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Das PJ, Kumar S, Choudhury M, Banik S, Pegu SR, Kumar S, Deb R, Gupta VK. Characterization of the complete mitochondrial genome and identification of signature sequence of Indian wild pig. Gene 2024; 897:148070. [PMID: 38070787 DOI: 10.1016/j.gene.2023.148070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/15/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090th to 1099th position, deletion of a 10 bp sequence at the 755th position, insertion of (CA) at the 137th position, and substitution of AT to GA at the 638th position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species.
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Affiliation(s)
- Pranab Jyoti Das
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India.
| | - Satish Kumar
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Manasee Choudhury
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Santanu Banik
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Seema Rani Pegu
- Animal Health, ICAR-National Research Centre on Pig, Rani, Guiwahati-781131, Assam, India
| | - Sunil Kumar
- Animal Reproduction, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Rajib Deb
- Animal Health, ICAR-National Research Centre on Pig, Rani, Guiwahati-781131, Assam, India
| | - Vivek Kumar Gupta
- Animal Health, ICAR-National Research Centre on Pig, Rani, Guiwahati-781131, Assam, India
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2
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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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3
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Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, Dubcovsky J. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proc Natl Acad Sci U S A 2023; 120:e2306494120. [PMID: 37703281 PMCID: PMC10515147 DOI: 10.1073/pnas.2306494120] [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: 04/24/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.
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Affiliation(s)
- Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Hongchun Xiong
- Department of Plant Sciences, University of California, Davis, CA95616
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Germán F. Burguener
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Hans Vasquez-Gross
- Department of Plant Sciences, University of California, Davis, CA95616
- Nevada Bioinformatics Center, University of Nevada, Reno, NV89557
| | - Qiujie Liu
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Juan M. Debernardi
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Kimberly Garland-Campbell
- United States Department of Agriculture - Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA99164
| | - Shahryar F. Kianian
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN55108-6086
| | - Gina Brown-Guedira
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Unit, Raleigh, NC27695
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, SaskatoonS7N 5A8, Canada
| | - Justin D. Faris
- United States Department of Agriculture - Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND58102
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
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Koller D, Benítez-Burraco A, Polimanti R. Enrichment of self-domestication and neural crest function loci in the heritability of neurodevelopmental disorders. Hum Genet 2023; 142:1271-1279. [PMID: 36930228 PMCID: PMC10472204 DOI: 10.1007/s00439-023-02541-5] [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: 12/27/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Self-domestication could contribute to shaping the biology of human brain and consequently the predisposition to neurodevelopmental disorders. Leveraging genome-wide data from the Psychiatric Genomics Consortium, we tested the enrichment of self-domestication and neural crest function loci with respect to the heritability of autism spectrum disorder, schizophrenia (SCZ in East Asian and European ancestries, EAS and EUR, respectively), attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, and Tourette's syndrome (TS). Considering only self-domestication and neural-crest-function annotations in the linkage disequilibrium score regression (LDSC) model, our partitioned heritability analysis revealed statistically significant enrichments across all disorders investigated. The estimates of the heritability enrichments for self-domestication loci were similar across neurodevelopmental disorders, ranging from 0.902 (EAS SCZ, p = 4.55 × 10-20) to 1.577 (TS, p = 5.85 × 10-5). Conversely, a wider spectrum of heritability enrichment estimates was present for neural crest function with the highest enrichment observed for TS (enrichment = 3.453, p = 2.88 × 10-3) and the lowest for EAS SCZ (enrichment = 1.971, p = 3.81 × 10-3). Although these estimates appear to be strong, the enrichments for self-domestication and neural crest function were null once we included additional annotations related to different genomic features. This indicates that the effect of self-domestication on the polygenic architecture of neurodevelopmental disorders is not independent of other functions of human genome.
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Affiliation(s)
- Dora Koller
- Department of Psychiatry, Yale School of Medicine, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, 41004, Seville, Spain
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA.
- VA CT Healthcare Center, West Haven, CT, 06516, USA.
