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Van Goor A, Pasternak A, Walugembe M, Chehab N, Hamonic G, Dekkers JCM, Harding JCS, Lunney JK. Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus. Front Genet 2023; 14:1110463. [PMID: 36845393 PMCID: PMC9947478 DOI: 10.3389/fgene.2023.1110463] [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: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to Porcine reproductive and respiratory syndrome virus infection. However, the genetic control of T3 and T4 levels during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with Porcine reproductive and respiratory syndrome virus. Methods: Sera from 5-week-old pigs (N = 1792) at 11 days post inoculation (DPI) with Porcine reproductive and respiratory syndrome virus were assayed for T3 levels (piglet_T3). Sera from fetuses (N = 1,267) at 12 or 21 days post maternal inoculation (DPMI) with Porcine reproductive and respiratory syndrome virus of sows (N = 145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60 K Illumina or 650 K Affymetrix single nucleotide polymorphism (SNP) panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using Julia for Whole-genome Analysis Software (JWAS). Results: All three traits were low to moderately heritable (10%-16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26 ± 0.03 and 0.67 ± 0.14, respectively. Nine significant quantitative trait loci were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest quantitative trait loci identified on SSC5, explaining 15% of the genetic variation. Three significant quantitative trait loci were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the genetic variation. Five significant quantitative trait loci were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the genetic variation. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Discussion: Thyroid hormone levels following Porcine reproductive and respiratory syndrome virus infection were heritable and had positive genetic correlations with growth rate. Multiple quantitative trait loci with moderate effects were identified for T3 and T4 levels during challenge with Porcine reproductive and respiratory syndrome virus and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to Porcine reproductive and respiratory syndrome virus infection, revealing factors associated with genomic control of host resilience.
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Affiliation(s)
- Angelica Van Goor
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Alex Pasternak
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Glenn Hamonic
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jack C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - John C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joan K. Lunney
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States,*Correspondence: Joan K. Lunney,
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Botchway P, Amuzu-Aweh E, Naazie A, Aning G, Otsyina H, Saelao P, Wang Y, Zhou H, Walugembe M, Dekkers J, Lamont S, Gallardo R, Kelly T, Bunn D, Kayang B. Host response to successive challenges with lentogenic and velogenic Newcastle disease virus in local chickens of Ghana. Poult Sci 2022; 101:102138. [PMID: 36126448 PMCID: PMC9489513 DOI: 10.1016/j.psj.2022.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/10/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
Newcastle disease (ND) is a highly contagious viral disease that constantly threatens poultry production. The velogenic (highly virulent) form of ND inflicts the most damage and can lead to 100% mortality in unvaccinated village chicken flocks. This study sought to characterize responses of local chickens in Ghana after challenging them with lentogenic and velogenic Newcastle disease virus (NDV) strains. At 4 wk of age, chicks were challenged with lentogenic NDV. Traits measured were pre- and post-lentogenic infection growth rates (GR), viral load at 2 and 6 d post-lentogenic infection (DPI), viral clearance rate and antibody levels at 10 DPI. Subsequently, the chickens were naturally exposed to velogenic NDV (vNDV) after anti-NDV antibody titers had waned to levels ≤1:1,700. Body weights and blood samples were again collected for analysis. Finally, chickens were euthanized and lesion scores (LS) across tissues were recorded. Post-velogenic exposure GR; antibody levels at 21 and 34 days post-velogenic exposure (DPE); LS for trachea, proventriculus, intestines, and cecal tonsils; and average LS across tissues were measured. Variance components and heritabilities were estimated for all traits using univariate animal models. Mean pre- and post-lentogenic NDV infection GRs were 6.26 g/day and 7.93 g/day, respectively, but mean post-velogenic NDV exposure GR was −1.96 g/day. Mean lesion scores ranged from 0.52 (trachea) to 1.33 (intestine), with males having significantly higher (P < 0.05) lesion scores compared to females. Heritability estimates for the lentogenic NDV trial traits ranged from moderate (0.23) to high (0.55) whereas those for the vNDV natural exposure trial were very low (≤ 0.08). Therefore, in contrast to the vNDV exposure trial, differences in the traits measured in the lentogenic challenge were more affected by genetics and thus selection for these traits may be more feasible compared to those following vNDV exposure. Our results can form the basis for identifying local chickens with improved resilience in the face of NDV infection for selective breeding to improve productivity.
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Shi S, Shao D, Yang L, Liang Q, Han W, Xue Q, Qu L, Leng L, Li Y, Zhao X, Dong P, Walugembe M, Kayang BB, Muhairwa AP, Zhou H, Tong H. Whole Genome Analyses Reveal Novel Genes Associated with Chicken Adaptation to Tropical and Frigid Environments. J Adv Res 2022; 47:13-25. [PMID: 35907630 PMCID: PMC10173185 DOI: 10.1016/j.jare.2022.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/17/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. CONCLUSION Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.
