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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Paul K, Restoux G, Phocas F. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Genet Sel Evol 2024; 56:13. [PMID: 38389056 PMCID: PMC10882880 DOI: 10.1186/s12711-024-00884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. RESULTS Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). CONCLUSIONS Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.
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Affiliation(s)
- Katy Paul
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gwendal Restoux
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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Yin ZT, Li XQ, Sun YX, Smith J, Hincke M, Yang N, Hou ZC. Selection on the promoter regions plays an important role in complex traits during duck domestication. BMC Biol 2023; 21:303. [PMID: 38129834 PMCID: PMC10740227 DOI: 10.1186/s12915-023-01801-0] [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: 02/01/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the noncoding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood. RESULTS We constructed a genomics, transcriptomics, and epigenomics map of the duck genome and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the overexpression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment. CONCLUSIONS This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.
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Affiliation(s)
- Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiao-Qin Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Maxwell Hincke
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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Nayak SS, Panigrahi M, Rajawat D, Ghildiyal K, Sharma A, Parida S, Bhushan B, Mishra BP, Dutt T. Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data. Mamm Genome 2023; 34:615-631. [PMID: 37843569 DOI: 10.1007/s00335-023-10021-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023]
Abstract
The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - B P Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
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Benítez-Burraco A, Uriagereka J, Nataf S. The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development. Dev Genes Evol 2023; 233:123-135. [PMID: 37552321 PMCID: PMC10746608 DOI: 10.1007/s00427-023-00709-7] [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: 02/26/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain.
- Área de Lingüística General, Departamento de Lengua Española, Lingüística y Teoría de la Literatura, Facultad de Filología, Universidad de Sevilla, C/ Palos de la Frontera s/n., 41007-, Sevilla, España.
| | - Juan Uriagereka
- Department of Linguistics and School of Languages, Literatures & Cultures, University of Maryland, College Park, MD, USA
| | - Serge Nataf
- Stem-cell and Brain Research Institute, 18 avenue de Doyen Lépine, F-69500, Bron, France
- University of Lyon 1, 43 Bd du 11 Novembre 1918, F-69100, Villeurbanne, France
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d'Arsonval, F-69003, Lyon, France
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Wang J, Hua G, Chen J, Cui K, Yang Z, Han D, Yang X, Dong X, Ma Y, Cai G, Zhang Y, Li J, Tai Y, Da L, Li X, Ma L, Ma Q, Li R, Liu J, Darwish HYA, Wu K, Rong W, Liu W, Zhao Y, Deng X. Epigenetic mechanism of Gtl2-miRNAs causes the primitive sheep characteristics found in purebred Merino sheep. Cell Biosci 2023; 13:190. [PMID: 37828606 PMCID: PMC10571318 DOI: 10.1186/s13578-023-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND It is not uncommon for some individuals to retain certain primitive characteristics even after domestication or long-term intensive selection. Wild ancestors or original varieties of animals typically possess strong adaptability to environmental preservation, a trait that is often lacking in highly artificially selected populations. In the case of the Merino population, a world-renowned fine wool sheep breed, a phenotype with primitive coarse wool characteristic has re-emerged. It is currently unclear whether this characteristic is detrimental to the production of fine wool or whether it is linked to the adaptability of sheep. The underlying genetic/epigenetic mechanisms behind this trait are also poorly understood. RESULTS This study identified lambs with an ancestral-like coarse (ALC) wool type that emerged during the purebred breeding of Merino fine wool sheep. The presence of this primitive sheep characteristic resulted in better environmental adaptability in lambs, as well as improved fine wool yield in adulthood. Reciprocal cross experiments revealed that the ALC phenotype exhibited maternal genetic characteristics. Transcriptomic SNP analysis indicated that the ALC phenotype was localized to the imprinted Gtl2-miRNAs locus, and a significant correlation was found between the ALC wool type and a newly identified short Interstitial Telomeric Sequences (s-ITSs) at this locus. We further confirmed that a novel 38-nt small RNA transcribed from these s-ITSs, in combination with the previously reported 22-nt small RNAs cluster from the Gtl2-miRNAs locus, synergistically inhibited PI3K/AKT/Metabolic/Oxidative stress and subsequent apoptotic pathways in wool follicle stem cells, resulting in the ALC wool type. The necessity of Gtl2-miRNAs in controlling primary hair follicle morphogenesis, as well as the wool follicle type for ALC wool lambs, was verified using intergenic differentially methylated region-knockout mice. CONCLUSION The ALC wool type of Merino sheep, which does not reduce wool quality but increases yield and adaptability, is regulated by epigenetic mechanisms in the imprinted Gtl2-miRNAs region on sheep chromosome 18, with the maternally expressed imprinted gene responsible for the ALC phenotype. This study highlights the significance of epigenetic regulation during embryonic and juvenile stages and emphasizes the advantages of early adaptation breeding for maternal parents in enhancing the overall performance of their offspring.