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5
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Wen F, Wang J, Shang D, Yan H, Yuan X, Wang Y, Xia Q, Wang G. Non-classical digestive lipase BmTGL selected by gene amplification reduces the effects of mulberry inhibitor during silkworm domestication. Int J Biol Macromol 2023; 229:589-599. [PMID: 36587639 DOI: 10.1016/j.ijbiomac.2022.12.294] [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: 10/05/2022] [Revised: 12/09/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022]
Abstract
Efficient utilization of dietary lipids is crucial for Bombyx mori, also known as domesticated silkworms. However, the effects of domestication on the genes encoding lipases remain unknown. In this study, we investigated the expression difference of one triacylglycerol lipase (BmTGL) between B.mori and wild (ancestor) silkworm strains (Bombyx mandarina). An immunofluorescence localization analysis showed that BmTGL was present in all parts of the gut and was released into the intestinal lumen. BmTGL expression was significantly enhanced in different domesticated silkworm strains compared to that in the B. mandarina strains. The BmTGL copy numbers in the genomes of the domesticated silkworm strains were 2-to-3 folds that of the B. mandarina strains and accounted for the enhanced expression of BmTGL in the domesticated silkworm strains. The Ser144Asn substitution in the Ser-Asp-His catalytic triads of BmTGL resulted in relatively lower lipase activity and reduced sensitivity to the lipase inhibitor morachalcone A. Moreover, BmTGL overexpression significantly increased the weights of the B. mori silkworms compared to those of the non-transgenic controls. Thus, the selection of BmTGL by gene amplification may be a trade-off between maintaining high enzymatic activity and reducing the effects of mulberry inhibitors during silkworm domestication.
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Affiliation(s)
- Feng Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Jing Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Deli Shang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Hao Yan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Xingli Yuan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China.
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6
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Liu T, Chen J, Jiang L, Qiao G. Human‐mediated eco‐evolutionary processes of the herbivorous insect
Hyalopterus arundiniformis
during the Holocene. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tongyi Liu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
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8
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Adeola AC, Sola-Ojo FE, Opeyemi YA, Oguntunji AO, Nneji LM, Ewuola MK, Bello SF, Olaniyi WA, Adesoji AT, Karuno AP, Sanke OJ, Daniel EL. Genetic diversity and population structure of muscovy duck ( Cairina moschata) from Nigeria. PeerJ 2022; 10:e13236. [PMID: 35444865 PMCID: PMC9014852 DOI: 10.7717/peerj.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 01/15/2023] Open
Abstract
The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (F ST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
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Affiliation(s)
- Adeniyi C. Adeola
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Foluke E. Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Yusuf A. Opeyemi
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Abel O. Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, Osun, Nigeria
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States
| | - Muslim K. Ewuola
- Animal Breeding and Genetics Unit/Department of Animal Science, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics/Breeding and Reproduction/College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adeosun T. Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, Kano, Nigeria
| | - Alex P. Karuno
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
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9
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Yang Y, Xu C, Shen Z, Yan C. Crop Quality Improvement Through Genome Editing Strategy. Front Genome Ed 2022; 3:819687. [PMID: 35174353 PMCID: PMC8841430 DOI: 10.3389/fgeed.2021.819687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Good quality of crops has always been the most concerning aspect for breeders and consumers. However, crop quality is a complex trait affected by both the genetic systems and environmental factors, thus, it is difficult to improve through traditional breeding strategies. Recently, the CRISPR/Cas9 genome editing system, enabling efficiently targeted modification, has revolutionized the field of quality improvement in most crops. In this review, we briefly review the various genome editing ability of the CRISPR/Cas9 system, such as gene knockout, knock-in or replacement, base editing, prime editing, and gene expression regulation. In addition, we highlight the advances in crop quality improvement applying the CRISPR/Cas9 system in four main aspects: macronutrients, micronutrients, anti-nutritional factors and others. Finally, the potential challenges and future perspectives of genome editing in crop quality improvement is also discussed.
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Affiliation(s)
- Yihao Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
- Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Chenda Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
| | - Ziyan Shen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
| | - Changjie Yan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
- Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
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10
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Orbán L, Shen X, Phua N, Varga L. Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals? Front Genet 2021; 12:506754. [PMID: 33968125 PMCID: PMC8097054 DOI: 10.3389/fgene.2021.506754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.