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Affiliation(s)
- Shourong Shi
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Dan Shao
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Lingyun Yang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Wei Han
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Qian Xue
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Liang Qu
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Li Leng
- College of Animal Science and technology, Northeast Agricultural University, Harbin, Heilongjiang, 150038, China
| | - Yishu Li
- Tropical Crop Germplasm Research Institute, Haikou, Hainan, 571101, China
| | - Xiaogang Zhao
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Ping Dong
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Boniface B Kayang
- Department of Animal Science, University of Ghana, Legon, Accra 233, Ghana
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Huaijun Zhou
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China.
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Rathje T, Jakubowski A, Diaz IDPS, Mauch E, Walugembe M, Cross A. 44 Development and Application of Novel Phenotyping Technologies to Swine Production and Breeding. J Anim Sci 2022. [DOI: 10.1093/jas/skac064.023] [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
Advancement within numerous categories of technology are beginning to see application for improving production and genetic advancement in pigs. Digital technologies, particularly video, are creating a step change in improved animal environments, biosecurity, vaccine management and disease intervention. For breeders, video technology creates opportunity to begin assessing animal behavior on a useful scale and to expand the quantity and type of animals measured for growth rate, body composition, structural integrity and feed efficiency. A seemingly endless stream of ‘omics’ data is becoming less costly to obtain and includes such datasets as common SNP arrays in addition to DNA sequence, transcriptome, proteome, metabolome, gut microbiome and more. Leveraging the capabilities of these data to predict a phenotype is key to unlocking the full potential of ‘omics’ data. Novel, at least to animal scientists, analytical techniques are required to understand gene networks and their associated expression profiles. These techniques apply equally to video data, which in its purest form, is an interpretation of complex patterns. Scaling and applying these techniques will be important over the coming decade. There exists today a very applied approach to using these technologies in the swine industry. One of the most complex and well-trained pattern recognition technologies lies within our own brain. Experienced managers reviewing video of pigs within facilities, team members entering and performing critical activities impacting biosecurity and coordinating these observations with simple interventions can make large, positive improvements in productivity. Investing in hardware and time will produce results that reduce stressors, improve processes that protect the farm from pathogens and result in better overall animal well-being. This talk will focus on examples of current applications that are of benefit today. In addition, we hope to promote discussion around priorities for genetic improvement, pig management and the practical needs to move a variety of technologies from research to development in the field.
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Van Goor AG, Pasternak A, Walugembe M, Hamonic G, Dekkers J, Harding JCS, Lunney JK. Complex immunogenomic control of serum thyroid hormone levels in fetuses and piglets challenged with Porcine Reproductive and Respiratory Syndrome Virus. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.19.04] [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] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. However, the interaction between host immunity and hormone homeostasis is not completely understood but piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to PRRSV infection. Our objective was to estimate genetic parameters, identify QTL, and uncover nearby candidate genes for T3 and/or T4 levels of piglets and fetuses challenged with PRRSV2. Serum from 5-week old pigs (N=1792) at 11 days post infection (dpi) with PRRSV2 were assayed for T3 levels (piglet_T3). While serum from fetuses (N=1267) at 12 or 21 dpi from sows (N=150) challenged with PRRSV2 in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped for 60K or 650K SNPs, heritabilities were estimated and genome wide association studies were performed for each trait separately. We found all three traits to be moderately heritable (18–28%) and the significant QTL (N=37) across several chromosomes collectively explained 24–34% of the genetic variation. A shared QTL identified for all traits on chromosome 6 contained the IL12RB2 and IFI44 genes. The largest QTL identified for both piglet_T3 and fetal_T3 on chromosome 5 contained IL17RA. A large QTL identified for piglet_T3 on chromosome 7 contained 9 MHC genes (e.g., SLA-DMA, SLA-DOA, SLA-DQA, SLA-DRA, and MHC-IA7). In conclusion, our data support the concept that there are complex interactions between thyroid hormone levels and multiple immunogenetic pathways during PRRSV infection, and that there is potential to select for pleiotropic QTL to simultaneously improve host immunity for reproductive and respiratory PRRS.
