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Sparling BA, Ng TT, Carlo-Allende A, McCarthy FM, Taylor RL, Drechsler Y. Immunoglobulin-like receptors in chickens: identification, functional characterization, and renaming to cluster homolog of immunoglobulin-like receptors. Poult Sci 2024; 103:103292. [PMID: 38100950 PMCID: PMC10764270 DOI: 10.1016/j.psj.2023.103292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The cluster homolog of immunoglobulin-like receptors (CHIRs), previously known as the "chicken homolog of immunogloublin-like receptors," represents is a large group of transmembrane glycoproteins that direct the immune response. However, the full repertoire of putatively activating, inhibitory, or dual function CHIRA, CHIRB, and CHIRAB on chickens' immune responses is poorly understood. Herein, the study objective was to determine the genes encoding CHIR proteins and predict their function by searching canonical protein structure. A bioinformatics pipeline based on previous work was employed to search for the CHIRs from the newly updated broiler and layer genomes. The categorization into CHIRA, CHIRB, and CHIRAB types was assigned through motif searches, multiple sequence alignment, and phylogeny. In total, 150 protein-encoding genes on Chromosome 31 were identified as CHIRs. Gene members of each functional group (CHIRA, CHIRB, CHIRAB) were classified in accordance with previously recognized proteins. The genes were renamed to "cluster homolog of immunoglobulin-like receptors" (CHIRs) to allow for the naming of orthologous genes in other avian species. Additionally, expression analysis of the classified CHIRs across various reinforces their importance as immune regulators and activation in inflammatory tissues. Furthermore, over 1,000 diverse and rare CHIRs variants associated with differential Marek's disease response (P < 0.05) emphasize the impact of CHIRs on shaping avian immune responses in diverse contexts. The practical applications of these findings encompass advancing immunology, improving poultry health management, optimizing breeding programs for disease resistance, and enhancing overall animal health through a deeper understanding of the roles and functions of CHIRA, CHIRB, and CHIRAB types in avian immune responses.
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Affiliation(s)
- Brandi A Sparling
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA; Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Theros T Ng
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Anaid Carlo-Allende
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Fiona M McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Yvonne Drechsler
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA; Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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2
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Zhu F, Yin ZT, Zhao QS, Sun YX, Jie YC, Smith J, Yang YZ, Burt DW, Hincke M, Zhang ZD, Yuan MD, Kaufman J, Sun CJ, Li JY, Shao LW, Yang N, Hou ZC. A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 2023; 6:1233. [PMID: 38057566 PMCID: PMC10700341 DOI: 10.1038/s42003-023-05619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
A set of high-quality pan-genomes would help identify important genes that are still hidden/incomplete in bird reference genomes. In an attempt to address these issues, we have assembled a de novo chromosome-level reference genome of the Silkie (Gallus gallus domesticus), which is an important avian model for unique traits, like fibromelanosis, with unclear genetic foundation. This Silkie genome includes the complete genomic sequences of well-known, but unresolved, evolutionarily, endocrinologically, and immunologically important genes, including leptin, ovocleidin-17, and tumor-necrosis factor-α. The gap-less and manually annotated MHC (major histocompatibility complex) region possesses 38 recently identified genes, with differentially regulated genes recovered in response to pathogen challenges. We also provide whole-genome methylation and genetic variation maps, and resolve a complex genetic region that may contribute to fibromelanosis in these animals. Finally, we experimentally show leptin binding to the identified leptin receptor in chicken, confirming an active leptin ligand-receptor system. The Silkie genome assembly not only provides a rich data resource for avian genome studies, but also lays a foundation for further functional validation of resolved genes.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Qiang-Sen Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Yu-Chen Jie
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, 100101, Beijing, China
| | - David W Burt
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Maxwell Hincke
- Department of Cellular and Molecular Medicine, Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, KIH 8M5, Canada
| | - Zi-Ding Zhang
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Meng-Di Yuan
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Cong-Jiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jun-Ying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Li-Wa Shao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
- Sanya Institute of China Agricultural University, Beijing, China.
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3
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Johnsson M. Genomics in animal breeding from the perspectives of matrices and molecules. Hereditas 2023; 160:20. [PMID: 37149663 PMCID: PMC10163706 DOI: 10.1186/s41065-023-00285-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND This paper describes genomics from two perspectives that are in use in animal breeding and genetics: a statistical perspective concentrating on models for estimating breeding values, and a sequence perspective concentrating on the function of DNA molecules. MAIN BODY This paper reviews the development of genomics in animal breeding and speculates on its future from these two perspectives. From the statistical perspective, genomic data are large sets of markers of ancestry; animal breeding makes use of them while remaining agnostic about their function. From the sequence perspective, genomic data are a source of causative variants; what animal breeding needs is to identify and make use of them. CONCLUSION The statistical perspective, in the form of genomic selection, is the more applicable in contemporary breeding. Animal genomics researchers using from the sequence perspective are still working towards this the isolation of causative variants, equipped with new technologies but continuing a decades-long line of research.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, Uppsala, 75007, Sweden.
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Ribatti D, Annese T. Chick embryo in experimental embryology and more. Pathol Res Pract 2023; 245:154478. [PMID: 37100021 DOI: 10.1016/j.prp.2023.154478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023]
Abstract
Chicken remains an undisputed, powerful, useful, and practical model in developmental research. Chick embryos have been used as model systems for studies in experimental embryology and teratology. As the chicken embryo develops outside the mother, effects of external stresses on cardiovascular development can be studied without interferences of maternal hormonal, metabolic, or hemodynamic alterations. In 2004, the first draft sequence of the complete chicken genome was released, allowing broad genetic analysis and comparison to humans, and enabling expansion of transgenic techniques within the chick model. The chick embryo is relatively simple, quick, and low-cost model. The main advantages of the chick as a model system for experimental embryology are the ease with cells and tissues can be labeled, transplanted, and cultured, along with its similarity to mammalian systems.
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Affiliation(s)
- Domenico Ribatti
- Department of Translational Biomedicine and Neurosciences University of Bari Medical School, Piazza Giulio Cesare, 11, Policlinico, 70124 Bari, Italy.
| | - Tiziana Annese
- Department of Translational Biomedicine and Neurosciences University of Bari Medical School, Piazza Giulio Cesare, 11, Policlinico, 70124 Bari, Italy; Department of Medicine and Surgery, University LUM Giuseppe Degennaro, 70010 Casamassima (Ba), Italy
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Zhang Y, Jiang F, Yang B, Wang S, Wang H, Wang A, Xu D, Fan W. Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads. Gigascience 2022; 11:6833030. [PMID: 36399059 PMCID: PMC9673493 DOI: 10.1093/gigascience/giac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/27/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Background Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. Results We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the “RNA complete” criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. Conclusions HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host–microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.