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Affiliation(s)
- László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - László Varga
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllõ, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllõ, Hungary
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11
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Xie HB, Wang LG, Fan CY, Zhang LC, Adeniyi CA, Yin X, Zeng ZB, Wang LX, Zhang YP. Genetic architecture underlying nascent speciation - The evolution of Eurasian pigs under domestication. Mol Biol Evol 2021; 38:3556-3566. [PMID: 33892509 PMCID: PMC8382894 DOI: 10.1093/molbev/msab117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in the advanced stages of speciation, the genetics of reproductive isolation in nascent stage of speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying the early stages of speciation in great details. Pig breeds have not evolved the large X-effect of hybrid incompatibility commonly observed between “good species.” Instead, deleterious epistatic interactions among multiple autosomal loci are common. These weak Dobzhansky–Muller incompatibilities confer partial hybrid inviability with sex biases in crosses between European and East Asian domestic pigs. The genomic incompatibility is enriched in pathways for angiogenesis, androgen receptor signaling and immunity, with an observation of many highly differentiated cis-regulatory variants. Our study suggests that partial hybrid inviability caused by pervasive but weak interactions among autosomal loci may be a hallmark of nascent speciation in mammals.
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Affiliation(s)
- Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li-Gang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chen-Yu Fan
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Science, Yunnan University, Kunming, China
| | - Long-Chao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - C Adeola Adeniyi
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xue Yin
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Science, Yunnan University, Kunming, China
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Li-Xian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Science, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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12
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Guo X, He XX, Chen H, Wang ZC, Li HF, Wang JX, Wang MS, Jiang RS. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zool Res 2021; 42:43-50. [PMID: 33269825 PMCID: PMC7840458 DOI: 10.24272/j.issn.2095-8137.2020.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.
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Affiliation(s)
- Xing Guo
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xin-Xin He
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hong Chen
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhi-Cheng Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hui-Fang Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Jiang-Xian Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95064, USA. E-mail:
| | - Run-Shen Jiang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China. E-mail:
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13
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Liu Y, Liu B, Liu C, Hu Y, Liu C, Li X, Li X, Zhang X, Irwin DM, Wu Z, Chen Z, Jin Q, Zhang S. Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch. BMC Vet Res 2021; 17:112. [PMID: 33676490 PMCID: PMC7937242 DOI: 10.1186/s12917-021-02815-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 02/23/2021] [Indexed: 01/24/2023] Open
Abstract
Background Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared with captive wolves. We surveyed the gut bacterial diversity of 27 domestic dogs, which were fed commercial dog food, and 31 wolves, which were fed uncooked meat, by 16S rRNA sequencing. In addition, we collected fecal samples from 5 dogs and 5 wolves for shotgun metagenomic sequencing to explore changes in the functions of their gut microbiome. Results Differences in the abundance of core bacterial genera were observed between dogs and wolves. Together with shotgun metagenomics, the gut microbiome of dogs was found to be enriched in bacteria resistant to clinical drugs (P < 0.001), while wolves were enriched in bacteria resistant to antibiotics used in livestock (P < 0.001). In addition, a higher abundance of putative α-amylase genes (P < 0.05; P < 0.01) was observed in the dog samples. Conclusions Living environment of dogs and domestic wolves has led to increased numbers of bacteria with antibiotic resistance genes, with exposure to antibiotics through direct and indirect methods. In addition, the living environment of dogs has allowed the adaptation of their microbiota to a starch-rich diet. These observations align with a domestic lifestyle for domestic dogs and captive wolves, which might have consequences for public health.