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Affiliation(s)
- Jiankui Wang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Guoying Hua
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jianfei Chen
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Kai Cui
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100086, China
| | - Zu Yang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Deping Han
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xue Yang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xianggui Dong
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuhao Ma
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Ganxian Cai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jinnan Li
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yurong Tai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Lai Da
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031, China
| | - Xinhai Li
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Hesham Y A Darwish
- Department of Applied Biotechnology, Molecular Biology Researches & Studies Institute, Assiut University, Assiut, 71526, Egypt
| | - Keliang Wu
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiheng Rong
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031, China
| | - Wansheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yaofeng Zhao
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuemei Deng
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
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Wang J, Hua G, Cai G, Ma Y, Yang X, Zhang L, Li R, Liu J, Ma Q, Wu K, Zhao Y, Deng X. Genome-wide DNA methylation and transcriptome analyses reveal the key gene for wool type variation in sheep. J Anim Sci Biotechnol 2023; 14:88. [PMID: 37420295 DOI: 10.1186/s40104-023-00893-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/07/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wool fibers are valuable materials for textile industry. Typical wool fibers are divided into medullated and non-medullated types, with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles. The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding. The fine wool sheep have a non-medullated coat. However, the critical period determining the type of wool follicles is the embryonic stage, which limits the phenotypic observation and variant contrast, making both selection and studies of wool type variation fairly difficult. RESULTS During the breeding of a modern fine (MF) wool sheep population with multiple-ovulation and embryo transfer technique, we serendipitously discovered lambs with ancestral-like coarse (ALC) wool. Whole-genome resequencing confirmed ALC wool lambs as a variant type from the MF wool population. We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals, and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs. Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes. An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former. Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles. CONCLUSION In this study, we conducted genome-wide differential methylation site association analysis on differential wool type trait, and located the only CpG locus that strongly associated with primary wool follicle development. Combined with transcriptome analysis, SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin. The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.
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Affiliation(s)
- Jiankui Wang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Guoying Hua
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Ganxian Cai
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yuhao Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xue Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Letian Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qing Ma
- Animal Science Institute of Ningxia Agriculture and Forestry Academy, Yinchuan, 750002, China
| | - Keliang Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xuemei Deng
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
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8
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Population structure and hybridisation in a population of Hawaiian feral chickens. Heredity (Edinb) 2023; 130:154-162. [PMID: 36725960 PMCID: PMC9981564 DOI: 10.1038/s41437-022-00589-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.
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9
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Nagasawa T, Kimura Y, Masuda K, Uchiyama H. Physiological Assessment of the Health and Welfare of Domestic Cats-An Exploration of Factors Affecting Urinary Cortisol and Oxytocin. Animals (Basel) 2022; 12:ani12233330. [PMID: 36496851 PMCID: PMC9738311 DOI: 10.3390/ani12233330] [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: 10/12/2022] [Revised: 11/15/2022] [Accepted: 11/26/2022] [Indexed: 11/30/2022] Open
Abstract
Physiological samples are beneficial in assessing the health and welfare of cats. However, most studies have been conducted in specialized environments, such as shelters or laboratories, and have not focused on cats living in domestic settings. In addition, most studies have assessed physiological stress states in cats based on cortisol, and none have quantified positive indicators, such as oxytocin. Here, we collected urine samples from 49 domestic cats and quantified urinary cortisol, oxytocin, and creatinine using ELISA. To identify factors influencing hormone levels, owners responded to questionnaires regarding their housing environment, individual cat information, and the frequency of daily interactions with their cats. Using principal component analysis, principal component scores for daily interactions were extracted. These results showed that the frequency of tactile and auditory signal-based communication by owners was positively correlated with the mean concentration of oxytocin in the urine. Additionally, this communication was more frequent in younger cats or cats that had experienced a shorter length of cohabitation with the owner. However, no factors associated with urinary cortisol concentration were identified. Our study indicates that interactions and relationships with the owner influence the physiological status of cats and suggests that oxytocin is a valuable parameter for assessing their health and welfare.