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Affiliation(s)
- Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
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6
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Bruno S, Landi V, Senczuk G, Brooks SA, Almathen F, Faye B, Gaouar SSB, Piro M, Kim KS, David X, Eggen A, Burger P, Ciani E. Refining the Camelus dromedarius Myostatin Gene Polymorphism through Worldwide Whole-Genome Sequencing. Animals (Basel) 2022; 12:2068. [PMID: 36009658 PMCID: PMC9404819 DOI: 10.3390/ani12162068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Myostatin (MSTN) is a highly conserved negative regulator of skeletal muscle in mammals. Inactivating mutations results in a hyper-muscularity phenotype known as "double muscling" in several livestock and model species. In Camelus dromedarius, the gene structure organization and the sequence polymorphisms have been previously investigated, using Sanger and Next-Generation Sequencing technologies on a limited number of animals. Here, we carried out a follow-up study with the aim to further expand our knowledge about the sequence polymorphisms at the myostatin locus, through the whole-genome sequencing data of 183 samples representative of the geographical distribution range for this species. We focused our polymorphism analysis on the ±5 kb upstream and downstream region of the MSTN gene. A total of 99 variants (77 Single Nucleotide Polymorphisms and 22 indels) were observed. These were mainly located in intergenic and intronic regions, with only six synonymous Single Nucleotide Polymorphisms in exons. A sequence comparative analysis among the three species within the Camelus genus confirmed the expected higher genetic distance of C. dromedarius from the wild and domestic two-humped camels compared to the genetic distance between C. bactrianus and C. ferus. In silico functional prediction highlighted: (i) 213 differential putative transcription factor-binding sites, out of which 41 relative to transcription factors, with known literature evidence supporting their involvement in muscle metabolism and/or muscle development; and (ii) a number of variants potentially disrupting the canonical MSTN splicing elements, out of which two are discussed here for their potential ability to generate a prematurely truncated (inactive) form of the protein. The distribution of the considered variants in the studied cohort is discussed in light of the peculiar evolutionary history of this species and the hypothesis that extremely high muscularity, associated with a homozygous condition for mutated (inactivating) alleles at the myostatin locus, may represent, in arid desert conditions, a clear metabolic disadvantage, emphasizing the thermoregulatory and water availability challenges typical of these habitats.
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Affiliation(s)
- Silvia Bruno
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Valenzano, 70010 Bari, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Samantha Ann Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA
| | - Faisal Almathen
- Department of Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | | | | | - Mohammed Piro
- Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, Rabat BP 6202, Morocco
| | - Kwan Suk Kim
- Department of Animal Sciences, Chungbuk National University, Chungbuk 28644, Korea
| | | | | | - Pamela Burger
- Research Institute of Wildlife Ecology, Vetmeduni, 1160 Vienna, Austria
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, 70126 Bari, Italy
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7
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Heidaritabar M, Carney V, Groenen MAM, Plastow G. Assessing the genomic diversity and relatedness in 10 Canadian heritage chicken lines using whole-genome sequence data. J Anim Breed Genet 2022; 139:556-573. [PMID: 35579203 DOI: 10.1111/jbg.12720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
In the past 50 years, there has been a steep increase in the demand for poultry products, met by increasing production along with genetic selection for improved growth, efficiency, health and reproduction. The selection tends to reduce the number and type of genetic resources contributing to the majority of production. The University of Alberta maintains 10 heritage chicken lines (Brown Leghorn (BL), Light Sussex (LS), New Hampshire (NH), Saskatchewan Barred Rock (SaskBR), Shaver Barred Rock (ShaverBR), Shaver Rhode Island Red (RIR), White Leghorn (WL) and three commercial crosses called Alberta Meat Control strains 1957 (AMC-1957), 1978 sire line (AMC-1978-20S) and 1978 dam line (AMC-1978-30D), that played a large role in the evolution of the poultry industry in Canada. Since these lines have not been subjected to the same intensive selection pressures as commercial counterparts, they may contain unique genetic variants lost in commercial lines. Thus, for conservation management of these lines, the first step is to assess their genetic diversity. 71 male samples from across 10 lines were analysed using whole-genome sequencing and patterns of genetic diversity and relatedness among these lines were explored. AMC-1978-30D showed the highest genetic diversity as reflected in observed and expected heterozygosity (0.327 and 0.250), percentage of polymorphic markers (~ 65%) and average recent inbreeding coefficient (-0.039), followed by AMC-1978-20S and AMC-1957. BL showed the lowest genetic diversity as reflected in observed and expected heterozygosity (0.130 and 0.116), percentage of polymorphic markers (~31%) and average recent inbreeding coefficient (0.577), followed by LS, WL and NH. Our findings highlight the need for special attention for the populations of BL, WL, LS and NH, with the largest levels of inbreeding. Our results can be used to develop a breeding strategy to optimize and conserve the genetic variation present in heritage lines.
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Affiliation(s)
- Marzieh Heidaritabar
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Valerie Carney
- Poultry Innovation Partnership, University of Alberta, Edmonton, Alberta, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
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8
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Gu H, Wang L, Lv X, Yang W, Chen Y, Li K, Zhang J, Jia Y, Ning Z, Qu L. RNA-Seq Analysis Reveals Expression Regulatory Divergence of W-Linked Genes between Two Contrasting Chicken Breeds. Animals (Basel) 2022; 12:ani12091218. [PMID: 35565645 PMCID: PMC9103786 DOI: 10.3390/ani12091218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Understanding the mode of gene expression and regulation is essential for understanding the evolutionary process. Many previous studies tried to explain regulatory changes at the autosomal level, but little research has extended these explorations to the field of sex chromosomes due to their complex sex-limit features. Here, we first adopted an innovative method of identifying regulatory divergence of W-linked genes. Compared with cis-regulatory divergence, trans acting genes were more extensive in the W chromosome. We also found that divergent sex specific selection cannot strongly affect the expression evolution of the W chromosome. This insensitivity to selection may be one of the reasons why regulatory divergence is so small between autosomal and sex chromosomes. Abstract The regulation of gene expression is a complex process involving organism function and phenotypic diversity, and is caused by cis- and trans- regulation. While prior studies identified the regulatory pattern of the autosome rewiring in hybrids, the role of gene regulation in W sex chromosomes is not clear due to their degradation and sex-limit expression. Here, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibited broad differences in gender-related traits, and assessed the expression of the genes on the W chromosome to disentangle the contribution of cis- and trans-factors to expression divergence. We found that female-specific selection does not have a significant effect on W chromosome gene-expression patterns. For different tissues, there were most parental divergence expression genes in muscle, and also more heterosis compared with two other tissues. Notably, a broader pattern of trans regulation in the W chromosome was observed, which is consistent with autosomes. Taken together, this work describes the regulatory divergence of W-linked genes between two contrasting breeds and indicates sex chromosomes have a unique regulation and expression mechanism.
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Affiliation(s)
- Hongchang Gu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.G.); (Z.N.)
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (L.W.); (X.L.); (W.Y.); (Y.C.); (K.L.); (J.Z.)
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (L.W.); (X.L.); (W.Y.); (Y.C.); (K.L.); (J.Z.)
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (L.W.); (X.L.); (W.Y.); (Y.C.); (K.L.); (J.Z.)
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (L.W.); (X.L.); (W.Y.); (Y.C.); (K.L.); (J.Z.)
| | - Kaiyang Li
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (L.W.); (X.L.); (W.Y.); (Y.C.); (K.L.); (J.Z.)
| | - Jianwei Zhang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (L.W.); (X.L.); (W.Y.); (Y.C.); (K.L.); (J.Z.)
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.G.); (Z.N.)
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.G.); (Z.N.)