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Affiliation(s)
- Yuting Liu
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Bo Liu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengwu Liu
- Shenyang Police Dog Technical College, Shenyang, China
| | - Yumiao Hu
- Shenyang Forest Zoological Garden, Shenyang, China
| | - Chang Liu
- Changchun Animals and Plants Park, Changchun, China
| | - Xiaoping Li
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xibao Li
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaoshuang Zhang
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Zhiqiang Wu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zeliang Chen
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuyi Zhang
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
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14
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Mauki DH, Adeola AC, Ng’ang’a SI, Tijjani A, Akanbi IM, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Gwakisa PS, Yin TT, Peng MS, Zhang YP. Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers. PeerJ 2021; 9:e10607. [PMID: 33717663 PMCID: PMC7938780 DOI: 10.7717/peerj.10607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/29/2020] [Indexed: 01/29/2023] Open
Abstract
The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.
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Affiliation(s)
- David H. Mauki
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | | | - Ibikunle Mark Akanbi
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Oyo, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
| | | | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jebi Ibrahim
- College of veterinary medicine, department of theriogenology, University of agriculture, Makurdi, Makurdi, Benue, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, Nigeria
| | | | - Paul S. Gwakisa
- Department of Microbiology, Parasitology and Biotechnology/ Genome Science Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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15
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Graf L, Shin Y, Yang JH, Choi JW, Hwang IK, Nelson W, Bhattacharya D, Viard F, Yoon HS. A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida. Nat Ecol Evol 2021; 5:360-368. [PMID: 33495590 PMCID: PMC7929912 DOI: 10.1038/s41559-020-01378-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Human activity is an important driver of ecological and evolutionary change on our planet. In particular, domestication and biological introductions have important and long-lasting effects on species' genomic architecture and diversity. However, genome-wide analysis of independent domestication and introduction events within a single species has not previously been performed. The Pacific kelp Undaria pinnatifida provides such an opportunity because it has been cultivated in its native range in Northeast Asia but also introduced to four other continents in the past 50 years. Here we present the results of a genome-wide analysis of natural, cultivated and introduced populations of U. pinnatifida to elucidate human-driven evolutionary change. We demonstrate that these three categories of origin can be distinguished at the genome level, reflecting the combined influence of neutral (demography and migration) and non-neutral (selection) processes.
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Affiliation(s)
- Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Younhee Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Il Ki Hwang
- Aquaculture Management Division, National Institute of Fisheries Science, Busan, South Korea
| | - Wendy Nelson
- National Institute of Water & Atmospheric Research, Wellington, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Frédérique Viard
- Sorbonne Université, CNRS, AD2M, Station Biologique de Roscoff, Roscoff, France
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.
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16
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Liu X, Li Z, Yan Y, Li Y, Wu H, Pei J, Yan P, Yang R, Guo X, Lan X. Selection and introgression facilitated the adaptation of Chinese native endangered cattle in extreme environments. Evol Appl 2021; 14:860-873. [PMID: 33767758 PMCID: PMC7980270 DOI: 10.1111/eva.13168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/31/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Although persistent efforts have identified and characterized a few candidate genes and related biological processes with potential functions in the adaptation of many species to extreme environments, few works have been conducted to determine the genomic basis of adaptation in endangered livestock breeds that have been living in extreme conditions for more than thousands of years. To fill this gap, we sequenced the whole genomes of nine individuals from three Chinese native endangered cattle breeds that are living in high-altitude or arid environments. Phylogenetic and evolutionary history analyses of these three and other six breeds showed that the genetic structure of the cattle populations is primarily related to geographic location. Interestingly, we identified pervasive introgression from the yak to Zhangmu cattle (ZMC) that cover several genes (e.g., NOS2, EGLN1 and EPAS1) involved in the hypoxia response and previously identified as positive selection genes in other species, which suggested that the adaptive introgression from yak may have contributed to the adaptation of ZMC to high-altitude environments. In addition, by contrasting the breeds in opposite living conditions, we revealed a set of candidate genes with various functions from hypoxia response, water metabolism, immune response and body shape change to embryo development and skeletal system development, etc., that may be related to high-altitude or arid adaptation. Our research provides new insights into the recovery and adaptation of endangered native cattle and other species in extreme environments and valuable resources for future research on animal husbandry to cope with climate change.