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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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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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Mushi JR, Chiwanga GH, Amuzu-Aweh EN, Walugembe M, Max RA, Lamont SJ, Kelly TR, Mollel EL, Msoffe PL, Dekkers J, Gallardo R, Zhou H, Muhairwa AP. Phenotypic variability and population structure analysis of Tanzanian free-range local chickens. BMC Vet Res 2020; 16:360. [PMID: 32993651 PMCID: PMC7523039 DOI: 10.1186/s12917-020-02541-x] [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: 02/07/2020] [Accepted: 08/25/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Free-range local chickens (FRLC) farming is an important activity in Tanzania, however, they have not been well-characterized. This study aimed to phenotypically characterize three Tanzanian FRLCs and to determine their population structure. A total of 389 mature breeder chickens (324 females and 65 males) from three popular Tanzanian FRLC ecotypes (Kuchi, Morogoro-medium and Ching'wekwe) were used for the phenotypic characterization. Progenies of these chickens were utilized to assess population structure. The ecotypes were collected from four geographical zones across Tanzania: Lake, Central, Northern and Coastal zones. Body weights and linear measurements were obtained from the mature breeders, including body, neck, shanks, wingspan, chest girth, and shank girth. Descriptive statistics were utilized to characterize the chickens. Correlations between the linear measurements and differences among the means of measured linear traits between ecotypes and between sexes were assessed. A total of 1399 progeny chicks were genotyped using a chicken 600 K high density single nucleotide polymorphism (SNP) panel for determination of population structure. RESULTS The means for most traits were significantly higher in Kuchi relative to Ching'wekwe and Morogoro-medium. However, shank length and shank girth were similar between Kuchi and Morogoro-medium females. All traits were correlated with the exception of shank girth in Morogoro-medium. Admixture analyses revealed that Morogoro-medium and Ching'wekwe clustered together as one population, separate from Kuchi. CONCLUSIONS Phenotypic traits could be used to characterize FRLCs, however, there were variations in traits among individuals within ecotypes; therefore, complementary genomic methods should be considered to improve the characterization for selective breeding.
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Affiliation(s)
- James R Mushi
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Gaspar H Chiwanga
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Robert A Max
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Terra R Kelly
- School of Veterinary Medicine, University of California, Davis, 95616, USA
| | - Esther L Mollel
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Peter L Msoffe
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Jack Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Rodrigo Gallardo
- School of Veterinary Medicine, University of California, Davis, 95616, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, 95616, USA
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania.
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Walugembe M, Amuzu-Aweh EN, Botchway PK, Naazie A, Aning G, Wang Y, Saelao P, Kelly T, Gallardo RA, Zhou H, Lamont SJ, Kayang BB, Dekkers JCM. Genetic Basis of Response of Ghanaian Local Chickens to Infection With a Lentogenic Newcastle Disease Virus. Front Genet 2020; 11:739. [PMID: 32849779 PMCID: PMC7402339 DOI: 10.3389/fgene.2020.00739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/25/2020] [Accepted: 06/19/2020] [Indexed: 11/13/2022] Open
Abstract
Newcastle disease (ND) is a global threat to domestic poultry, especially in rural areas of Africa and Asia, where the loss of entire backyard local chicken flocks often threatens household food security and income. To investigate the genetics of Ghanaian local chicken ecotypes to Newcastle disease virus (NDV), in this study, three popular Ghanaian chicken ecotypes (regional populations) were challenged with a lentogenic NDV strain at 28 days of age. This study was conducted in parallel with a similar study that used three popular Tanzanian local chicken ecotypes and after two companion studies in the United States, using Hy-line Brown commercial laying birds. In addition to growth rate, NDV response traits were measured following infection, including anti-NDV antibody levels [pre-infection and 10 days post-infection (dpi)], and viral load (2 and 6 dpi). Genetic parameters were estimated, and two genome-wide association study analysis methods were used on data from 1,440 Ghanaian chickens that were genotyped on a chicken 600K Single Nucleotide Polymorphism (SNP) chip. Both Ghana and Tanzania NDV challenge studies revealed moderate to high (0.18 – 0.55) estimates of heritability for all traits, except viral clearance where the heritability estimate was not different from zero for the Tanzanian ecotypes. For the Ghana study, 12 quantitative trait loci (QTL) for growth and/or response to NDV from single-SNP analyses and 20 genomic regions that explained more than 1% of genetic variance using the Bayes B method were identified. Seven of these windows were also identified as having at least one significant SNP in the single SNP analyses for growth rate, anti-NDV antibody levels, and viral load at 2 and 6 dpi. An important gene for growth during stress, CHORDC1 associated with post-infection growth rate was identified as a positional candidate gene, as well as other immune related genes, including VAV2, IL12B, DUSP1, and IL17B. The QTL identified in the Ghana study did not overlap with those identified in the Tanzania study. However, both studies revealed QTL with genes vital for growth and immune response during NDV challenge. The Tanzania parallel study revealed an overlapping QTL on chromosome 24 for viral load at 6 dpi with the US NDV study in which birds were challenged with NDV under heat stress. This QTL region includes genes related to immune response, including TIRAP, ETS1, and KIRREL3. The moderate to high estimates of heritability and the identified QTL suggest that host response to NDV of local African chicken ecotypes can be improved through selective breeding to enhance increased NDV resistance and vaccine efficacy.