- Correspondence:
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9
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Whitacre LK, Wildhaber ML, Johnson GS, Durbin HJ, Rowan TN, Tribe P, Schnabel RD, Mhlanga-Mutangadura T, Tabor VM, Fenner D, Decker JE. Exploring genetic variation and population structure in a threatened species, Noturus placidus, with whole-genome sequence data. G3 (BETHESDA, MD.) 2022; 12:jkac046. [PMID: 35188205 PMCID: PMC8982419 DOI: 10.1093/g3journal/jkac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. For conservation efforts, we generated whole-genome sequence data from 10 Neosho madtom individuals originating from 3 geographically separated populations to evaluate genetic diversity and population structure. A Neosho madtom genome was de novo assembled, and genome size and content were assessed. Single nucleotide polymorphisms were assessed from de Bruijn graphs, and via reference alignment with both the channel catfish (Ictalurus punctatus) reference genome and Neosho madtom reference genome. Principal component analysis and structure analysis indicated weak population structure, suggesting fish from the 3 locations represent a single population. Using a novel method, genome-wide conservation and divergence between the Neosho madtom, channel catfish, and zebrafish (Danio rerio) was assessed by pairwise contig alignment, which demonstrated that genes important to embryonic development frequently had conserved sequences. This research in a threatened species with no previously published genomic resources provides novel genetic information to guide current and future conservation efforts and demonstrates that using whole-genome sequencing provides detailed information of population structure and demography using only a limited number of rare and valuable samples.
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Affiliation(s)
- Lynsey K Whitacre
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Mark L Wildhaber
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO 65201, USA
| | - Gary S Johnson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Harly J Durbin
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Peoria Tribe
- The Peoria Tribe of Indians of Oklahoma, Miami, OK 74354, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
| | - Tendai Mhlanga-Mutangadura
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Vernon M Tabor
- U.S. Fish and Wildlife Service, Kansas Ecological Services Field Office, Manhattan, KS 66502, USA
| | - Daniel Fenner
- U.S. Fish and Wildlife Service, Oklahoma Ecological Services Field Office, Tulsa, OK 74129, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Division of Animal Sciences , University of Missouri, Columbia, MO 65211, USA
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OHAGENYI IFEMMAJ, NDOFOR-FOLENG HARRIETM, UGWU SIMEONOC, OKWELUM NGOZI. Polymorphism of ghrelin genes among four Nigerian chicken populations as tool for improvement of chickens. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i3.122264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Research on polymorphism of ghrelin (GHRL), an acylated peptide that stimulates the release of growth hormone from the pituitary, has shown that it is associated with some essential growth genes in chicken, hence veritable in genomic selection. There is porous information on the polymorphism of GHRL genes among Nigerian chickens. The objective of this study was to determine polymorphism of ghrelin gene among four Nigerian chicken populations. Blood sample (0.5 ml) was collected from the wing vein of 102 birds for DNA extraction. Tested PCR products were sequenced following Macrogen INC. The SNPs were determined using the sequence alignment program, CLUSTAL W, implemented in MEGA software. The sequence results showed 25 SNPs. The Nigerian chickens varied in polymorphic sites from Ogun chickens (348 and 535) to Nsukka chickens (558 and 696) at the GHRL 1 and GHRL2 loci respectively. Polymorphic sites and diversity were higher among the Nsukka chicken than other populations of the Nigerian chickens. SNPs common to one geographic varied in another. The result revealed that genomic selection based on ghrelin SNPs may yield higher predictive accuracy, while Nsukka chickens could be useful for the creation of more superior lines for the global poultry industry. Since past studies have revealed that ghrelin gene stimulates the pituitary and hypothalamus for releasing growth factor (GF) hormone and have strong effect on many organs, we suggest an association study of ghrelin gene and growth traits.
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Abstract
The lack of preclinical models of spontaneous ovarian cancer (OVCA), a fatal gynecological malignancy, is a significant barrier to generating information on early changes indicative of OVCA. In contrast to rodents, laying hens develop OVCA spontaneously, with remarkable similarities to OVCA in women regarding tumor histology, OVCA dissemination, immune responses, and risk factors. These important features of OVCA will be useful to develop an early detection test for OVCA, which would significantly reduce mortality rates; preventive strategies; immunotherapeutics; prevention of resistance to chemotherapeutics; and exploration of gene therapies. A transvaginal ultrasound (TVUS) imaging method for imaging of hen ovarian tumors has been developed. Hens can be monitored prospectively by using serum markers, together with TVUS imaging, to detect early-stage OVCA, provided that a panel of serum markers can be established and imaging agents developed. Recent sequencing of the chicken genome will further facilitate the hen model to explore gene therapies against OVCA.
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Affiliation(s)
- Animesh Barua
- Laboratory of Translational Research on Ovarian Cancer, Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, Illinois, USA;
| | - Janice M Bahr
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
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12
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Zhang Y, Zhang N, Liu L, Wang Y, Xing J, Li X. Transcriptome Analysis of Effects of Folic Acid Supplement on Gene Expression in Liver of Broiler Chickens. Front Vet Sci 2021; 8:686609. [PMID: 34604366 PMCID: PMC8481781 DOI: 10.3389/fvets.2021.686609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/23/2021] [Indexed: 12/30/2022] Open
Abstract
Folic acid is a water-soluble B vitamin, and plays an important role in regulating gene expression and methylation. The liver is the major site of lipid biosynthesis in the chicken. Nevertheless, how gene expression and regulatory networks are affected by folic acid in liver of broilers are poorly understood. This paper conducted the RNA-seq technology on the liver of broilers under folic acid challenge investigation. First, 405 differentially expressed genes (DEGs), including 157 significantly upregulated and 248 downregulated, were detected between the control group (C) and the 5 mg folic acid group (M). Second, 68 upregulated DEGs and 142 downregulated DEGs were determined between C group and 10 mg folic acid group (H). Third, there were 165 upregulated genes and 179 downregulated genes between M and H groups. Of these DEGs, 903 DEGs were successfully annotated in the public databases. The functional classification based on GO and KEEGG showed that “general function prediction only” represented the largest functional classes, “cell cycle” (C vs. M; M vs. H), and “neuroactive ligand-receptor interaction” (C vs. H) were the highest unique sequences among three groups. SNP analysis indicated that numbers of C, M and H groups were 145,450, 146,131, and 123,004, respectively. Total new predicted alternative splicing events in C, M, and H groups were 9,521, 9,328, and 8,929, respectively. A protein-protein interaction (PPI) network was constructed, and the top 10 hub genes were evaluated among three groups. The results of real time PCR indicated that mRNA abundance of PPARγ and FAS in abdominal fat of M and H groups were reduced compared with the C group (P < 0.05). Ultramicroscopy results showed that folic acid could reduce lipid droplets in livers from chickens. Finally, contents of LPL, PPARγ, and FAS in abdominal fat were decreased with the folic acid supplmented diets (P < 0.01). These findings reveal the effects of folic acid supplemention on gene expression in liver of broilers, which can provide information for understanding the molecular mechanisms of folic acid regulating liver lipid metabolism.
