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Cecil RF, Strohl L, Thomas MK, Schwartz JL, Timoshevskaya N, Smith JJ, Voss SR. Tyrp1 is the mendelian determinant of the Axolotl (Ambystoma mexicanum) copper mutant. Sci Rep 2024; 14:22399. [PMID: 39333770 PMCID: PMC11436669 DOI: 10.1038/s41598-024-73283-1] [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: 06/05/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Several dozen Mendelian mutants have been discovered in axolotl (Ambystoma mexicanum) populations, including several that affect pigmentation. Four recessive mutants have been described in the scientific literature and genes for three of these have been identified. Here we describe and genetically dissect copper, a mutant with an albino-like phenotype known only from the pet trade. We performed a cross segregating copper and wildtype color phenotypes and used bulked segregant RNA-Seq to identify a region on chromosome 6 that was enriched for single-nucleotide polymorphisms (SNPs) between the color phenotypes. This region included Tyrosinase-like Protein 1 (Tyrp1), a melanin synthesis protein that when mutated, is associated with lighter than black melanin coloration in animal models and oculocutaneous albinism in humans. Inspection of RNA-Seq reads identified a single nucleotide deletion that is predicted to change the coding frame, introduce a premature stop codon in exon 6 and yield a truncated Tyrp1 protein in copper individuals. Using CRISPR-Cas9 editing, we show that wildtype Tyrp1 crispants exhibit copper pigmentation, thus confirming Tyrp1 as the copper locus. Our results suggest that commercial and hobbyist axolotl populations may harbor useful mutants for biological research.
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Affiliation(s)
- Raissa F Cecil
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA
| | | | - Maddie K Thomas
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA
| | - James L Schwartz
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA
| | | | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | - S Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA.
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2
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Kinoshita K, Tanabe K, Nakamura Y, Nishijima KI, Suzuki T, Okuzaki Y, Mizushima S, Wang MS, Khan SU, Xu K, Jamal MA, Wei T, Zhao H, Su Y, Sun F, Liu G, Zhu F, Zhao HY, Wei HJ. PGC-based cryobanking, regeneration through germline chimera mating, and CRISPR/Cas9-mediated TYRP1 modification in indigenous Chinese chickens. Commun Biol 2024; 7:1127. [PMID: 39271811 PMCID: PMC11399235 DOI: 10.1038/s42003-024-06775-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Primordial germ cells (PGCs) are vital for producing sperm and eggs and are crucial for conserving chicken germplasm and creating genetically modified chickens. However, efforts to use PGCs for preserving native chicken germplasm and genetic modification via CRISPR/Cas9 are limited. Here we show that we established 289 PGC lines from eight Chinese chicken populations with an 81.6% success rate. We regenerated Piao chickens by repropagating cryopreserved PGCs and transplanting them into recipient chickens, achieving a 12.7% efficiency rate. These regenerated chickens carried mitochondrial DNA from female donor PGC and the rumplessness mutation from both male and female donors. Additionally, we created the TYRP1 (tyrosinase-related protein 1) knockout (KO) PGC lines via CRISPR/Cas9. Transplanting KO cells into male recipients and mating them with wild-type hens produced four TYRP1 KO chickens with brown plumage due to reduced eumelanin production. Our work demonstrates efficient PGC culture, cryopreservation, regeneration, and gene editing in chickens.
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Affiliation(s)
- Keiji Kinoshita
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Kumiko Tanabe
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Yoshiaki Nakamura
- Laboratory of Animal Breeding and Genetics, Graduate School of Integrated Sciences for Life and School of Applied Biological Science, Hiroshima University, Hiroshima, 739-8528, Japan
| | - Ken-Ichi Nishijima
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Takayuki Suzuki
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, 558-8585, Japan
| | - Yuya Okuzaki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Shusei Mizushima
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Ming-Shan Wang
- State Key Laboratory of Genetic resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sami Ullah Khan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Kaixiang Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Muhammad Ameen Jamal
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory of Genetic resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Taiyun Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Heng Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Yanhua Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Feizhou Sun
- National Center for Preservation of Animal Genetic Resources, National Animal Husbandry Service, Beijing, 100125, China
| | - Gang Liu
- National Center for Preservation of Animal Genetic Resources, National Animal Husbandry Service, Beijing, 100125, China
| | - Fangxian Zhu
- National Center for Preservation of Animal Genetic Resources, National Animal Husbandry Service, Beijing, 100125, China
| | - Hong-Ye Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
| | - Hong-Jiang Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
- State Key Laboratory of Genetic resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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3
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Amiri Roudbar M, Rosengren MK, Mousavi SF, Fegraeus K, Naboulsi R, Meadows JRS, Lindgren G. Effect of an endothelial regulatory module on plasma proteomics in exercising horses. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101265. [PMID: 38906044 DOI: 10.1016/j.cbd.2024.101265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/23/2024]
Abstract
Elite performing exercise requires an intricate modulation of the blood pressure to support the working muscles with oxygen. We have previously identified a genomic regulatory module that associates with differences in blood pressures of importance for elite performance in racehorses. This study aimed to determine the effect of the regulatory module on the protein repertoire. We sampled plasma from 12 Coldblooded trotters divided into two endothelial regulatory module haplotype groups, a sub-elite performing haplotype (SPH) and an elite performing haplotype (EPH), each at rest and exercise. The haplotype groups and their interaction were interrogated in two analyses, i) individual paired ratio analysis for identifying differentially abundant proteins of exercise (DAPE) and interaction (DAPI) between haplotype and exercise, and ii) unpaired ratio analysis for identifying differentially abundant protein of haplotype (DAPH). The proteomics analyses revealed a widespread change in plasma protein content during exercise, with a decreased tendency in protein abundance that is mainly related to lung function, tissue fluids, metabolism, calcium ion pathway and cellular energy metabolism. Furthermore, we provide the first investigation of the proteome variation due to the interaction between exercise and related blood pressure haplotypes, which this difference was related to a faster switch to the lipoprotein and lipid metabolism during exercise for EPH. The molecular signatures identified in the present study contribute to an improved understanding of exercise-related blood pressure regulation.