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Affiliation(s)
- Xinfeng Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Zhaohong Li
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Yubin Yan
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Ye Li
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Hui Wu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Jie Pei
- Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural SciencesLanzhouChina
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural SciencesLanzhouChina
| | - Ruolin Yang
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural SciencesLanzhouChina
| | - Xianyong Lan
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
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17
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Du H, Diao C, Zhao P, Zhou L, Liu JF. Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads. Brief Bioinform 2021; 22:6082823. [PMID: 33429431 DOI: 10.1093/bib/bbaa399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 11/12/2022] Open
Abstract
With the rapid progress of sequencing technologies, various types of sequencing reads and assembly algorithms have been designed to construct genome assemblies. Although recent studies have attempted to evaluate the appropriate type of sequencing reads and algorithms for assembling high-quality genomes, it is still a challenge to set the correct combination for constructing animal genomes. Here, we present a comparative performance assessment of 14 assembly combinations-9 software programs with different short and long reads of Duroc pig. Based on the results of the optimization process for genome construction, we designed an integrated hybrid de novo assembly pipeline, HSCG, and constructed a draft genome for Duroc pig. Comparison between the new genome and Sus scrofa 11.1 revealed important breakpoints in two S. scrofa 11.1 genes. Our findings may provide new insights into the pan-genome analysis studies of agricultural animals, and the integrated assembly pipeline may serve as a guide for the assembly of other animal genomes.
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Affiliation(s)
- Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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18
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Torres-Sánchez M. Variation under domestication in animal models: the case of the Mexican axolotl. BMC Genomics 2020; 21:827. [PMID: 33228551 PMCID: PMC7685626 DOI: 10.1186/s12864-020-07248-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864. RESULTS Using gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations. CONCLUSIONS Awareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.
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Affiliation(s)
- María Torres-Sánchez
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center & Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA.
- Present address: Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.
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19
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Yan H, Liu Q, Wen F, Bai B, Wen Y, Chen W, Lu W, Lin Y, Xia Q, Wang G. Characterization and potential application of an α-amylase (BmAmy1) selected during silkworm domestication. Int J Biol Macromol 2020; 167:1102-1112. [PMID: 33188814 DOI: 10.1016/j.ijbiomac.2020.11.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Efficient resource utilization plays a central role in the high productivity of domesticated plants and animals. Whether artificial selection acts on digestive enzymes in the domesticated silkworm (Bombyx mori), which is larger than its wild ancestor, Bombyx mandarina (B. mandarina), remains unknown. In this study, we present the characteristics of a novel alpha-amylase, BmAmy1, in B. mori. The activity of recombinant BmAmy1 was maximal at 35 °C and pH 9.0, and could be suppressed by amylase inhibitors from mulberry, the exclusive food source of silkworms. Three different transposable element fragments, which were independently inserted in the 5'-upstream regulatory region, might be responsible for the enhanced expression of BmAmy1 in different domesticated silkworm strains as revealed by dual-luciferase reporter assay. The BmAmy1 overexpression increased the weight of female and male B. mori by 11.9% and 6.8%, respectively, compared with non-transgenic controls. Our results emphasize that, by exploring the genetic mechanisms of human-selected traits, the domestication process could be further accelerated through genetic engineering and targeted breeding.
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Affiliation(s)
- Hao Yan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingsong Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Feng Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Bingchuan Bai
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Yuchan Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wenwen Chen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Ying Lin
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China.
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20
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Wang MS, Thakur M, Peng MS, Jiang Y, Frantz LAF, Li M, Zhang JJ, Wang S, Peters J, Otecko NO, Suwannapoom C, Guo X, Zheng ZQ, Esmailizadeh A, Hirimuthugoda NY, Ashari H, Suladari S, Zein MSA, Kusza S, Sohrabi S, Kharrati-Koopaee H, Shen QK, Zeng L, Yang MM, Wu YJ, Yang XY, Lu XM, Jia XZ, Nie QH, Lamont SJ, Lasagna E, Ceccobelli S, Gunwardana HGTN, Senasige TM, Feng SH, Si JF, Zhang H, Jin JQ, Li ML, Liu YH, Chen HM, Ma C, Dai SS, Bhuiyan AKFH, Khan MS, Silva GLLP, Le TT, Mwai OA, Ibrahim MNM, Supple M, Shapiro B, Hanotte O, Zhang G, Larson G, Han JL, Wu DD, Zhang YP. 863 genomes reveal the origin and domestication of chicken. Cell Res 2020; 30:693-701. [PMID: 32581344 PMCID: PMC7395088 DOI: 10.1038/s41422-020-0349-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/20/2020] [Indexed: 01/10/2023] Open
Abstract
Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.