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Affiliation(s)
- Yujie Zhang
- School of Life Sciences, Linyi University, Linyi, China
| | - Ningbo Zhang
- School of Agriculture and Forestry Sciences, Linyi University, Linyi, China
| | - Lin Liu
- School of Pharmacy, Linyi University, Linyi, China
| | - Yan Wang
- School of Life Sciences, Linyi University, Linyi, China
| | - Jinyi Xing
- School of Life Sciences, Linyi University, Linyi, China
| | - Xiuling Li
- School of Life Sciences, Linyi University, Linyi, China
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13
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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14
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Yuan Y, Zhang H, Yi G, You Z, Zhao C, Yuan H, Wang K, Li J, Yang N, Lian L. Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations. Front Genet 2021; 12:710770. [PMID: 34484301 PMCID: PMC8414643 DOI: 10.3389/fgene.2021.710770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.
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Affiliation(s)
- Yiming Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huanmin Zhang
- United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhen You
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunfang Zhao
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haixu Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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15
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Guo Y, Ou J, Zan Y, Wang Y, Li H, Zhu C, Chen K, Zhou X, Hu X, Carlborg Ö. Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history. Evol Appl 2021; 15:553-564. [PMID: 35505888 PMCID: PMC9046761 DOI: 10.1111/eva.13241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In‐depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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Affiliation(s)
- Ying Guo
- State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing China
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
| | - Jen‐Hsiang Ou
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
| | - Yanjun Zan
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
| | - Yuzhe Wang
- State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China
| | - Huifang Li
- Jiangsu Institute of Poultry Science Yangzhou China
| | - Chunhong Zhu
- Jiangsu Institute of Poultry Science Yangzhou China
| | - Kuanwei Chen
- Jiangsu Institute of Poultry Science Yangzhou China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing China
| | - Xiaoxiang Hu
- State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China
- National Engineering Laboratory for Animal Breeding China Agricultural University Beijing China
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
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16
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Brocklehurst N, Field DJ. Macroevolutionary dynamics of dentition in Mesozoic birds reveal no long-term selection towards tooth loss. iScience 2021; 24:102243. [PMID: 33763634 PMCID: PMC7973866 DOI: 10.1016/j.isci.2021.102243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/16/2020] [Accepted: 02/25/2021] [Indexed: 11/28/2022] Open
Abstract
Several potential drivers of avian tooth loss have been proposed, although consensus remains elusive as fully toothless jaws arose independently numerous times among Mesozoic avialans and dinosaurs more broadly. The origin of crown bird edentulism has been discussed in terms of a broad-scale selective pressure or trend toward toothlessness, although this has never been quantitatively tested. Here, we find no evidence for models whereby iterative acquisitions of toothlessness among Mesozoic Avialae were driven by an overarching selective trend. Instead, our results support modularity among jaw regions underlying heterogeneous tooth loss patterns and indicate a substantially later transition to complete crown bird edentulism than previously hypothesized (∼90 mya). We show that patterns of avialan tooth loss adhere to Dollo's law and suggest that the exclusive survival of toothless birds to the present represents lineage-specific selective pressures, irreversibility of tooth loss, and the filter of the Cretaceous-Paleogene (K–Pg) mass extinction. The evolutionary processes underlying tooth loss in Mesozoic birds are debated Analyses reveal no long-term selective pressure or trend toward toothlessness Tooth loss was likely a result of local selective pressures on individual lineages The transition to crown bird toothlessness occurred later than previously hypothesized
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Affiliation(s)
- Neil Brocklehurst
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, UK
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17
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An interplay between compositional constraint and natural selection dictates the codon usage pattern among select Galliformes. Biosystems 2021; 204:104390. [PMID: 33636205 DOI: 10.1016/j.biosystems.2021.104390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 11/20/2022]
Abstract
Galliformes are believed to be the first avian order that started living in human association and became domesticated. Members of this order ranged from common to rare species. Next-generation sequencing has availed researchers with the whole genome sequences of five Galliformes; chicken, helmeted Guinea fowl, turkey, Japanese quail, and peafowl. Bioinformatic analysis based on codon usage, evolution, and species-specific functional enrichment can provide some crucial information aiding proper understanding of their genomic strategies. In this study, we investigated the genomic features of chicken, helmeted guinea fowl, turkey, and Japanese quail. Their genomes were AT biased although the potentially highly expressed genes contained more GC than AT. Cytosine dominated the third position of frequently used optimal codons. Mutational pressures in the analyzed Galliformes were in the range of 0.2-0.6%. Neutrality plot, translational selection index, and mutational responsive index indicated the dominance of selection pressure over mutational pressure among Galliformes. A pair of di-nucleotides, TpA and CpG, was found to be used less frequently than others in protein-coding genes since both of them are associated with the conversion of euchromatin to heterochromatin. Functional enrichment analysis revealed the dominance of proteins associated with fundamental biological processes. In turkey, chicken and helmeted Guinea fowl proteins with immunity-boosting capacity prevailed along with proteins needed for signal transduction and maintenance of central dogma. Evolutionary analysis indicated a bias towards synonymous substitution than non-synonymous mutation.
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18
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Polymorphisms of AMY1A gene and their association with growth, carcass traits and feed intake efficiency in chickens. Genomics 2021; 113:583-594. [PMID: 33485951 DOI: 10.1016/j.ygeno.2020.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 10/09/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022]
Abstract
Investigations on the association between chicken traits and genetic variations can provide basic information to improve production performance in chickens. In our previous work, we genotyped 450 male chickens with a 600 K SNP array [1] and found that several SNPs in the genomic regions of the amylase alpha 1A (AMY1A) gene were significantly associated with feed intake efficiency and carcass traits. Given the lower accuracy of the SNP array, we performed direct sequencing with male and female chickens to further test chicken AMY1A polymorphisms and investigate their association with 17 traits in chickens. The results showed that 7 SNPs in the 5' flanking region, exon, intron and 3' UTR (3' untranslated region) of AMY1A, were significantly associated with daily gain (DG), average daily feed intake (ADFI), leg muscle weight (LMW) and abdominal fat (AF) (p < 0.05). Additionally, the haplotypes based on three SNPs, rs15910189, rs314354067 and rs316026696, showed significant associations with DG (p < 0.01), ADFI and AF (p < 0.05). To better understand the transcriptional regulation of AMY1A, we cloned its 5' flanking region and found that the SNPs rs316436216 and rs314213090 which might change the transcriptional regulator binding sites, were in the suppressor and enhancer regions, respectively. In addition, luciferase assays revealed that the SNP rs314613110 in the 3' UTR influenced the binding of the miRNA gga-miR-1764-3p. To validate whether there is any copy number variation in AMY1A in our population, we performed a genome-wide assessment of CNVs through whole-genome resequencing data. However, no CNV was found in AMY1A in our population, which is different from the increased copy number of AMY1A found in humans who consume a high-starch diet. Therefore, the present study provides substantial evidence for the association of AMY1A polymorphisms with growth traits and feed intake efficiency, which might contribute to chicken breeding programs.
