong positive genetic correlations with LWG (+0.24 to +0.54; < 0.05). However, SFI did not have a significant genetic correlation with LWG. These genetic correlations suggest that SFI during lactation is predominantly used for reducing sow body tissue losses, rather than for milk production. Estimates of genetic correlations for the same trait measured in parities 1 and 2 ranged from 0.64 to 0.98, which suggests that first and later parities should be treated as genetically different for some traits. Genetic correlations estimated between traits in parities 1 and 2 indicated that BWF and BWL measured in parity 1 can be used as indicator traits for SFI and SRFI measured in parities 1 and 2. In conclusion, traits associated with lactation in sows have a sizable genetic component and show potential for genetic improvement.
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Talenti A, Bertolini F, Pagnacco G, Pilla F, Ajmone-Marsan P, Rothschild MF, Crepaldi P. The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions. Mamm Genome 2017; 28:114-128. [PMID: 28255622 DOI: 10.1007/s00335-017-9678-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/26/2017] [Indexed: 01/10/2023]
Abstract
The Valdostana goat is an alpine breed, raised only in the northern Italian region of the Aosta Valley. This breed's main purpose is to produce milk and meat, but is peculiar for its involvement in the "Batailles de Chèvres," a recent tradition of non-cruel fight tournaments. At both the genetic and genomic levels, only a very limited number of studies have been performed with this breed and there are no studies about the genomic signatures left by selection. In this work, 24 unrelated Valdostana animals were screened for runs of homozygosity to identify highly homozygous regions. Then, six different approaches (ROH comparison, Fst single SNPs and windows based, Bayesian, Rsb, and XP-EHH) were applied comparing the Valdostana dataset with 14 other Italian goat breeds to confirm regions that were different among the comparisons. A total of three regions of selection that were also unique among the Valdostana were identified and located on chromosomes 1, 7, and 12 and contained 144 genes. Enrichment analyses detected genes such as cytokines and lymphocyte/leukocyte proliferation genes involved in the regulation of the immune system. A genetic link between an aggressive challenge, cytokines, and immunity has been hypothesized in many studies both in humans and in other species. Possible hypotheses associated with the signals of selection detected could be therefore related to immune-related factors as well as with the peculiar battle competition, or other breed-specific traits, and provided insights for further investigation of these unique regions, for the understanding and safeguard of the Valdostana breed.
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Affiliation(s)
- Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | | | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, via Francesco De Sanctis s.n.c., 86100, Campobasso, Italy
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
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Van Goor A, Ashwell CM, Persia ME, Rothschild MF, Schmidt CJ, Lamont SJ. Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat. PLoS One 2017; 12:e0171414. [PMID: 28166270 PMCID: PMC5293231 DOI: 10.1371/journal.pone.0171414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/20/2017] [Indexed: 01/25/2023] Open
Abstract
Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus (lipopolysaccharide (LPS) or saline), and temperature (35°C or 25°C). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change ≥ 2 and FDR ≤ 0.05) in the broiler (N = 283) than the Fayoumi (N = 85), whereas heat treatment resulted in fewer DEG in broiler (N = 22) compared to Fayoumi (N = 107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat. The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens.
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Affiliation(s)
- Angelica Van Goor
- Department of Animal Science, Iowa State University, Ames, IA, United States of America
| | - Chris M. Ashwell
- Department of Poultry Science, North Carolina State University, Raleigh, NC, United States of America
| | - Michael E. Persia
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States of America
| | - Carl J. Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States of America
| | - Susan J. Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States of America
- * E-mail:
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Msalya G, Kim ES, Laisser ELK, Kipanyula MJ, Karimuribo ED, Kusiluka LJM, Chenyambuga SW, Rothschild MF. Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses. PLoS One 2017; 12:e0171088. [PMID: 28129396 PMCID: PMC5271371 DOI: 10.1371/journal.pone.0171088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/16/2017] [Indexed: 11/29/2022] Open
Abstract
Background More than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them. Methodology/Principal findings The Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain. Conclusions Population admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle.