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Affiliation(s)
- Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran.
| | - Maria K Rosengren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Seyedeh Fatemeh Mousavi
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Kim Fegraeus
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Sweden.
| | - Rakan Naboulsi
- Department of Women's and Children's Health, Karolinska Institute, Tomtebodavägen 18A, Stockholm 17177, Sweden.
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132 Uppsala, Sweden.
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium.
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4
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Fegraeus K, Rosengren MK, Naboulsi R, Orlando L, Åbrink M, Jouni A, Velie BD, Raine A, Egner B, Mattsson CM, Lång K, Zhigulev A, Björck HM, Franco-Cereceda A, Eriksson P, Andersson G, Sahlén P, Meadows JRS, Lindgren G. An endothelial regulatory module links blood pressure regulation with elite athletic performance. PLoS Genet 2024; 20:e1011285. [PMID: 38885195 PMCID: PMC11182536 DOI: 10.1371/journal.pgen.1011285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024] Open
Abstract
The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.
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Affiliation(s)
- Kim Fegraeus
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Maria K. Rosengren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Rakan Naboulsi
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Stockholm
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Toulouse, France
| | - Magnus Åbrink
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ahmad Jouni
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Brandon D. Velie
- School of Life & Environmental Sciences, University of Sydney, Sydney, Australia
| | - Amanda Raine
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Beate Egner
- Department of Cardio-Vascular Research, Veterinary Academy of Higher Learning, Babenhausen, Germany
| | - C Mikael Mattsson
- Silicon Valley Exercise Analytics (svexa), MenloPark, CA, United States of America
| | - Karin Lång
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Artemy Zhigulev
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Hanna M. Björck
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Anders Franco-Cereceda
- Section of Cardiothoracic Surgery, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Göran Andersson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
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5
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Zhang C, Asadollahpour Nanaei H, Jafarpour Negari N, Amiri Roudbar M, Amiri Ghanatsaman Z, Niyazbekova Z, Yang X. Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats. BMC Genomics 2024; 25:477. [PMID: 38745140 PMCID: PMC11094986 DOI: 10.1186/s12864-024-10387-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: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Since domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate. RESULTS To explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (- 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds. CONCLUSIONS The results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions.
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Affiliation(s)
- Chenxi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hojjat Asadollahpour Nanaei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | | | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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6
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Gabriel V, Zdyrski C, Sahoo DK, Ralston A, Wickham H, Bourgois-Mochel A, Ahmed B, Merodio MM, Paukner K, Piñeyro P, Kopper J, Rowe EW, Smith JD, Meyerholz D, Kol A, Viall A, Elbadawy M, Mochel JP, Allenspach K. Adult Animal Stem Cell-Derived Organoids in Biomedical Research and the One Health Paradigm. Int J Mol Sci 2024; 25:701. [PMID: 38255775 PMCID: PMC10815683 DOI: 10.3390/ijms25020701] [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: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Preclinical biomedical research is limited by the predictiveness of in vivo and in vitro models. While in vivo models offer the most complex system for experimentation, they are also limited by ethical, financial, and experimental constraints. In vitro models are simplified models that do not offer the same complexity as living animals but do offer financial affordability and more experimental freedom; therefore, they are commonly used. Traditional 2D cell lines cannot fully simulate the complexity of the epithelium of healthy organs and limit scientific progress. The One Health Initiative was established to consolidate human, animal, and environmental health while also tackling complex and multifactorial medical problems. Reverse translational research allows for the sharing of knowledge between clinical research in veterinary and human medicine. Recently, organoid technology has been developed to mimic the original organ's epithelial microstructure and function more reliably. While human and murine organoids are available, numerous other organoids have been derived from traditional veterinary animals and exotic species in the last decade. With these additional organoid models, species previously excluded from in vitro research are becoming accessible, therefore unlocking potential translational and reverse translational applications of animals with unique adaptations that overcome common problems in veterinary and human medicine.