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Affiliation(s)
- Takumi Nagasawa
- Department of Human and Animal-Plant Relationships, Graduate School of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan
| | - Yuichi Kimura
- Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan
| | - Koji Masuda
- Department of Human and Animal-Plant Relationships, Graduate School of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan
- Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan
| | - Hidehiko Uchiyama
- Department of Human and Animal-Plant Relationships, Graduate School of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan
- Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan
- Correspondence: ; Tel.: +81-046-270-6263
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10
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Cunha F, Stingo-Hirmas D, Cardoso RF, Wright D, Henriksen R. Neuronal and non-neuronal scaling across brain regions within an intercross of domestic and wild chickens. Front Neuroanat 2022; 16:1048261. [PMID: 36506870 PMCID: PMC9732670 DOI: 10.3389/fnana.2022.1048261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2022] Open
Abstract
The allometric scaling of the brain size and neuron number across species has been extensively studied in recent years. With the exception of primates, parrots, and songbirds, larger brains have more neurons but relatively lower neuronal densities than smaller brains. Conversely, when considering within-population variability, it has been shown that mice with larger brains do not necessarily have more neurons but rather more neurons in the brain reflect higher neuronal density. To what extent this intraspecific allometric scaling pattern of the brain applies to individuals from other species remains to be explored. Here, we investigate the allometric relationships among the sizes of the body, brain, telencephalon, cerebellum, and optic tectum, and the numbers of neurons and non-neuronal cells of the telencephalon, cerebellum, and optic tectum across 66 individuals originated from an intercross between wild and domestic chickens. Our intercross of chickens generates a population with high variation in brain size, making it an excellent model to determine the allometric scaling of the brain within population. Our results show that larger chickens have larger brains with moderately more neurons and non-neuronal cells. Yet, absolute number of neurons and non-neuronal cells correlated strongly and positively with the density of neurons and non-neuronal cells, respectively. As previously shown in mice, this scaling pattern is in stark contrast with what has been found across different species. Our findings suggest that neuronal scaling rules across species are not a simple extension of the neuronal scaling rules that apply within a species, with important implications for the evolutionary developmental origins of brain diversity.
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11
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Xu B, Yang G, Jiao B, Zhu H. Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication. Front Genet 2022; 13:944933. [PMID: 36276948 PMCID: PMC9579347 DOI: 10.3389/fgene.2022.944933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs’ potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.
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Affiliation(s)
- Baoyan Xu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Medical Engineering Department, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Guixian Yang
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Hao Zhu,
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12
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Does the Domestication Syndrome Apply to the Domestic Pig? Not Completely. Animals (Basel) 2022; 12:ani12182458. [PMID: 36139318 PMCID: PMC9495052 DOI: 10.3390/ani12182458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 01/21/2023] Open
Abstract
The ‘domestication syndrome’ defines a suite of features that domesticated animals possess as the result of the artificial selection operated by Homo sapiens since the Neolithic. An interesting anthropological question is whether such features, including increased tameness and reduced aggression, apply to all domesticated forms. We investigated this issue in the domestic pig (Sus scrofa). We video-recorded and analysed aggression and social play (mostly play-fighting) sessions from piglets (three litters; n = 24) and wild boar hybrids (domestic pig mother x wild boar father; three litters; n = 27) from 6–50 days of age, raised in the same woodland/grassland habitat and extensive farming management (ethical farm ‘Parva Domus’, Cavagnolo, Torino). Play and aggression session structure was assessed via Asymmetry (AI; offensive/defensive pattern balance), Shannon (H′; pattern variability), and Pielou (J; pattern evenness) indices. We found that piglets played more (especially after the 20th day of life) and engaged in less variable and uniform sessions than wild boar hybrids. Compared to hybrids, piglets showed less variable but more frequent (especially when approaching weaning) and asymmetrical aggressive events. Thus, the domestication syndrome does not seem to fully apply to either social play or aggression, possibly because artificial selection has produced greater tameness of pigs towards humans than towards conspecifics.
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13
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Machová K, Málková A, Vostrý L. Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes. Genes (Basel) 2022; 13:genes13040613. [PMID: 35456419 PMCID: PMC9025449 DOI: 10.3390/genes13040613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/26/2022] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
- Correspondence:
| | - Anežka Málková
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Luboš Vostrý
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
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14
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Lesch R, Kitchener AC, Hantke G, Kotrschal K, Fitch WT. Cranial volume and palate length of cats, Felis spp., under domestication, hybridization and in wild populations. ROYAL SOCIETY OPEN SCIENCE 2022; 9:210477. [PMID: 35116138 PMCID: PMC8790375 DOI: 10.1098/rsos.210477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 12/21/2021] [Indexed: 05/07/2023]
Abstract
Reduced brain size, compared with wild individuals, is argued to be a key characteristic of domesticated mammal species, and often cited as a key component of a putative 'domestication syndrome'. However, brain size comparisons are often based on old, inaccessible literature and in some cases drew comparisons between domestic animals and wild species that are no longer thought to represent the true progenitor species of the domestic species in question. Here we replicate studies on cranial volumes in domestic cats that were published in the 1960s and 1970s, comparing wildcats, domestic cats and their hybrids. Our data indicate that domestic cats indeed, have smaller cranial volumes (implying smaller brains) relative to both European wildcats (Felis silvestris) and the wild ancestors of domestic cats, the African wildcats (Felis lybica), verifying older results. We further found that hybrids of domestic cats and European wildcats have cranial volumes that cluster between those of the two parent species. Apart from replicating these studies, we also present new data on palate length in Felis cat skulls, showing that domestic cat palates are shorter than those of European wildcats but longer than those of African wildcats. Our data are relevant to current discussions of the causes and consequences of the 'domestication syndrome' in domesticated mammals.