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19
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Tian S, Zhou X, Phuntsok T, Zhao N, Zhang D, Ning C, Li D, Zhao H. Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens. iScience 2020; 23:101644. [PMID: 33103083 PMCID: PMC7578744 DOI: 10.1016/j.isci.2020.101644] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/19/2020] [Accepted: 09/30/2020] [Indexed: 12/05/2022] Open
Abstract
The genetic footprints of adaptations to naturally occurring tropical stress along with domestication are poorly reported in chickens. Here, by conducting population genomic analyses of 67 chickens inhabiting distinct climates, we found signals of gene flow from Tibetan chickens to Sri Lankan and Saudi Arabian breeds and identified 12 positively selected genes that are likely involved in genetic adaptations to both tropical desert and tropical monsoon island climates. Notably, in tropical desert climate, advantageous alleles of TLR7 and ZC3HAV1, which could inhibit replication of viruses in cells, suggest immune adaptation to the defense against zoonotic diseases in chickens. Furthermore, comparative genomic analysis showed that four genes (OC90, PLA2G12B, GPR17 and TNFRSF11A) involved in arachidonic acid metabolism have undergone convergent adaptation to tropical desert climate between birds and mammals. Our study offers insights into the genetic mechanisms of adaptations to tropical climates in birds and other animals and provides practical value for breeding design and medical research on avian viruses.
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Affiliation(s)
- Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Tashi Phuntsok
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Ning Zhao
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Dejing Zhang
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Chunyou Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
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20
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Chen YC, Kuo HC, Lo WS, Hung CM. Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence. BMC Evol Biol 2020; 20:147. [PMID: 33160317 PMCID: PMC7648321 DOI: 10.1186/s12862-020-01711-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving. Results Phylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, different pairs of orders with convergent foot-propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot-propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds. Conclusions Our analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of first studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution.
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Affiliation(s)
- Yu-Chi Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Sui Lo
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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21
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Katajamaa R, Jensen P. Tameness correlates with domestication related traits in a Red Junglefowl intercross. GENES BRAIN AND BEHAVIOR 2020; 20:e12704. [PMID: 32969588 PMCID: PMC7988571 DOI: 10.1111/gbb.12704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 01/21/2023]
Abstract
Early animal domestication may have been driven by selection on tameness. Selection on only tameness can bring about correlated selection responses in other traits, not intentionally selected upon, which may be one cause of the domesticated phenotype. We predicted that genetically reduced fear towards humans in Red Junglefowl, ancestors of domesticated chickens, would be correlated to other traits included in the domesticated phenotype. Fear level was determined by a standardised behaviour test, where the reaction towards an approaching human was recorded. We first selected birds for eight generations for either high or low fear levels in this test, to create two divergent selection lines. An F3 intercross, with birds from the eighth generation as parentals, was generated to study correlations between fear‐of‐human scores and other unselected phenotypes, possibly caused by pleiotropy or linkage. Low fear‐of‐human scores were associated with higher body weight and growth rates, and with increased activity in an open field test, indicating less general fearfulness. In females, low fear‐of‐human scores were also associated with more efficient fear habituation and in males with an increased tendency to emit food calls in a mirror test, indicating increased social dominance. Low fear‐of‐human scores were also associated with smaller brain relative to body weight, and with larger cerebrum relative to total brain weight in females. All these effects are in line with the changes observed in domesticated chickens compared to their ancestors, and we conclude that tameness may have been a driving factor underlying some aspects of the domesticated phenotype.
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Affiliation(s)
| | - Per Jensen
- IFM Biology, Linköping University, Linköping, Sweden
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Mucksová J, Reinišová M, Kalina J, Lejčková B, Hejnar J, Trefil P. Conservation of chicken male germline by orthotopic transplantation of primordial germ cells from genetically distant donors†. Biol Reprod 2020; 101:200-207. [PMID: 30980659 DOI: 10.1093/biolre/ioz064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/31/2019] [Accepted: 04/12/2019] [Indexed: 02/07/2023] Open
Abstract
Successful derivation and cultivation of primordial germ cells (PGCs) opened the way to efficient transgenesis and genome editing in the chicken. Furthermore, implantation of male PGCs from non-chicken galliform species into the chicken embryos resulted in cross-species germline chimeras and viable offspring. We have recently improved the PGC technology by demonstrating that chicken male PGCs transplanted into the testes of adult cockerel recipients mature into functional sperms. However, the availability of this orthotopic transplantation for cross-species transfer remains to be explored. Here we tested the capacity of genetically distant male PGCs to mature in the microenvironment of adult testes. We derived PGCs from the Chinese black-bone Silkie and transplanted them into infertile White Leghorn cockerels. Within 15-18 weeks after transplantation, we observed restoration of spermatogenesis in recipient cockerels and production of healthy progeny derived from the transplanted PGCs. Our findings also indicate the possibility of cross-species orthotopic transplantation of PGCs. Thus, our results might contribute to the preservation of endangered avian species and maintaining the genetic variability of the domestic chicken.
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Affiliation(s)
- Jitka Mucksová
- BIOPHARM, Research Institute of Biopharmacy and Veterinary Drugs, Jílové u Prahy, Czech Republic
| | - Markéta Reinišová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Kalina
- BIOPHARM, Research Institute of Biopharmacy and Veterinary Drugs, Jílové u Prahy, Czech Republic
| | - Barbora Lejčková
- BIOPHARM, Research Institute of Biopharmacy and Veterinary Drugs, Jílové u Prahy, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Trefil
- BIOPHARM, Research Institute of Biopharmacy and Veterinary Drugs, Jílové u Prahy, Czech Republic
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Gao G, Zhang K, Zhao X, Wu R, Zhong H, Li J, Li C, Xie Y, Wang Q. Molecular cloning of the goose GnRH gene and identification of GnRH polymorphisms associated with laying traits. Br Poult Sci 2020; 61:502-507. [PMID: 32306753 DOI: 10.1080/00071668.2020.1758298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
1. Egg-laying traits are important economic characteristics in goose production (Anser cygnoides). The gene GnRH, which encodes gonadotropin-releasing hormone, is a strong candidate gene for egg-laying traits in avian species. 2. In this study, a 3520 bp genomic sequence and a 279 bp mRNA sequence for GnRH, which encoded 92 amino acids, were determined. The GnRH DNA sequence contains four exons and three introns, and the DNA and deduced amino acid sequences were highly conserved across mammals (human, macaque, cow, and sheep) and avians (chicken, fulmar and quail). 3. Using a direct sequencing method, 46 single nucleotide polymorphisms (SNPs) were identified in the GnRH genomic sequence that were shared between two Sichuan White goose populations (217 and 208 individuals). Furthermore, 44 haplotypes were constructed using a sliding window approach. Association analysis between the SNPs and haplotypes and egg-laying traits showed that 10 SNPs affected the first egg weight, average egg weight, egg number at 48 weeks and egg number at 64 weeks. 4. These results lay the foundation for further studies of the function of GnRH in geese and provide a theoretical basis for marker-assisted selection of egg-laying traits in the Sichuan white goose population.