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Affiliation(s)
- Vojtech Gabriel
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | | | - Dipak K. Sahoo
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
| | - Abigail Ralston
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
| | - Hannah Wickham
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | - Agnes Bourgois-Mochel
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
| | - Basant Ahmed
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | - Maria M. Merodio
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
| | - Karel Paukner
- Atherosclerosis Research Laboratory, Centre for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
| | - Pablo Piñeyro
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.P.); (J.D.S.)
| | - Jamie Kopper
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
| | - Eric W. Rowe
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | - Jodi D. Smith
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.P.); (J.D.S.)
| | - David Meyerholz
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA;
| | - Amir Kol
- Department of Pathology, University of California, Davis, CA 94143, USA; (A.K.); (A.V.)
| | - Austin Viall
- Department of Pathology, University of California, Davis, CA 94143, USA; (A.K.); (A.V.)
| | - Mohamed Elbadawy
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30530, USA;
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Jonathan P. Mochel
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30530, USA;
| | - Karin Allenspach
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30530, USA;
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7
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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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8
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Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, Wang MS, Jiang L, Dai LH, Wang JR, Chu XH, Zeng YQ, Fang LZ, Wu DD, Zhang Q, Ding XD. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 2023; 26:106119. [PMID: 36852268 PMCID: PMC9958381 DOI: 10.1016/j.isci.2023.106119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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Affiliation(s)
- Yi-Fan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chong-Long Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ru-Hai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen-Wen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Li-He Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jie-Ru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao-Hong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Ling-Zhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Xiang-Dong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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9
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Loengbudnark W, Chankitisakul V, Boonkum W. The genetic impact of heat stress on the egg production of Thai native chickens (Pradu Hang dum). PLoS One 2023; 18:e0281328. [PMID: 36735733 PMCID: PMC9897533 DOI: 10.1371/journal.pone.0281328] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Sustainable poultry production in adverse weather conditions is a widely debated issue, which has led to research into the development of breeds of poultry that are genetically resistant to heat. This study aimed to investigate the effects of heat stress on the genetics of monthly egg production and examine the threshold point of heat stress for preventing thermal stress and its effects on chicken productivity. The data of 5,965 monthly egg production records of 629 Thai native Pradu Hang dum chickens were used for analysis in combination with the temperature-humidity index (THI) calculated by meteorological data near the testing station. The average THI throughout the year was 76.6, and the highest was 82. The THI data were subsequently used to find the threshold point of heat stress. The THI equation used in this study was chosen by its highest correlation (-0.306) between THI values and monthly egg production. At a THI of 74, the lowest -2 logL was found and was considered the threshold point of heat stress. This means that monthly egg production would start decreasing when the THI was 74. Heritability was 0.15±0.03, and genetic and permanent environmental correlations were -0.29 and -0.48, respectively. The threshold point was used to estimate the estimated breeding values (EBVs) of the monthly egg production and heat stress individually, and EBVs were calculated into the selection index. The selection index values when the animal was selected for the replacement herd for all chickens (top 50%, 30%, 20%, and 10%) were 0.14, 0.90, 1.27, 1.53, and 1.91, respectively, and the genetic progress was 0.55, 0.60, 0.68, 0.75, and 0.77, respectively. This shows that the selection index values are lower if there are many selected animals. The recommendation for animal genetic selection is that the top 10% is appropriately because it seems to be most preferred. Therefore, using a selection index for high egg production and heat tolerance in Thai native chickens is possible to achieve genetic assessment in a large population.
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Affiliation(s)
- Wipas Loengbudnark
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
- The Research and Development Network Center of Animal Breeding and Omics, Khon Kaen University, Khon Kaen, Thailand
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
- The Research and Development Network Center of Animal Breeding and Omics, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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10
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Liu Y, Fu Y, Yang Y, Yi G, Lian J, Xie B, Yao Y, Chen M, Niu Y, Liu L, Wang L, Zhang Y, Fan X, Tang Y, Yuan P, Zhu M, Li Q, Zhang S, Chen Y, Wang B, He J, Lu D, Liachko I, Sullivan ST, Pang B, Chen Y, He X, Li K, Tang Z. Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs. GENETICS SELECTION EVOLUTION 2022; 54:62. [PMID: 36104777 PMCID: PMC9476355 DOI: 10.1186/s12711-022-00754-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.
Results
We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.
Conclusions
Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.