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Affiliation(s)
- Raffaela Lesch
- Department of Behavioral and Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Institute of Animal Welfare Science, University for Veterinary Medicine, Vienna, Austria
| | | | - Georg Hantke
- Department Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Kurt Kotrschal
- Department of Behavioral and Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - W. Tecumseh Fitch
- Department of Behavioral and Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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15
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Núñez-León D, Cordero GA, Schlindwein X, Jensen P, Stoeckli E, Sánchez-Villagra MR, Werneburg I. Shifts in growth, but not differentiation, foreshadow the formation of exaggerated forms under chicken domestication. Proc Biol Sci 2021; 288:20210392. [PMID: 34130497 DOI: 10.1098/rspb.2021.0392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Domestication provides an outstanding opportunity for biologists to explore the underpinnings of organismal diversification. In domesticated animals, selective breeding for exaggerated traits is expected to override genetic correlations that normally modulate phenotypic variation in nature. Whether this strong directional selection affects the sequence of tightly synchronized events by which organisms arise (ontogeny) is often overlooked. To address this concern, we compared the ontogeny of the red junglefowl (RJF) (Gallus gallus) to four conspecific lineages that underwent selection for traits of economic or ornamental value to humans. Trait differentiation sequences in embryos of these chicken breeds generally resembled the representative ancestral condition in the RJF, thus revealing that early ontogeny remains highly canalized even during evolution under domestication. This key finding substantiates that the genetic cost of domestication does not necessarily compromise early ontogenetic steps that ensure the production of viable offspring. Instead, disproportionate beak and limb growth (allometry) towards the end of ontogeny better explained phenotypes linked to intense selection for industrial-scale production over the last 100 years. Illuminating the spatial and temporal specificity of development is foundational to the enhancement of chicken breeds, as well as to ongoing research on the origins of phenotypic variation in wild avian species.
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Affiliation(s)
- Daniel Núñez-León
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, 8006, Zürich, Switzerland
| | - Gerardo A Cordero
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls, Universität Tübingen, Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Xenia Schlindwein
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls, Universität Tübingen, Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Per Jensen
- IFM Biologi, AVIAN Behavioural Genomics and Physiology group, Linköping University, SE-58183 Linköping, Sweden
| | - Esther Stoeckli
- Department of Molecular Life Sciences, Universität Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Marcelo R Sánchez-Villagra
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, 8006, Zürich, Switzerland
| | - Ingmar Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls, Universität Tübingen, Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität Tübingen, Tübingen, Germany
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16
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Šimić G, Vukić V, Kopić J, Krsnik Ž, Hof PR. Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective. Biomolecules 2020; 11:E2. [PMID: 33375093 PMCID: PMC7822183 DOI: 10.3390/biom11010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.
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Affiliation(s)
- Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Vana Vukić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Janja Kopić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Željka Krsnik
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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17
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Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 2020; 11:6014. [PMID: 33293529 PMCID: PMC7723042 DOI: 10.1038/s41467-020-19813-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition. A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys.
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18
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Höglund A, Henriksen R, Fogelholm J, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 2020; 4:1713-1724. [PMID: 32958860 DOI: 10.1038/s41559-020-01310-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/26/2020] [Indexed: 01/06/2023]
Abstract
Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.