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Affiliation(s)
- G Gao
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - K Zhang
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - X Zhao
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - R Wu
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China
| | - H Zhong
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - J Li
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - C Li
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - Y Xie
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
| | - Q Wang
- Poultry Science Department, Chongqing Academy of Animal Science , Chongqing, China.,Poultry Science Department, Chongqing Engineering Research Center of Goose Genetic Improvement , Chongqing, China
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Li XZ. What can PIWI-interacting RNA research learn from chickens, and vice versa? CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
P-element induced wimpy testis (PIWI) interacting RNA (piRNA) are essential for fertility, by protecting the integrity of the germ-line genome via silencing of transposable elements (TE). Because new TE are constantly invading the host genome, piRNA-producing loci are under continuous pressure to undergo rapid evolution. This arms race between TE and piRNA is a prime example of the genome being more plastic than previously thought. Historically, the study of piRNA and TE has benefited from the use of diverse model organisms, including worms, fruit fly, zebrafish, frogs, and mice. In domestic chickens, we recently identified a new mode of piRNA acquisition in which the host hijacks and converts a pre-existing provirus into a piRNA-producing locus to defend against Avian leukosis virus, an adaptive immune strategy similar to the prokaryotic CRISPR–Cas [clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas)] system. This finding reveals a previously unrecognized mechanism of the host piRNA repertoire to rapidly evolve and target TE specifically. In this review, we will focus on both the unique and common features of chicken piRNA, as well as the advantages of using chickens as a model system, to address fundamental questions regarding piRNA acquisition in hosts. We will also comment on the potential application of piRNA for improving poultry health and reproductive efficiency.
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Affiliation(s)
- Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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25
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Guo Y, Lillie M, Zan Y, Beranger J, Martin A, Honaker CF, Siegel PB, Carlborg Ö. A genomic inference of the White Plymouth Rock genealogy. Poult Sci 2019; 98:5272-5280. [PMID: 31309227 PMCID: PMC6863967 DOI: 10.3382/ps/pez411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/01/2019] [Indexed: 11/20/2022] Open
Abstract
Crossing of populations has been, and still is, a central component in domestication and breed and variety formation. It is a way for breeders to utilize heterosis and to introduce new genetic variation into existing plant and livestock populations. During the mid-19th century, several chicken breeds that had been introduced to America from Europe and Asia became the founders for those formed in the USA. Historical records about the genealogy of these populations are often unclear and inconsistent. Here, we used genomics in an attempt to describe the ancestry of the White Plymouth Rock (WPR) chicken. In total, 150 chickens from the WPR and 8 other stocks that historical records suggested contributed to its formation were whole-genome re-sequenced. The admixture analyses of the autosomal and sex chromosomes showed that the WPR was likely founded as a cross between a paternal lineage that was primarily Dominique, and a maternal lineage where Black Java and Cochin contributed in essentially equal proportions. These results were consistent and provided quantification with the historical records that they were the main contributors to the WPR. The genomic analyses also revealed genome-wide contributions (<10% each) by Brahma, Langshan, and Black Minorca. When viewed on an individual chromosomal basis, contributions varied considerably among stocks.
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Affiliation(s)
- Y Guo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - M Lillie
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Y Zan
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - J Beranger
- The Livestock Conservancy, Pittsboro, NC 27312
| | - A Martin
- The Livestock Conservancy, Pittsboro, NC 27312
| | - C F Honaker
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
| | - P B Siegel
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Ö Carlborg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
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27
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Rebel J, Balk F, Post J, Van Hemert S, Zekarias B, Stockhofe N. Malabsorption syndrome in broilers. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps200481] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J.M.J. Rebel
- Animal Sciences Group, Division Animal Resources Development, P.O. Box 65, 8200AB Lelystad, The Netherlands
| | - F.R.M. Balk
- Animal Sciences Group, Division Animal Resources Development, P.O. Box 65, 8200AB Lelystad, The Netherlands
| | - J. Post
- Animal Sciences Group, Division Animal Resources Development, P.O. Box 65, 8200AB Lelystad, The Netherlands
| | - S. Van Hemert
- Animal Sciences Group, Division Animal Resources Development, P.O. Box 65, 8200AB Lelystad, The Netherlands
| | - B. Zekarias
- Animal Sciences Group, Division Animal Resources Development, P.O. Box 65, 8200AB Lelystad, The Netherlands
| | - N. Stockhofe
- Animal Sciences Group, Division Animal Resources Development, P.O. Box 65, 8200AB Lelystad, The Netherlands
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28
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Contributions and perspectives of chicken genomics in Brazil: from biological model to export commodity. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s004393390700164x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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30
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31
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32
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Affiliation(s)
- P.M. Hocking
- Roslin Institute, Roslin, Midlothian, Scotland, EH25 9PS
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33
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34
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35
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36
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Affiliation(s)
- Mirte Bosse
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- * E-mail:
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37
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Ono T, Kouguchi T, Ishikawa A, Nagano AJ, Takenouchi A, Igawa T, Tsudzuki M. Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens. Poult Sci 2019; 98:1096-1101. [PMID: 30329107 DOI: 10.3382/ps/pey493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/10/2018] [Indexed: 12/18/2022] Open
Abstract
The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction-site associated DNA sequencing (RAD-seq). An F2 resource family was generated by mating Oh-Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main-effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome-wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and -0.31 in males and -0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD-seq.
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Affiliation(s)
- Takashi Ono
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | | | - Akira Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Atsushi Takenouchi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takeshi Igawa
- Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masaoki Tsudzuki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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38
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O'Hare EA, Antin PB, Delany ME. Two Proximally Close Priority Candidate Genes for diplopodia-1, an Autosomal Inherited Craniofacial-Limb Syndrome in the Chicken: MRE11 and GPR83. J Hered 2019; 110:194-210. [PMID: 30597046 PMCID: PMC6399517 DOI: 10.1093/jhered/esy071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/29/2018] [Indexed: 11/12/2022] Open
Abstract
Next-generation sequencing (NGS) and expression technologies were utilized to investigate the genes and sequence elements in a 586 kb region of chicken chromosome 1 associated with the autosomal recessive diplopodia-1 (dp-1) mutation. This mutation shows a syndromic phenotype similar to known human developmental abnormalities (e.g., cleft palate, polydactyly, omphalocele [exposed viscera]). Toward our goal to ascertain the variant responsible, the entire 586 kb region was sequenced following utilization of a specifically designed capture array and to confirm/validate fine-mapping results. Bioinformatic analyses identified a total of 6142 sequence variants, which included SNPs, indels, and gaps. Of these, 778 SNPs, 146 micro-indels, and 581 gaps were unique to the UCD-Dp-1.003 inbred congenic line; those found within exons and splice sites were studied for contribution to the mutant phenotype. Upon further validation with additional mutant samples, a smaller subset (of variants [51]) remains linked to the mutation. Additionally, utilization of specific samples in the NGS technology was advantageous in that fine-mapping methodologies eliminated an additional 326 kb of sequence information on chromosome 1. Predicted and confirmed protein-coding genes within the smaller 260 kb region were assessed for their developmental expression patterns over several stages of early embryogenesis in regions/tissues of interest (e.g., digits, craniofacial region). Based on these results and known function in other vertebrates, 2 genes within 5 kb of each other, MRE11 and GPR83, are proposed as high-priority candidates for the dp-1 mutation.