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11
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HOXC10 intronic duplication is associated with unsealed skull and crest in crested chicken with cerebral hernia. Gene 2022; 840:146758. [PMID: 35905851 DOI: 10.1016/j.gene.2022.146758] [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: 08/23/2021] [Revised: 06/21/2022] [Accepted: 07/24/2022] [Indexed: 11/22/2022]
Abstract
The genetic basis and developmental mechanism of unsealed skull in crested chicken with cerebral hernia remain unclear. Here, a genomic region including six HOXC genes was mapped by bulked segregant analysis (BSA) in a crested chicken resource population. A 195-bp intronic tandem duplication was further confirmed in the HOXC10 gene. HOXC genes, particularly HOXC10, were expressed ectopically in fetal skin and meningeal tissues of crested chicken with cerebral hernia, indicating its impact on the cranial mesenchymal tissues that drive the development of scalp skin, frontal bone, and meninges. The restricted expansion of frontal bone progenitors labeled with anti-RUNX2 antibody in the supraorbital mesenchyme of the fetal head implied abnormal migration, which contributed to the formation of the unsealed skull. This study suggests that HOXC genes were potent drivers for the abnormalities of the head crest and unsealed skull observed in crested chicken with cerebral hernia.
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12
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Hanly JJ, Livraghi L, Heryanto C, McMillan WO, Jiggins CD, Gilbert LE, Martin A. A large deletion at the cortex locus eliminates butterfly wing patterning. G3 GENES|GENOMES|GENETICS 2022; 12:6517782. [PMID: 35099556 PMCID: PMC8982378 DOI: 10.1093/g3journal/jkac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/21/2022] [Indexed: 11/21/2022]
Abstract
As the genetic basis of natural and domesticated variation has been described in recent years, a number of hotspot genes have been repeatedly identified as the targets of selection, Heliconius butterflies display a spectacular diversity of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here, we sought to identify the mechanism behind an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78-kb deletion at the cortex wing patterning locus, a gene which has been associated with wing pattern evolution in H. melpomene and 10 divergent lepidopteran species. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable while heterozygotes are the targets of artificial selection, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations.
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Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
| | - Luca Livraghi
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christa Heryanto
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Lawrence E Gilbert
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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13
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Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens. BMC Genomics 2022; 23:224. [PMID: 35317755 PMCID: PMC8939082 DOI: 10.1186/s12864-022-08434-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Background Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes. To detect genomic signatures of adaptation, we applied nucleotide diversity (θπ) and FST statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits. Results By generating whole-genome data, we assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (~ 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits. Conclusions The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08434-7.
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14
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Flores-Santin J, Burggren WW. Beyond the Chicken: Alternative Avian Models for Developmental Physiological Research. Front Physiol 2021; 12:712633. [PMID: 34744759 PMCID: PMC8566884 DOI: 10.3389/fphys.2021.712633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/13/2021] [Indexed: 12/23/2022] Open
Abstract
Biomedical research focusing on physiological, morphological, behavioral, and other aspects of development has long depended upon the chicken (Gallus gallus domesticus) as a key animal model that is presumed to be typical of birds and generally applicable to mammals. Yet, the modern chicken in its many forms is the result of artificial selection more intense than almost any other domesticated animal. A consequence of great variation in genotype and phenotype is that some breeds have inherent aberrant physiological and morphological traits that may show up relatively early in development (e.g., hypertension, hyperglycemia, and limb defects in the broiler chickens). While such traits can be useful as models of specific diseases, this high degree of specialization can color general experimental results and affect their translational value. Against this background, in this review we first consider the characteristics that make an animal model attractive for developmental research (e.g., accessibility, ease of rearing, size, fecundity, development rates, genetic variation, etc.). We then explore opportunities presented by the embryo to adult continuum of alternative bird models, including quail, ratites, songbirds, birds of prey, and corvids. We conclude by indicating that expanding developmental studies beyond the chicken model to include additional avian groups will both validate the chicken model as well as potentially identify even more suitable avian models for answering questions applicable to both basic biology and the human condition.
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Affiliation(s)
- Josele Flores-Santin
- Facultad de Ciencias, Biologia, Universidad Autónoma del Estado de Mexico, Toluca, Mexico
| | - Warren W. Burggren
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas Denton, Denton, TX, United States
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15
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Anello M, Daverio MS, Rodríguez SS, Romero SR, Renieri C, Vidal Rioja L, Di Rocco F. The ASIP gene in the llama (Lama glama): Alternative transcripts, expression and relation with color phenotypes. Gene 2021; 809:146018. [PMID: 34655720 DOI: 10.1016/j.gene.2021.146018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/15/2021] [Accepted: 10/11/2021] [Indexed: 11/27/2022]
Abstract
The Agouti gene (ASIP) is one of the most important genes for coat color determination in mammals. It has a complex structure with several promoters and alternative non-coding first exons that are transcribed into mRNAs with different 5'UTR. These mRNA isoforms regulate the temporal and spatial expression of the gene, producing diverse pigmentation patterns. Here, we studied ASIP transcriptional variants and their expression in the skin of llamas with different coat color phenotypes. We also described the ASIP locus, including promoter usage and the splicing events that originate each transcript variant. Using 5'RACE-PCR we isolated seven ASIP transcripts with alternative 5'UTR, where exons 1A, 1A', 1C, 1D, and a novel non-coding exon 1A" were identified. Additionally, new alternative spliced forms were found. The diversity of ASIP 5'UTRs is originated by a complex pattern of alternative promoter usage, multiple transcription start sites and splicing events that include exon skipping and alternative 3' splicing site selection. We found that ASIP was highly expressed in llamas with white and brown phenotypes while black animals presented very low expression. The main responsible for this difference was a fusion transcript between ASIP and NCOA6 genes, which was present in the skin of white and brown llamas but not in the black ones. The rest of ASIP transcripts presented very low expression in the skin, indicating that the main regulation point for ASIP gene expression is at the transcriptional level. Nevertheless, the characteristics of the 5'UTRs sequences suggest that alternative transcripts could be regulated differently at the protein synthesis level.