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Affiliation(s)
- Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M Guerrero-Bosagna
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.,Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
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19
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Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
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20
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Hou Y, Qi F, Bai X, Ren T, Shen X, Chu Q, Zhang X, Lu X. Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals. BMC Genomics 2020; 21:204. [PMID: 32131728 PMCID: PMC7057487 DOI: 10.1186/s12864-020-6613-1] [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: 05/25/2019] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
Background In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cognition, which partly or indirectly result in consequences for economic productivity. Such independent adaptations provide an excellent model to investigate molecular mechanisms and patterns of evolutionary convergence driven by artificial selection. Results First performing population genomic and brain transcriptional comparisons in 68 wild and domesticated chickens, we revealed evolutionary trajectories, genetic architectures and physiologic bases of adaptively behavioral alterations. To extensively decipher molecular convergence on behavioral changes thanks to domestication, we investigated selection signatures in hundreds of genomes and brain transcriptomes across chicken and 6 other domesticated mammals. Although no shared substitution was detected, a common enrichment of the adaptive mutations in regulatory sequences was observed, presenting significance to drive adaptations. Strong convergent pattern emerged at levels of gene, gene family, pathway and network. Genes implicated in neurotransmission, semaphorin, tectonic protein and modules regulating neuroplasticity were central focus of selection, supporting molecular repeatability of homoplastic behavior reshapes. Genes at nodal positions in trans-regulatory networks were preferably targeted. Consistent down-regulation of majority brain genes may be correlated with reduced brain size during domestication. Up-regulation of splicesome genes in chicken rather mammals highlights splicing as an efficient way to evolve since avian-specific genomic contraction of introns and intergenics. Genetic burden of domestication elicits a general hallmark. The commonly selected genes were relatively evolutionary conserved and associated with analogous neuropsychiatric disorders in human, revealing trade-off between adaption to life with human at the cost of neural changes affecting fitness in wild. Conclusions After a comprehensive investigation on genomic diversity and evolutionary trajectories in chickens, we revealed basis, pattern and evolutionary significance of molecular convergence in domesticated bird and mammals, highlighted the genetic basis of a compromise on utmost adaptation to the lives with human at the cost of high risk of neurophysiological changes affecting animals’ fitness in wild.
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Affiliation(s)
- Yali Hou
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,China National Center for Bioinformation, Beijing, People's Republic of China.
| | - Furong Qi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xue Bai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China
| | - Tong Ren
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xu Shen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Xiquan Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China.
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, People's Republic of China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China.
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21
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Gleeson BT. Masculinity and the Mechanisms of Human Self-Domestication. ADAPTIVE HUMAN BEHAVIOR AND PHYSIOLOGY 2020. [DOI: 10.1007/s40750-019-00126-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Fogelholm J, Henriksen R, Höglund A, Huq N, Johnsson M, Lenz R, Jensen P, Wright D. CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken. Sci Rep 2020; 10:1161. [PMID: 31980681 PMCID: PMC6981141 DOI: 10.1038/s41598-020-57710-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 12/28/2019] [Indexed: 01/12/2023] Open
Abstract
Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic × wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.
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Affiliation(s)
- J Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - R Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - A Höglund
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - N Huq
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - M Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, United Kingdom.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - R Lenz
- ITN Dept of Science and Technology, Linköping University, Linköping, 58183, Sweden
| | - P Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - D Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden.
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23
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Benítez-Burraco A. Genes Positively Selected in Domesticated Mammals Are Significantly Dysregulated in the Blood of Individuals with Autism Spectrum Disorders. Mol Syndromol 2020; 10:306-312. [PMID: 32021604 PMCID: PMC6995977 DOI: 10.1159/000505116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Human self-domestication (i.e., the presence of traits in our species that are commonly found in domesticated animals) has been hypothesized to have contributed to the emergence of many human-specific features, including aspects of our cognition and behavior. Signs of self-domestication have been claimed to be attenuated in individuals with autism spectrum disorders (ASD), this conceivably accounting for facets of their distinctive cognitive and behavioral profile, although this possibility needs to be properly tested. In this study, we have found that candidate genes for mammal domestication, but not for neural crest development and function, are significantly dysregulated in the blood of subjects with ASD. The set of differentially expressed genes (DEGs) is enriched in biological and molecular processes, as well as in pathological phenotypes, of relevance for the etiology of ASD, like lipid metabolism, cell apoptosis, the activity of the insulin-like growth factor, gene expression regulation, skin/hair anomalies, musculoskeletal abnormalities, and hearing impairment. Moreover, among the DEGs, there are known candidates for ASD and/or genes involved in biological processes known to be affected in ASD. Our findings give support to the view that one important aspect of the etiopathogenesis of ASD is the abnormal manifestation of features of human self-domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
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24
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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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25