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Affiliation(s)
- Elizabeth A O'Hare
- Department of Animal Science, University of California, Davis, CA.,Elizabeth A. O'Hare is now at the Department of Biological Sciences, Towson University, Towson, MD
| | - Parker B Antin
- Department of Molecular and Cellular Medicine, University of Arizona, Tucson, AZ
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, CA
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Shultz AJ, Sackton TB. Immune genes are hotspots of shared positive selection across birds and mammals. eLife 2019; 8:e41815. [PMID: 30620335 PMCID: PMC6338464 DOI: 10.7554/elife.41815] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/08/2019] [Indexed: 12/16/2022] Open
Abstract
Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.
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Affiliation(s)
- Allison J Shultz
- Informatics GroupHarvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
- Museum of Comparative ZoologyHarvard UniversityCambridgeUnited States
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40
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Świderská Z, Šmídová A, Buchtová L, Bryjová A, Fabiánová A, Munclinger P, Vinkler M. Avian Toll-like receptor allelic diversity far exceeds human polymorphism: an insight from domestic chicken breeds. Sci Rep 2018; 8:17878. [PMID: 30552359 PMCID: PMC6294777 DOI: 10.1038/s41598-018-36226-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023] Open
Abstract
Immune genes show remarkable levels of adaptive variation shaped by pathogen-mediated selection. Compared to humans, however, population polymorphism in animals has been understudied. To provide an insight into immunogenetic diversity in birds, we sequenced complete protein-coding regions of all Toll-like receptor (TLR) genes with direct orthology between mammals and birds (TLR3, TLR4, TLR5 and TLR7) in 110 domestic chickens from 25 breeds and compared their variability with a corresponding human dataset. Chicken TLRs (chTLRs) exhibit on average nine-times higher nucleotide diversity than human TLRs (hTLRs). Increased potentially functional non-synonymous variability is found in chTLR ligand-binding ectodomains. While we identified seven sites in chTLRs under positive selection and found evidence for convergence between alleles, no selection or convergence was detected in hTLRs. Up to six-times more alleles were identified in fowl (70 chTLR4 alleles vs. 11 hTLR4 alleles). In chTLRs, high numbers of alleles are shared between the breeds and the allelic frequencies are more equal than in hTLRs. These differences may have an important impact on infectious disease resistance and host-parasite co-evolution. Though adaptation through high genetic variation is typical for acquired immunity (e.g. MHC), our results show striking levels of intraspecific polymorphism also in poultry innate immune receptors.
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Grants
- 504214 Grantová Agentura, Univerzita Karlova (Charles University Grant Agency)
- 504214 Grantová Agentura, Univerzita Karlova (Charles University Grant Agency)
- 204069 Univerzita Karlova v Praze (Charles University)
- 204069 Univerzita Karlova v Praze (Charles University)
- PRIMUS/17/SCI/12 Univerzita Karlova v Praze (Charles University)
- SVV 260434/2018 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- INTER-COST LTC18060 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- SVV 260434/2018 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- P502/12/P179 Grantová Agentura České Republiky (Grant Agency of the Czech Republic)
- Grantov&#x00E1; Agentura, Univerzita Karlova (Charles University Grant Agency)
- Ministerstvo &#x0160;kolstv&#x00ED;, Ml&#x00E1;de&#x017E;e a T&#x011B;lov&#x00FD;chovy (Ministry of Education, Youth and Sports)
- Grantov&#x00E1; Agentura &#x010C;esk&#x00E9; Republiky (Grant Agency of the Czech Republic)
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Affiliation(s)
- Zuzana Świderská
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
- Charles University, Faculty of Science, Department of Cell Biology, Viničná 7, Prague, 12843, Czech Republic
| | - Adéla Šmídová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Lucie Buchtová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Anna Bryjová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
- The Czech Academy of Sciences, Institute of Vertebrate Biology, v.v.i., Květná 8, Brno, 60365, Czech Republic
| | - Anežka Fabiánová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Pavel Munclinger
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic.
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42
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Moreira GCM, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Pértille F, Ledur MC, Moura ASAMT, Garrick DJ, Coutinho LL. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. Sci Rep 2018; 8:16222. [PMID: 30385857 PMCID: PMC6212401 DOI: 10.1038/s41598-018-34364-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.
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Affiliation(s)
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
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43
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Tilak MK, Botero-Castro F, Galtier N, Nabholz B. Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA. Genome Biol Evol 2018; 10:616-622. [PMID: 29385572 PMCID: PMC5808798 DOI: 10.1093/gbe/evy022] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 02/06/2023] Open
Abstract
Standard Illumina libraries are biased toward sequences of intermediate GC-content. This results in an underrepresentation of GC-rich regions in sequencing projects of genomes with heterogeneous base composition, such as mammals and birds. We developed a simple, cost-effective protocol to enrich sheared genomic DNA in its GC-rich fraction by subtracting AT-rich DNA. This was achieved by heating DNA up to 90 °C before applying Illumina library preparation. We tested the new approach on chicken DNA and found that heated DNA increased average coverage in the GC-richest chromosomes by a factor up to six. Using a Taq polymerase supposedly appropriate for PCR amplification of GC-rich sequences had a much weaker effect. Our protocol should greatly facilitate sequencing and resequencing of the GC-richest regions of heterogeneous genomes, in combination with standard short-read and long-read technologies.
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Affiliation(s)
- Marie-Ka Tilak
- Institut des Sciences de l'Evolution, ISEM, Université de Montellier, CNRS, IRD, EPHE, France
| | - Fidel Botero-Castro
- Institut des Sciences de l'Evolution, ISEM, Université de Montellier, CNRS, IRD, EPHE, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, ISEM, Université de Montellier, CNRS, IRD, EPHE, France
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution, ISEM, Université de Montellier, CNRS, IRD, EPHE, France
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44
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The habu genome reveals accelerated evolution of venom protein genes. Sci Rep 2018; 8:11300. [PMID: 30050104 PMCID: PMC6062510 DOI: 10.1038/s41598-018-28749-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/29/2018] [Indexed: 01/11/2023] Open
Abstract
Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 non-venom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole-genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition.
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45
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Ren GJ, Fan XC, Liu TL, Wang SS, Zhao GH. Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection. BMC Genomics 2018; 19:356. [PMID: 29747577 PMCID: PMC5946474 DOI: 10.1186/s12864-018-4754-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/02/2018] [Indexed: 01/17/2023] Open
Abstract
Background Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were still not available. Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in regulating occurrence and progression of many diseases and are identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of host mRNAs, lncRNAs and circRNAs associated with C. baileyi infection were investigated for the first time. Results The tracheal tissues of experimental (C. baileyi infection) and control chickens were collected for deep RNA sequencing, and 545,479,934 clean reads were obtained. Of them, 1376 novel lncRNAs were identified, including 1161 long intergenic non-coding RNAs (lincRNAs) and 215 anti-sense lncRNAs. A total of 124 lncRNAs were found to be significantly differentially expressed between the experimental and control groups. Additionally, 14,698 mRNAs and 9085 circRNAs were identified, and significantly different expressions were observed for 1317 mRNAs and 104 circRNAs between two groups. Bioinformatic analyses of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for their targets and source genes suggested that these dysregulated genes may be involved in the interaction between the host and C. baileyi. Conclusions The present study revealed the expression profiles of mRNAs, lncRNAs and circRNAs during C. baileyi infection for the first time, and sheds lights on the roles of lncRNAs and circRNAs underlying the pathogenesis of Cryptosporidium infection. Electronic supplementary material The online version of this article (10.1186/s12864-018-4754-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guan-Jing Ren
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Xian-Cheng Fan
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Ting-Li Liu
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Sha-Sha Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Guang-Hui Zhao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
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46
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Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK. Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture. Crit Rev Biotechnol 2018; 38:1157-1175. [PMID: 29631431 DOI: 10.1080/07388551.2018.1451819] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.