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Affiliation(s)
- George Msalya
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
- * E-mail:
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Emmanuel L. K. Laisser
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
- Ministry of Education and Vocational Training, Inspectorate Department Eastern Zone, Morogoro, Tanzania
| | | | - Esron D. Karimuribo
- Department of Veterinary Medicine and Public Health, SUA, Morogoro, Tanzania
| | - Lughano J. M. Kusiluka
- Department of Veterinary Medicine and Public Health, SUA, Morogoro, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Sebastian W. Chenyambuga
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
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Zurbrigg K, van Dreumel T, Rothschild MF, Alves D, Friendship R, O'Sullivan T. Pig-level risk factors for in-transit losses in swine: a review. Can J Anim Sci 2017. [DOI: 10.1139/cjas-2016-0193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bertolini F, Harding JCS, Mote B, Ladinig A, Plastow GS, Rothschild MF. Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks. Anim Genet 2016; 48:228-232. [PMID: 27943331 PMCID: PMC7159462 DOI: 10.1111/age.12522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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] [Accepted: 09/29/2016] [Indexed: 12/01/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome-wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean Fst value was calculated in 1-Mb non-overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected-five on chromosome 2, one on chromosome 4 and one on chromosome 15-in total encompassing 152 genes. Several of these genes are either under- or overexpressed in many virus infections, including Coronaviridae (such as SARS-CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.
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Affiliation(s)
- F Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA
| | - J C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - B Mote
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
| | - A Ladinig
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Wien, 1210, Austria
| | - G S Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA
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Fleming DS, Koltes JE, Fritz-Waters ER, Rothschild MF, Schmidt CJ, Ashwell CM, Persia ME, Reecy JM, Lamont SJ. Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences. BMC Genomics 2016; 17:812. [PMID: 27760519 PMCID: PMC5070165 DOI: 10.1186/s12864-016-3147-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 12/31/2015] [Accepted: 10/05/2016] [Indexed: 11/22/2022] Open
Abstract
Background Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. Results Downstream fixation test (FST) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high FST values for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. Conclusions Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - J E Koltes
- Iowa State University, Ames, IA, USA.,Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | | | | | | | - C M Ashwell
- North Carolina State University, Raleigh, NC, USA
| | - M E Persia
- Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - J M Reecy
- Iowa State University, Ames, IA, USA
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Abell CE, Fernando RL, Serenius TV, Rothschild MF, Gray KA, Stalder KJ. Genetic relationship between purebred and crossbred sow longevity. J Anim Sci Biotechnol 2016; 7:51. [PMID: 27606062 PMCID: PMC5013583 DOI: 10.1186/s40104-016-0112-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 01/08/2016] [Accepted: 08/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background The overall breeding objective for a nucleus swine selection program is to improve crossbred commercial performance. Most genetic improvement programs are based on an assumed high degree of positive relationship between purebred performance in a nucleus herd and their relatives’ crossbred performance in a commercial herd. The objective of this study was to examine the relationship between purebred and crossbred sow longevity performance. Sow longevity was defined as a binary trait with a success occurring if a sow remained in the herd for a certain number of parities and including the cumulative number born alive as a measure of reproductive success. Heritabilities, genetic correlations, and phenotypic correlations were estimated using THRGIBBS1F90. Results Results indicated little to no genetic correlations between crossbred and purebred reproductive traits. This indicates that selection for longevity or lifetime performance at the nucleus level may not result in improved longevity and lifetime performance at the crossbred level. Early parity performance was highly correlated with lifetime performance indicating that an indicator trait at an early parity could be used to predict lifetime performance. This would allow a sow to have her own record for the selection trait before she has been removed from the herd. Conclusions Results from this study aid in quantifying the relationship between purebred and crossbred performance and provide information for genetic companies to consider when developing a selection program where the objective is to improve crossbred sow performance. Utilizing crossbred records in a selection program would be the best way to improve crossbred sow productivity.
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Affiliation(s)
- C E Abell
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
| | - R L Fernando
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
| | - T V Serenius
- Figen Ltd., PO Box 319, 60101 Seinäjoki, Finland
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
| | - K A Gray
- Smithfield Premium Genetics, 316 W. Charity Rd, Rose Hill, NC 28458 USA
| | - K J Stalder
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
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