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Xu W, Yang T, Qiu L, Chapman MA, Li D, Liu A. Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi-woody crop. PLANT DIRECT 2019; 3:e00173. [PMID: 31641699 PMCID: PMC6802463 DOI: 10.1002/pld3.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication origin, genomic variation, and potential targets of selection underlying domestication traits remain unknown. Here, we performed a phylogenetic analysis, which suggests that the wild accessions were distinctively separated from the cultivated accessions. Genome sequencing of three accessions (one each wild, landrace, and cultivar) showed a large number of genetic variants between wild and cultivated castor bean (ZB306 or Hale), and relatively few variants between cultivar ZB306 and Hale. Comparative genome analysis revealed many candidate genes of selection and key pathways potentially involved in the transition from a perennial woody tree to annual crop. Interestingly, among 16 oil-related genes only three showed evidence of selection and the remainder showed low genetic variation at the population level, suggesting strong purifying selection in both the wild and domesticated gene pools. These results extend our understanding of the origin, genomic variation, and domestication, and provide a valuable resource for future gene-trait associations and castor bean breeding.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Tianquan Yang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lijun Qiu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Mark A. Chapman
- Biological Sciences and Centre for Underutilised CropsUniversity of SouthamptonSouthamptonUK
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Aizhong Liu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of ChinaMinistry of EducationSouthwest Forestry UniversityKunmingChina
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26
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Gering E, Incorvaia D, Henriksen R, Wright D, Getty T. Maladaptation in feral and domesticated animals. Evol Appl 2019; 12:1274-1286. [PMID: 31417614 PMCID: PMC6691326 DOI: 10.1111/eva.12784] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/10/2019] [Accepted: 02/07/2019] [Indexed: 12/14/2022] Open
Abstract
Selection regimes and population structures can be powerfully changed by domestication and feralization, and these changes can modulate animal fitness in both captive and natural environments. In this review, we synthesize recent studies of these two processes and consider their impacts on organismal and population fitness. Domestication and feralization offer multiple windows into the forms and mechanisms of maladaptation. Firstly, domestic and feral organisms that exhibit suboptimal traits or fitness allow us to identify their underlying causes within tractable research systems. This has facilitated significant progress in our general understandings of genotype-phenotype relationships, fitness trade-offs, and the roles of population structure and artificial selection in shaping domestic and formerly domestic organisms. Additionally, feralization of artificially selected gene variants and organisms can reveal or produce maladaptation in other inhabitants of an invaded biotic community. In these instances, feral animals often show similar fitness advantages to other invasive species, but they are also unique in their capacities to modify natural ecosystems through introductions of artificially selected traits. We conclude with a brief consideration of how emerging technologies such as genome editing could change the tempos, trajectories, and ecological consequences of both domestication and feralization. In addition to providing basic evolutionary insights, our growing understanding of mechanisms through which artificial selection can modulate fitness has diverse and important applications-from enhancing the welfare, sustainability, and efficiency of agroindustry, to mitigating biotic invasions.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior ProgramMichigan State UniversityEast LansingMichigan
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior ProgramMichigan State UniversityEast LansingMichigan
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology GroupLinköping UniversitySweden
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology GroupLinköping UniversitySweden
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior ProgramMichigan State UniversityEast LansingMichigan
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27
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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28
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Muñoz M, Bozzi R, García F, Núñez Y, Geraci C, Crovetti A, García-Casco J, Alves E, Škrlep M, Charneca R, Martins JM, Quintanilla R, Tibau J, Kušec G, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernández AI, Óvilo C. Diversity across major and candidate genes in European local pig breeds. PLoS One 2018; 13:e0207475. [PMID: 30458028 PMCID: PMC6245784 DOI: 10.1371/journal.pone.0207475] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.
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Affiliation(s)
- María Muñoz
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | | | - Fabián García
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | | | | | | | - Rui Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Jose M. Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | | | - Joan Tibau
- Programa de Genética y Mejora Animal, IRTA, Barcelona, Spain
| | - Goran Kušec
- University of Osijek, Faculty of Agrobiotechnical Sciences, Osijek, Croatia
| | | | | | - Juliette Riquet
- Génétique Physiologie et Système d’Elevage, INRA, Castanet-Tolosan, France
| | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Jose P. Araujo
- Instituto Politecnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Čedomir Radović
- Institute for Animal Husbandry-Pig Research Department, Belgrade-Zemun, Serbia
| | - Radomir Savić
- University of Belgrade, Faculty of agriculture, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of animal science, Faculty of agriculture, University of Zagreb, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Roma, Italy
| | | | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Cristina Óvilo
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
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29
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Yurchenko AA, Daetwyler HD, Yudin N, Schnabel RD, Vander Jagt CJ, Soloshenko V, Lhasaranov B, Popov R, Taylor JF, Larkin DM. Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation. Sci Rep 2018; 8:12984. [PMID: 30154520 PMCID: PMC6113280 DOI: 10.1038/s41598-018-31304-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/16/2018] [Indexed: 01/08/2023] Open
Abstract
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, 3083, Victoria, Australia
| | - Nikolay Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Victoria, Australia
| | | | | | - Ruslan Popov
- Yakutian Research Institute of Agriculture, 677001, Yakutsk, Russia
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia.