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Affiliation(s)
- M Anello
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina
| | - M S Daverio
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina; Cátedra de Biología, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - S S Rodríguez
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina
| | - S R Romero
- Instituto de Investigaciones y Desarrollo Tecnológico para la Agricultura Familiar- Región NOA (IPAF NOA) INTA - Posta de Hornillos, Maimara, Jujuy, Argentina
| | - C Renieri
- School of Pharmacy, University of Camerino, Camerino, Marche, Italia
| | - L Vidal Rioja
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina
| | - F Di Rocco
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina.
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16
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Krause A, Kreiser M, Puppe B, Tuchscherer A, Düpjan S. The effect of age on discrimination learning and self-control in a marshmallow test for pigs. Sci Rep 2021; 11:18287. [PMID: 34521956 PMCID: PMC8440626 DOI: 10.1038/s41598-021-97770-x] [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: 04/06/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
Both humans and nonhuman animals need to show self-control and wait for a larger or better reward instead of a smaller or less preferred but instant reward on an everyday basis. We investigated whether this ability undergoes ontogenetic development in domestic pigs (similar to what is known in human infants) by testing if and for how long nine- and 16-week-old pigs wait for a larger amount of their preferred reward. In a delay-of-gratification task, animals first learned that a small reward was hidden under a white cup and a large reward under a black cup, and then the delay to deliver the large reward was gradually increased. The results show that older pigs could wait longer for a larger reward than younger pigs (10.6 ± 1.3 s vs. 5.2 ± 1.5 s), thereby confirming our hypothesis of ontogenetic development of self-control in pigs. This self-control is likely to be regulated by the behavioural inhibition system and associated systems. Self-control or, more specifically the lack of it may be involved in the development of abnormal behaviours, not only in humans but also in animals. Therefore, research on self-control in decision-making might provide a new perspective on abnormal behaviours in captive animals.
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Affiliation(s)
- Annika Krause
- grid.418188.c0000 0000 9049 5051Institute of Behavioural Physiology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Maren Kreiser
- grid.418188.c0000 0000 9049 5051Institute of Behavioural Physiology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Birger Puppe
- grid.418188.c0000 0000 9049 5051Institute of Behavioural Physiology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany ,grid.10493.3f0000000121858338Behavioural Sciences, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Armin Tuchscherer
- grid.418188.c0000 0000 9049 5051Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Sandra Düpjan
- grid.418188.c0000 0000 9049 5051Institute of Behavioural Physiology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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17
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Henkel J, Dubacher A, Bangerter E, Herren U, Ammann P, Drögemüller C, Flury C, Leeb T. Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats. J Hered 2021; 112:452-457. [PMID: 34050662 DOI: 10.1093/jhered/esab024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The Valais Blackneck goat is a Swiss goat breed with a characteristic coat color phenotype. Before the revision of the breed standard in 1938, 4 different color varieties of Valais goats were known. Besides Blackneck animals resembling the modern breed standard, the brown and white Copperneck goat, the white Capra Sempione, and the greyish Grüenochte comprised the historic Valais goats. The brown pigmentation of Copperneck goats had previously been traced back to an introgression of a mutant TYRP1 allele from Toggenburg goats. In the present study, we identified additional introgression events of distinct ASIP alleles causing the remaining 2 rare coat color patterns within the Valais Blackneck goat breed. We identified the introgression of the AWt allele from Appenzell or Saanen goats in white Capra Sempione goats. Similarly, introgression of the Apc allele from Peacock goats resulted in the greyish Grüenochte phenotype. These results demonstrate past hybridization events between breeds that are separated today. A perfect genotype-phenotype association in 393 Valais goats supported the causality of the genotyped variants for the different coat color phenotypes. Our study gives insights into the introgression of functionally relevant copy number variant (CNV) alleles controlling pigmentation between goat breeds with strikingly different coat color patterns.