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Affiliation(s)
- Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Esinam N Amuzu-Aweh
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of Ghana, Accra, Ghana
| | - Princess K Botchway
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of Ghana, Accra, Ghana
| | - Augustine Naazie
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of Ghana, Accra, Ghana
| | - George Aning
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of Ghana, Accra, Ghana
| | - Ying Wang
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Perot Saelao
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Terra Kelly
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of California, Davis, Davis, CA, United States.,School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rodrigo A Gallardo
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Huaijun Zhou
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Boniface B Kayang
- Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States.,Department of Animal Science, University of Ghana, Accra, Ghana
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Feed the Future Innovation Lab for Genomics to Improve Poultry, Department of Animal Science, University of California, Davis, Davis, CA, United States
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Walugembe M, Mushi JR, Amuzu-Aweh EN, Chiwanga GH, Msoffe PL, Wang Y, Saelao P, Kelly T, Gallardo RA, Zhou H, Lamont SJ, Muhairwa AP, Dekkers JCM. Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus. Genes (Basel) 2019; 10:genes10070546. [PMID: 31319636 PMCID: PMC6678660 DOI: 10.3390/genes10070546] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/21/2019] [Revised: 06/27/2019] [Accepted: 07/15/2019] [Indexed: 01/03/2023] Open
Abstract
Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18–0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes.
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Affiliation(s)
- Muhammed Walugembe
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - James R Mushi
- Department of Veterinary Medicine and Public Health, Sokoine University, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Esinam N Amuzu-Aweh
- Department of Animal Science, University of Ghana, P.O. Box LG 25 Legon, Accra, Ghana
| | - Gaspar H Chiwanga
- Department of Veterinary Medicine and Public Health, Sokoine University, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Peter L Msoffe
- Department of Veterinary Medicine and Public Health, Sokoine University, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Terra Kelly
- Department of Animal Science, University of California, Davis, CA 95616, USA
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Rodrigo A Gallardo
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, Sokoine University, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania.
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA.
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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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Walugembe M, Swantek PM, Honeyman MS, Mabry JW, Stalder KJ, Rothschild MF. Evaluation of growth, deposition of back fat, and loin muscle for purebred Berkshire pigs housed in bedded hoop buildings. J Anim Sci 2016; 94:800-4. [PMID: 27065150 DOI: 10.2527/jas.2015-9577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
This study was conducted to evaluate the accretion of BW, back fat, and loin muscle from purebred Berkshire pigs raised in bedded hoop barns in Iowa. The growth of a total of 144 purebred Berkshire pigs (18 barrows and 18 gilts per trial) was evaluated from 4 trials (2 winter and 2 summer trials). Pigs were fed ad libitum utilizing a 5-phase standard corn-soybean meal feeding program that met or exceeded NRC nutrient requirements. Pigs were housed in bedded hoop barns (unheated) to approximate common niche market requirements. At 21-d intervals, pigs were serially weighed, and ultrasonic back fat depth and loin muscle area (LMA) measurements were taken. Live BW measurements began at the trial initiation at approximately 18 to 32 kg, but ultrasonic scans for 10th-rib back fat depth and LMA began at between 36 and 45 kg until market weight of about 122 ± 2.5 kg. The rate (µ) of live body growth (weight) and ultrasonic back fat depth were influenced ( < 0.01) by trial and sex, with no significant interactions between trial and sex. Both live BW and back fat deposition were significantly greater in trial 1 than all other trials (2, 3, and 4). The rate of accretion and maximum growth of LMA depth were not affected ( > 0.05) by trial and sex. Overall, barrows averaged 31 mm of back fat at 125 kg, whereas gilts had an average of about 23 mm at 121 kg of market weight. Results suggest that because of the sex differences in growth and back fat deposition between Berkshire barrows and gilts, it may be important to formulate their diets differently in commercial pork production systems.
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Calderon Diaz JA, Danielson AM, Azarpajouh S, Mumm JM, Hirano S, Beam DL, Walugembe M, Stock JD, Dematawewa C, Stalder KJ. 014 The effect of temperament on pork quality. J Anim Sci 2016. [DOI: 10.2527/msasas2016-014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Walugembe M, Hsieh J, Koszewski N, Lamont S, Persia M, Rothschild M. Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks. Poult Sci 2015; 94:2351-9. [DOI: 10.3382/ps/pev242] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/05/2015] [Indexed: 01/14/2023] Open
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Walugembe M, Rothschild M, Persia M. Effects of high fiber ingredients on the performance, metabolizable energy and fiber digestibility of broiler and layer chicks. Anim Feed Sci Technol 2014. [DOI: 10.1016/j.anifeedsci.2013.09.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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