- Royal Veterinary College, University of London, NW01 0TU, London, UK.
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30
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Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli KP, Gulevich RG, Vladimirova AV, Hekman JP, Perelman PL, Graphodatsky AS, O'Brien SJ, Wang X, Clark AG, Acland GM, Trut LN, Zhang G. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2018; 2:1479-1491. [PMID: 30082739 DOI: 10.1038/s41559-018-0611-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes the main trafficking protein for AMPA glutamate receptors and neurexins and suggests a role for synaptic plasticity in fox domestication. Other regions identified as likely to have been under selection in foxes include genes implicated in human neurological disorders, mouse behaviour and dog domestication. The fox represents a powerful model for the genetic analysis of affiliative and aggressive behaviours that can benefit genetic studies of behaviour in dogs and other mammals, including humans.
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Affiliation(s)
- Anna V Kukekova
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA.
| | - Jennifer L Johnson
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA
| | - Xueyan Xiang
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Shaohong Feng
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Shiping Liu
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Halie M Rando
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA
| | - Anastasiya V Kharlamova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yury Herbeck
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Zijun Xiong
- China National Genebank, BGI -Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Violetta Beklemischeva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington DC, USA.,Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia
| | - Rimma G Gulevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya V Vladimirova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Jessica P Hekman
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Aleksander S Graphodatsky
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Pathobiology, Auburn University, Auburn, AL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Gregory M Acland
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Guojie Zhang
- China National Genebank, BGI -Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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31
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Fam BS, Paré P, Felkl AB, Vargas-Pinilla P, Paixão-Côrtes VR, Viscardi LH, Bortolini MC. Oxytocin and arginine vasopressin systems in the domestication process. Genet Mol Biol 2018; 41:235-242. [PMID: 29668014 PMCID: PMC5913714 DOI: 10.1590/1678-4685-gmb-2017-0069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/01/2017] [Indexed: 11/22/2022] Open
Abstract
Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication process. Furthermore, AVPR1a, which plays a role in social behavior, is under relaxed selective constraint in domesticated species. These results provide new insights into the nature of the domestication process and its impact on the OXT-AVP system.
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Affiliation(s)
- Bibiana S.O. Fam
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Pamela Paré
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Aline B. Felkl
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | | | | | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
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Derks MFL, Herrero-Medrano JM, Crooijmans RPMA, Vereijken A, Long JA, Megens HJ, Groenen MAM. Early and late feathering in turkey and chicken: same gene but different mutations. Genet Sel Evol 2018; 50:7. [PMID: 29566646 PMCID: PMC5863816 DOI: 10.1186/s12711-018-0380-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/15/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Sex-linked slow (SF) and fast (FF) feathering rates at hatch have been widely used in poultry breeding for autosexing at hatch. In chicken, the sex-linked K (SF) and k+ (FF) alleles are responsible for the feathering rate phenotype. Allele K is dominant and a partial duplication of the prolactin receptor gene has been identified as the causal mutation. Interestingly, some domesticated turkey lines exhibit similar slow- and fast-feathering phenotypes, but the underlying genetic components and causal mutation have never been investigated. In this study, our aim was to investigate the molecular basis of feathering rate at hatch in domestic turkey. RESULTS We performed a sequence-based case-control association study and detected a genomic region on chromosome Z, which is statistically associated with rate of feathering at hatch in turkey. We identified a 5-bp frameshift deletion in the prolactin receptor (PRLR) gene that is responsible for slow feathering at hatch. All female cases (SF turkeys) were hemizygous for this deletion, while 188 controls (FF turkeys) were hemizygous or homozygous for the reference allele. This frameshift mutation introduces a premature stop codon and six novel amino acids (AA), which results in a truncated PRLR protein that lacks 98 C-terminal AA. CONCLUSIONS We present the causal mutation for feathering rate in turkey that causes a partial C-terminal loss of the prolactin receptor, and this truncated PRLR protein is strikingly similar to the protein encoded by the slow feathering K allele in chicken.
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Affiliation(s)
- Martijn F L Derks
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Juan M Herrero-Medrano
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Richard P M A Crooijmans
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Addie Vereijken
- Hendrix Genetics Turkeys, Technolgy and Service B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Julie A Long
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Hendrik-Jan Megens
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Martien A M Groenen
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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33
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Chen J, Ni P, Li X, Han J, Jakovlić I, Zhang C, Zhao S. Population size may shape the accumulation of functional mutations following domestication. BMC Evol Biol 2018; 18:4. [PMID: 29351740 PMCID: PMC5775542 DOI: 10.1186/s12862-018-1120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . CONCLUSIONS Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.