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Affiliation(s)
- Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Alexandra Dubacher
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | - Ursula Herren
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
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18
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Li J, Lee M, Davis BW, Lamichhaney S, Dorshorst BJ, Siegel PB, Andersson L. Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken. Mol Biol Evol 2021; 37:2477-2486. [PMID: 32344431 PMCID: PMC7475036 DOI: 10.1093/molbev/msaa093] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Feathered leg is a trait in domestic chickens that has undergone intense selection by fancy breeders. Previous studies have shown that two major loci controlling feathered leg are located on chromosomes 13 and 15. Here, we present genetic evidence for the identification of candidate causal mutations at these loci. This was accomplished by combining classical linkage mapping using an experimental cross segregating for feathered leg and high-resolution identical-by-descent mapping using whole-genome sequence data from 167 samples of chicken with or without feathered legs. The first predicted causal mutation is a single-base change located 25 kb upstream of the gene for the forelimb-specific transcription factor TBX5 on chromosome 15. The second is a 17.7-kb deletion located ∼200 kb upstream of the gene for the hindlimb-specific transcription factor PITX1 on chromosome 13. These mutations are predicted to activate TBX5 and repress PITX1 expression, respectively. The study reveals a remarkable convergence in the evolution of the feathered-leg phenotype in domestic chickens and domestic pigeons, as this phenotype is caused by noncoding mutations upstream of the same two genes. Furthermore, the PITX1 causal variants are large overlapping deletions, 17.7 kb in chicken and 44 kb in pigeons. The results of the present study are consistent with the previously proposed model for pigeon that feathered leg is caused by reduced PITX1 expression and ectopic expression of TBX5 in hindlimb buds resulting in a shift of limb identity from hindlimb to more forelimb-like identity.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - MiOk Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ben J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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19
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He Y, Zhou X, Zheng R, Jiang Y, Yao Z, Wang X, Zhang Z, Zhang H, Li J, Yuan X. The Association of an SNP in the EXOC4 Gene and Reproductive Traits Suggests Its Use as a Breeding Marker in Pigs. Animals (Basel) 2021; 11:ani11020521. [PMID: 33671441 PMCID: PMC7921996 DOI: 10.3390/ani11020521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/07/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
In mammals, the exocyst complex component 4 (EXOC4) gene has often been reported to be involved in vesicle transport. The SNP rs81471943 (C/T) is located in the intron of porcine EXOC4, while six quantitative trait loci (QTL) within 5-10 Mb around EXOC4 are associated with ovary weight, teat number, total offspring born alive, and corpus luteum number. However, the molecular mechanisms between EXOC4 and the reproductive performance of pigs remains to be elucidated. In this study, rs81471943 was genotyped from a total of 994 Duroc sows, and the genotype and allele frequency of SNP rs81471943 (C/T) were statistically analyzed. Then, the associations between SNP rs81471943 and four reproductive traits, including number of piglets born alive (NBA), litter weight at birth (LWB), number of piglets weaned (NW), and litter weight at weaning (LWW), were determined. Sanger sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) were utilized to identify the rs81471943 genotype. We found that the genotype frequency of CC was significantly higher than that of CT and TT, and CC was the most frequent genotype for NBA, LWB, NW, and LWW. Moreover, 5'-deletion and luciferase assays identified a positive transcription regulatory element in the EXOC4 promoter. After exploring the EXOC4 promoter, SNP -1781G/A linked with SNP rs81471943 (C/T) were identified by analysis of the transcription activity of the haplotypes, and SNP -1781 G/A may influence the potential binding of P53, E26 transformation specific sequence -like 1 transcription factor (ELK1), and myeloid zinc finger 1 (MZF1). These findings provide useful information for identifying a molecular marker of EXOC4-assisted selection in pig breeding.
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Affiliation(s)
- Yingting He
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
| | - Xiaofeng Zhou
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
| | - Rongrong Zheng
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
| | - Yao Jiang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
| | - Zhixiang Yao
- Guangdong Dexing Food Co., Ltd., Shantou 515100, China;
| | - Xilong Wang
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510260, China;
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
- Correspondence: (J.L.); (X.Y.)
| | - Xiaolong Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (R.Z.); (Y.J.); (Z.Z.); (H.Z.)
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510260, China;
- Correspondence: (J.L.); (X.Y.)
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20
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Asadollahpour Nanaei H, Esmailizadeh A, Ayatollahi Mehrgardi A, Han J, Wu DD, Li Y, Zhang YP. Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony. BMC Genomics 2020; 21:496. [PMID: 32689947 PMCID: PMC7370493 DOI: 10.1186/s12864-020-06887-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
Background Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits. Results A number of protein-coding genes in windows with the top 1% values of FST (367 genes), XP-CLR (681 genes), and log2 (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size. Conclusions Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.
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Affiliation(s)
- Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran. .,State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China.
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
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21
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Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 2020; 16:e1008274. [PMID: 32433666 PMCID: PMC7239393 DOI: 10.1371/journal.pgen.1008274] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons. The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.