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Affiliation(s)
- Mrinmoy Ghosh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Neelesh Sharma
- b Department of Veterinary Science and Animal Husbandry , Sher-e-Kashmir University of Agricultural Sciences and Technology , R.S. Pura , India
| | - Amit Kumar Singh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Meeta Gera
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | | | - Dong Kee Jeong
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
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47
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Schoville SD, Chen YH, Andersson MN, Benoit JB, Bhandari A, Bowsher JH, Brevik K, Cappelle K, Chen MJM, Childers AK, Childers C, Christiaens O, Clements J, Didion EM, Elpidina EN, Engsontia P, Friedrich M, García-Robles I, Gibbs RA, Goswami C, Grapputo A, Gruden K, Grynberg M, Henrissat B, Jennings EC, Jones JW, Kalsi M, Khan SA, Kumar A, Li F, Lombard V, Ma X, Martynov A, Miller NJ, Mitchell RF, Munoz-Torres M, Muszewska A, Oppert B, Palli SR, Panfilio KA, Pauchet Y, Perkin LC, Petek M, Poelchau MF, Record É, Rinehart JP, Robertson HM, Rosendale AJ, Ruiz-Arroyo VM, Smagghe G, Szendrei Z, Thomas GWC, Torson AS, Vargas Jentzsch IM, Weirauch MT, Yates AD, Yocum GD, Yoon JS, Richards S. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Sci Rep 2018; 8:1931. [PMID: 29386578 PMCID: PMC5792627 DOI: 10.1038/s41598-018-20154-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/13/2018] [Indexed: 01/04/2023] Open
Abstract
The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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Affiliation(s)
- Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, USA.
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | | | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Anita Bhandari
- Department of Molecular Physiology, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Kaat Cappelle
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Mei-Ju M Chen
- USDA-ARS National Agricultural Library, Beltsville, MD, USA
| | - Anna K Childers
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | | | | | - Justin Clements
- Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moskva, Russia
| | - Patamarerk Engsontia
- Department of Biology, Faculty of Science, Prince of Songkla University, Amphoe Hat Yai, Thailand
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chandan Goswami
- National Institute of Science Education and Research, Bhubaneswar, India
| | | | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, King Abdulaziz, Saudi Arabia
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | - Megha Kalsi
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Sher A Khan
- Department of Entomology, Texas A&M University, College Station, USA
| | - Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Fei Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
| | - Xingzhou Ma
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alexander Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nicholas J Miller
- Department of Biology, Illinois Institute of Technology, Chicago, USA
| | - Robert F Mitchell
- Department of Biology, University of Wisconsin-Oshkosh, Oshkosh, USA
| | - Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brenda Oppert
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | | | - Kristen A Panfilio
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, England, UK
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lindsey C Perkin
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Éric Record
- INRA, Aix-Marseille Université, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Joseph P Rinehart
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | | | - Guy Smagghe
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Zsofia Szendrei
- Department of Entomology, Michigan State University, East Lansing, USA
| | - Gregg W C Thomas
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, USA
| | - Alex S Torson
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | | | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Ashley D Yates
- Department of Entomology, The Ohio State University, Columbus, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, USA
| | - George D Yocum
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - June-Sun Yoon
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Stephen Richards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Zhai Y, Alexandre BC. A Poissonian Model of Indel Rate Variation for Phylogenetic Tree Inference. Syst Biol 2018; 66:698-714. [PMID: 28204784 DOI: 10.1093/sysbio/syx033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 01/27/2017] [Indexed: 01/22/2023] Open
Abstract
While indel rate variation has been observed and analyzed in detail, it is not taken into account by current indel-aware phylogenetic reconstruction methods. In this work, we introduce a continuous time stochastic process, the geometric Poisson indel process, that generalizes the Poisson indel process by allowing insertion and deletion rates to vary across sites. We design an efficient algorithm for computing the probability of a given multiple sequence alignment based on our new indel model. We describe a method to construct phylogeny estimates from a fixed alignment using neighbor joining. Using simulation studies, we show that ignoring indel rate variation may have a detrimental effect on the accuracy of the inferred phylogenies, and that our proposed method can sidestep this issue by inferring latent indel rate categories. We also show that our phylogenetic inference method may be more stable to taxa subsampling than methods that either ignore indels or indel rate variation. [evolutionary stochastic process; indel rate variation; Poisson indel process; TKF91.].
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Affiliation(s)
- Yongliang Zhai
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Bouchard-Côté Alexandre
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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49
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Balik-Meisner M, Truong L, Scholl EH, Tanguay RL, Reif DM. Population genetic diversity in zebrafish lines. Mamm Genome 2018; 29:90-100. [PMID: 29368091 PMCID: PMC5851690 DOI: 10.1007/s00335-018-9735-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/17/2018] [Indexed: 12/27/2022]
Abstract
Toxicological and pharmacological researchers have seized upon the many benefits of zebrafish, including the short generation time, well-characterized development, and early maturation as clear embryos. A major difference from many model organisms is that standard husbandry practices in zebrafish are designed to maintain population diversity. While this diversity is attractive for translational applications in human and ecological health, it raises critical questions on how interindividual genetic variation might contribute to chemical exposure or disease susceptibility differences. Findings from pooled samples of zebrafish support this supposition of diversity yet cannot directly measure allele frequencies for reference versus alternate alleles. Using the Tanguay lab Tropical 5D zebrafish line (T5D), we performed whole genome sequencing on a large group (n = 276) of individual zebrafish embryos. Paired-end reads were collected on an Illumina 3000HT, then aligned to the most recent zebrafish reference genome (GRCz10). These data were used to compare observed population genetic variation across species (humans, mice, zebrafish), then across lines within zebrafish. We found more single nucleotide polymorphisms (SNPs) in T5D than have been reported in SNP databases for any of the WIK, TU, TL, or AB lines. We theorize that some subset of the novel SNPs may be shared with other zebrafish lines but have not been identified in other studies due to the limitations of capturing population diversity in pooled sequencing strategies. We establish T5D as a model that is representative of diversity levels within laboratory zebrafish lines and demonstrate that experimental design and analysis can exert major effects when characterizing genetic diversity in heterogeneous populations.
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Affiliation(s)
- Michele Balik-Meisner
- Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA
| | - Robert L Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - David M Reif
- Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA.
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50
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Tohidi R, Javanmard A, Idris I. Immunogenetics applied to control salmonellosis in chicken: a review. JOURNAL OF APPLIED ANIMAL RESEARCH 2018. [DOI: 10.1080/09712119.2017.1301256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Reza Tohidi
- Department of Animal Science, Torbat-e Jam University of Agriculture, Torbat-e Jam, Iran
| | - Arash Javanmard
- Department of Animal Science, University of Tabriz, Tabriz, Iran
| | - Ismail Idris
- Department of Animal Science, Universiti Putra Malaysia, Serdang, Malaysia
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