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Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Chengjun Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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35
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Convergent and divergent genetic changes in the genome of Chinese and European pigs. Sci Rep 2017; 7:8662. [PMID: 28819228 PMCID: PMC5561219 DOI: 10.1038/s41598-017-09061-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/20/2017] [Indexed: 01/17/2023] Open
Abstract
Since 10,000 BC, continuous human selection has led to intense genetic and phenotypic changes in pig (Sus scrofa) domestication. Through whole genome analysis of 257 individuals, we demonstrated artificial unidirectional and bidirectional selection as the primary force to shape the convergent and divergent changes between Chinese domestic pigs (CHD) and European domestic pigs (EUD). We identified 31 genes in unidirectional selection regions that might be related to fundamental domestication requirements in pigs. And these genes belong predominantly to categories related to the nervous system, muscle development, and especially to metabolic diseases. In addition, 35 genes, representing different breeding preference, were found under bidirectional selection for the distinct leanness and reproduction traits between CHD and EUD. The convergent genetic changes, contributing physical and morphological adaption, represent the common concerns on pig domestication. And the divergent genetic changes reflect distinct breeding goals between Chinese and European pigs. Using ITPR3, AHR and NMU as examples, we explored and validated how the genetic variations contribute to the phenotype changes.
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36
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CRISPR/Cas9-mediated genome editing in wild-derived mice: generation of tamed wild-derived strains by mutation of the a (nonagouti) gene. Sci Rep 2017; 7:42476. [PMID: 28195201 PMCID: PMC5307340 DOI: 10.1038/srep42476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/11/2017] [Indexed: 12/31/2022] Open
Abstract
Wild-derived mice have contributed to experimental mouse genetics by virtue of their genetic diversity, which may help increase the chance of identifying novel modifier genes responsible for specific phenotypes and diseases. However, gene targeting using wild-derived mice has been unsuccessful because of the unavailability of stable embryonic stem cells. Here, we report that CRISPR/Cas9-mediated gene targeting can be applied to the Japanese wild-derived MSM/Ms strain (Mus musculus molossinus). We targeted the nonagouti (a) gene encoding the agouti protein that is localized in hair and the brain. We obtained three homozygous knockout mice as founders, all showing black coat colour. While homozygous knockout offspring were physiologically indistinguishable from wild-type litter-mates, they showed specific domesticated behaviours: hypoactivity in the dark phase and a decline in the avoidance of a human hand. These phenotypes were consistent over subsequent generations. Our findings support the empirical hypothesis that nonagouti is a domestication-linked gene, the loss of which might repress aggressive behaviour.
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Böhmer C, Böhmer E. Shape Variation in the Craniomandibular System and Prevalence of Dental Problems in Domestic Rabbits: A Case Study in Evolutionary Veterinary Science. Vet Sci 2017; 4:vetsci4010005. [PMID: 29056664 PMCID: PMC5606619 DOI: 10.3390/vetsci4010005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 12/20/2022] Open
Abstract
In contrast to wild lagomorphs, pet rabbits exhibit a noticeably high frequency of dental problems. Although dietary habits are considered as a major factor contributing to acquired malocclusions, the exact causes and interrelationships are still under debate. In this regard, an important aspect that has not been considered thoroughly to date is the effect of diet-induced phenotypic plasticity in skull morphology. Therefore, we conducted a geometric morphometric analysis on skull radiological images of wild and pet rabbits in order to quantify intraspecific variation in craniomandibular morphology. The statistical analyses reveal a significant morphological differentiation of the craniomandibular system between both groups. Furthermore, the analysis of covariance shows that the force-generating modules (cranium and mandible) vary independently from the force-receiving module (hypselodont teeth) in pet rabbits, which is in contrast to their wild relatives. Our findings suggest that the phenotypic changes in domestic rabbits impact mastication performance and, consequently, oral health. An adequate close-to-nature nutrition throughout the whole life and especially beginning early parallel to weaning (phase of increased phenotypic plasticity) is necessary to ensure a normal strain on the teeth by promoting physiological lateral gliding movements and avoiding direct axial loads.
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Affiliation(s)
- Christine Böhmer
- UMR 7179 CNRS, Muséum National d'Histoire Naturelle, CP 55, 57 rue Cuvier, 75231 Paris Cedex 05, France.
| | - Estella Böhmer
- Chirurgische und Gynäkologische Kleintierklinik ,Tierärztliche Fakultät, Ludwig-Maximilians-Universität München, Veterinärstr 13, München 80539, Germany.
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