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Affiliation(s)
- Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Hannah Van Hollebeke
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward J. Osborne
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Zev Kronenberg
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Emily Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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22
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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23
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Singh B, Mal G, Kues WA, Yadav PS. The domesticated buffalo - An emerging model for experimental and therapeutic use of extraembryonic tissues. Theriogenology 2020; 151:95-102. [PMID: 32320839 DOI: 10.1016/j.theriogenology.2020.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/12/2020] [Accepted: 04/04/2020] [Indexed: 12/16/2022]
Abstract
Large animals play important roles as model animals for biomedical sciences and translational research. The water buffalo (Bubalus bubalis) is an economically important, multipurpose livestock species. Important assisted reproduction techniques, such as in vitro fertilization, cryo-conservation of sperm and embryos, embryo transfer, somatic cell nuclear transfer, genetic engineering, and genome editing have been successfully applied to buffaloes. Recently, detailed whole genome data and transcriptome maps have been generated. In addition, rapid progress has been made in stem cell biology of the buffalo. Apart from embryonic stem cells, bubaline extra-embryonic stem cells have gained particular interest. The multipotency of non-embryonic stem cells has been revealed, and their utility in basic and applied research is currently investigated. In particular, success achieved in bubaline extra-embryonic stem cells may have important roles in experimental biology and therapeutic regenerative medicine. Progress in other farm animals in assisted reproduction techniques, stem cell biology and genetic engineering, which could be of importance for buffalo, will also be briefly summarized.
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Affiliation(s)
- Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station Palampur, 176 061, India
| | - Gorakh Mal
- ICAR-Indian Veterinary Research Institute, Regional Station Palampur, 176 061, India
| | | | - Prem S Yadav
- ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, India.
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24
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Lindblad-Toh K. What animals can teach us about evolution, the human genome, and human disease. Ups J Med Sci 2020; 125:1-9. [PMID: 32054372 PMCID: PMC7054949 DOI: 10.1080/03009734.2020.1722298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
During the past 20 years, since I started as a postdoc, the world of genetics and genomics has changed dramatically. My main research goal throughout my career has been to understand human disease genetics, and I have developed comparative genomics and comparative genetics to generate resources and tools for understanding human disease. Through comparative genomics I have worked to sequence enough mammals to understand the functional potential of each base in the human genome as well as chosen vertebrates to study the evolutionary changes that have given many species their key traits. Through comparative genetics, I have developed the dog as a model for human disease, characterising the genome itself and determining a list of germ-line loci and somatic mutations causing complex diseases and cancer in the dog. Pulling all these findings and resources together opens new doors for understanding genome evolution, the genetics of complex traits and cancer in man and his best friend.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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25
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Zhang L, Huang Y, Wang M, Guo Y, Liang J, Yang X, Qi W, Wu Y, Si J, Zhu S, Li Z, Li R, Shi C, Wang S, Zhang Q, Tang Z, Wang L, Li K, Fei JF, Lan G. Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease. iScience 2019; 19:162-176. [PMID: 31376679 PMCID: PMC6677790 DOI: 10.1016/j.isci.2019.07.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/11/2019] [Accepted: 07/13/2019] [Indexed: 01/10/2023] Open
Abstract
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism.
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Affiliation(s)
- Li Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuemeng Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Meng Wang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yafen Guo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenjing Qi
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yanjun Wu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinglei Si
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Siran Zhu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhe Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Chao Shi
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shuo Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qunjie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Zhonglin Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ji-Feng Fei
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
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26
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A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens. Genet Sel Evol 2019; 51:51. [PMID: 31533607 PMCID: PMC6751821 DOI: 10.1186/s12711-019-0492-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/29/2019] [Indexed: 12/27/2022] Open
Abstract
Background Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which causes high mortality. Furthermore, an outbreak of SP infection can result in a considerable number of carriers that become potential transmitters, thus, threatening fellow chickens and offspring. In this study, we conducted a genome-wide association study (GWAS) to detect potential genomic loci and candidate genes associated with two disease-related traits: death and carrier state. Methods In total, 818 birds were phenotyped for death and carrier state traits through a SP challenge experiment, and genotyped by using a 600 K high-density single nucleotide polymorphism (SNP) array. A GWAS using a single-marker linear mixed model was performed with the GEMMA software. RNA-sequencing on spleen samples was carried out for further identification of candidate genes. Results We detected a region that was located between 33.48 and 34.03 Mb on chicken chromosome 4 and was significantly associated with death, with the most significant SNP (rs314483802) accounting for 11.73% of the phenotypic variation. Two candidate genes, FBXW7 and LRBA, were identified as the most promising genes involved in resistance to SP. The expression levels of FBXW7 and LRBA were significantly downregulated after SP infection, which suggests that they may have a role in controlling SP infections. Two other significant loci and related genes (TRAF3 and gga-mir-489) were associated with carrier state, which indicates a different polygenic determinism compared with that of death. In addition, genomic inbreeding coefficients showed no correlation with resistance to SP within each breed in our study. Conclusions The results of this GWAS with a carefully organized Salmonella challenge experiment represent an important milestone in understanding the genetics of infectious disease resistance, offer a theoretical basis for breeding SP-resistant chicken lines using marker-assisted selection, and provide new information for salmonellosis research in humans and other animals.