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Affiliation(s)
- Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Ecology and Evolutionary Biology, Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mukesh Thakur
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Laurent Alain François Frantz
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Joris Peters
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany
- SNSB, Bavarian State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Newton Otieno Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhu-Qing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Nalini Yasoda Hirimuthugoda
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Hidayat Ashari
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Sri Suladari
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Moch Syamsul Arifin Zein
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Szilvia Kusza
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Saeed Sohrabi
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hamed Kharrati-Koopaee
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ya-Jiang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Xue-Mei Lu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin-Zheng Jia
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Qing-Hua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Susan Joy Lamont
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, Perugia, Italy
| | | | | | - Shao-Hong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong, China
| | - Jing-Fang Si
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (CAS-SEABRI), Yezin, Myanmar
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Cheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | | | | | - Thi-Thuy Le
- National Institute of Animal Husbandry, Hanoi, Vietnam
| | - Okeyo Ally Mwai
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | | | - Megan Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China.
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21
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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22
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Weng Z, Huang X. Highlighting the classification of mitochondrial DNA haplogroups C and D in chickens. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:218-219. [PMID: 32516055 DOI: 10.1080/24701394.2020.1773452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zhuoxian Weng
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas; Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken; School of Life Science of Jiaying University, Meizhou, China
| | - Xunhe Huang
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas; Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken; School of Life Science of Jiaying University, Meizhou, China
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23
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Kon T, Omori Y, Fukuta K, Wada H, Watanabe M, Chen Z, Iwasaki M, Mishina T, Matsuzaki SIS, Yoshihara D, Arakawa J, Kawakami K, Toyoda A, Burgess SM, Noguchi H, Furukawa T. The Genetic Basis of Morphological Diversity in Domesticated Goldfish. Curr Biol 2020; 30:2260-2274.e6. [PMID: 32392470 DOI: 10.1016/j.cub.2020.04.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/13/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
Abstract
Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these phenotypes is poorly understood. Here, based on analysis of transposable elements in the allotetraploid goldfish genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event in the ancestor of goldfish and common carp. We conducted whole-genome sequencing of 27 domesticated goldfish strains and wild goldfish. We identified more than 60 million genetic variations and established a population genetic structure of major goldfish strains. Genome-wide association studies and analysis of strain-specific variants revealed genetic loci associated with several goldfish phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, and heart-shaped tail. Our results suggest that accumulated mutations in the asymmetrically evolved subgenomes led to generation of diverse phenotypes in the goldfish domestication history. This study is a key resource for understanding the genetic basis of phenotypic diversity among goldfish strains.
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Affiliation(s)
- Tetsuo Kon
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yoshihiro Omori
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
| | - Kentaro Fukuta
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Hironori Wada
- College of Liberal Arts and Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Masakatsu Watanabe
- Laboratory of Pattern Formation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Miki Iwasaki
- College of Liberal Arts and Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Tappei Mishina
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | | | - Daiki Yoshihara
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Jumpei Arakawa
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Aichi, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan; Advanced Genomics Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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24
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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25
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Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
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Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
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26
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Rattanawannee A, Duangphakdee O, Chanchao C, Teerapakpinyo C, Warrit N, Wongsiri S, Oldroyd BP. Genetic Characterization of Exotic Commercial Honey Bee (Hymenoptera: Apidae) Populations in Thailand Reveals High Genetic Diversity and Low Population Substructure. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:34-42. [PMID: 31769836 DOI: 10.1093/jee/toz298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Indexed: 06/10/2023]
Abstract
Domestication of animal species is often associated with a reduction in genetic diversity. The honey bee, Apis mellifera Linnaeus, 1758, has been managed by beekeepers for millennia for both honey and wax production and for crop pollination. Here we use both microsatellite markers and sequence data from the mitochondrial COI gene to evaluate genetic variation of managed A. mellifera in Thailand, where the species is introduced. Microsatellite analysis revealed high average genetic diversity with expected heterozygosities ranging from 0.620 ± 0.184 to 0.734 ± 0.071 per locus per province. Observed heterozygosities were generally lower than those expected under Hardy-Weinberg equilibrium, both locally and across the population as a whole. Mitochondrial sequencing revealed that the frequency of two evolutionary linages (C-Eastern European and O-Middle Eastern) are similar to those observed in a previous survey 10 yr ago. Our results suggest that Thai beekeepers are managing their A. mellifera in ways that retain overall genetic diversity, but reduce genetic diversity between apiaries.