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27
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Sánchez‐Villagra MR, van Schaik CP. Evaluating the self‐domestication hypothesis of human evolution. Evol Anthropol 2019; 28:133-143. [DOI: 10.1002/evan.21777] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 12/12/2018] [Accepted: 03/03/2019] [Indexed: 12/17/2022]
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28
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Yang Y, Liu C, Adeola AC, Sulaiman X, Xie HB, Zhang YP. Artificial selection drives differential gene expression during pig domestication. J Genet Genomics 2019; 46:97-100. [PMID: 30850275 DOI: 10.1016/j.jgg.2018.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/08/2018] [Accepted: 09/04/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Yang Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Chaorui Liu
- National Pilot School of Software, Yunnan University, Kunming, 650500, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
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29
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Velie BD, Lillie M, Fegraeus KJ, Rosengren MK, Solé M, Wiklund M, Ihler CF, Strand E, Lindgren G. Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model. BMC Genomics 2019; 20:104. [PMID: 30717660 PMCID: PMC6360714 DOI: 10.1186/s12864-019-5484-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/28/2019] [Indexed: 01/07/2023] Open
Abstract
Background Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exists between breeds, making the horse particularly well suited for genetic studies of athleticism. To identify genomic regions associated with athleticism as it pertains to trotting racing ability in the horse, the current study applies a pooled sequence analysis approach using a unique Nordic horse model. Results Pooled sequence data from three Nordic horse populations were used for FST analysis. After strict filtering, FST analysis yielded 580 differentiated regions for trotting racing ability. Candidate regions on equine chromosomes 7 and 11 contained the largest number of SNPs (n = 214 and 147, respectively). GO analyses identified multiple genes related to intelligence, energy metabolism, and skeletal development as potential candidate genes. However, only one candidate region for trotting racing ability overlapped a known racing ability QTL. Conclusions Not unexpected for genomic investigations of complex traits, the current study identified hundreds of candidate regions contributing to trotting racing ability in the horse. Likely resulting from the cumulative effects of many variants across the genome, racing ability continues to demonstrate its polygenic nature with candidate regions implicating genes influencing both musculature and neurological development. Electronic supplementary material The online version of this article (10.1186/s12864-019-5484-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brandon D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. .,School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
| | - Mette Lillie
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kim Jäderkvist Fegraeus
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria K Rosengren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marina Solé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maja Wiklund
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carl-Fredrik Ihler
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Eric Strand
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
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30
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Jagannathan V, Gerber V, Rieder S, Tetens J, Thaller G, Drögemüller C, Leeb T. Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses. Anim Genet 2018; 50:74-77. [PMID: 30525216 DOI: 10.1111/age.12753] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2018] [Indexed: 11/29/2022]
Abstract
Whole-genome sequencing studies are vital to gain a thorough understanding of genomic variation. Here, we summarize the results of a whole-genome sequencing study comprising 88 horses and ponies from diverse breeds at 19.1× average coverage. The paired-end reads were mapped to the current EquCab3.0 horse reference genome assembly, and we identified approximately 23.5 million single nucleotide variants and 2.3 million short indel variants. Our dataset included at least 7 million variants that were not previously reported. On average, each individual horse genome carried ∼5.7 million single nucleotides and 0.8 million small indel variants with respect to the reference genome assembly. The variants were functionally annotated. We provide two examples for potentially deleterious recessive alleles that were identified in a heterozygous state in individual genome sequences. Appropriate management of such deleterious recessive alleles in horse breeding programs should help to improve fertility and reduce the prevalence of heritable diseases. This comprehensive dataset has been made publicly available, will represent a valuable resource for future horse genetic studies and supports the goal of accelerating the rates of genetic gain in domestic horse.
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Affiliation(s)
- V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - V Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland
| | - S Rieder
- Swiss National Stud Farm, Agroscope, 1580, Avenches, Switzerland
| | - J Tetens
- Department of Animal Sciences, Functional Breeding Group, Georg-August University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - G Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
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Abstract
In many birds, bright red plumage in males helps to attract females, a classic example of sexual selection. Studies in zebra finches and canaries have now identified the gene responsible for red coloration.
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Affiliation(s)
- Gregory Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94035, USA.
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32
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Menzi F, Keller I, Reber I, Beck J, Brenig B, Schütz E, Leeb T, Drögemüller C. Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation. Sci Rep 2016; 6:28438. [PMID: 27329507 PMCID: PMC4916431 DOI: 10.1038/srep28438] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023] Open
Abstract
The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.
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Affiliation(s)
- Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Irene Keller
- Department of Clinical Research and Swiss Institute of Bioinformatics, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Julia Beck
- Chronix Biomedical, Goetheallee 8, 37073 Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
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