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Affiliation(s)
- Atsalek Rattanawannee
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Orawan Duangphakdee
- King Mongkut's University of Technology Thonburi, Ratchaburi Campus, Bangmod, Thung Khru, Bangkok, Thailand
| | - Chanpen Chanchao
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nattapot Warrit
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Siriwat Wongsiri
- Agricultural Interdisciplinary Program, Graduate School, Maejo University, Chiang Mai, Thailand
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, Macleay Building A12, University of Sydney, Sydney, NSW, Australia
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27
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Ming L, Yuan L, Yi L, Ding G, Hasi S, Chen G, Jambl T, Hedayat-Evright N, Batmunkh M, Badmaevna GK, Gan-Erdene T, Ts B, Zhang W, Zulipikaer A, Hosblig, Erdemt, Natyrov A, Mamay P, Narenbatu, Meng G, Narangerel C, Khongorzul O, He J, Hai L, Lin W, Sirendalai, Sarentuya, Aiyisi, Li Y, Wang Z, Jirimutu. Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels. Commun Biol 2020; 3:1. [PMID: 31925316 PMCID: PMC6946651 DOI: 10.1038/s42003-019-0734-6] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/10/2019] [Indexed: 12/11/2022] Open
Abstract
The domestic Bactrian camels were treated as one of the principal means of locomotion between the eastern and western cultures in history. However, whether they originated from East Asia or Central Asia remains elusive. To address this question, we perform whole-genome sequencing of 128 camels across Asia. The extant wild and domestic Bactrian camels show remarkable genetic divergence, as they were split from dromedaries. The wild Bactrian camels also contribute little to the ancestry of domestic ones, although they share close habitat in East Asia. Interestingly, among the domestic Bactrian camels, those from Iran exhibit the largest genetic distance and the earliest split from all others in the phylogeny, despite evident admixture between domestic Bactrian camels and dromedaries living in Central Asia. Taken together, our study support the Central Asian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where native wild Bactrian camels inhabit. Ming, Yuan et al. performed whole-genome sequencing on 128 wild and domesticated Bactrian camels across Asia. They show that wild and domestic Bactrian camels are genetically diverged from dromedaries, and that wild camels contributed little to domestic camel ancestry despite sharing a habitat in East Asia.
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Affiliation(s)
- Liang Ming
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Liyun Yuan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Guohui Ding
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Gui'an Bio-Med Big Data Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Guiyang, China
| | - Surong Hasi
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot, China
| | - Gangliang Chen
- Bactrian Camel Academe of Altai, Xingjiang Wangyuan Camel Milk Limited Company, Fuhai County, Xijiang, China
| | - Tuyatsetseg Jambl
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | | | - Mijiddorj Batmunkh
- China-Mongolia Joint Laboratory for Biomacromolecule Research, Ulaanbaatar, Mongolia.,Mongolian Wild Camel Protection Area, Ministry of Nature and Environment, Ulaanbaatar, Mongolia
| | | | - Tudeviin Gan-Erdene
- Institute of Chemistry and Chemical Technology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Batsukh Ts
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | - Wenbin Zhang
- Bactrian Camel Institute of Alxa, Inner Mongolia, China
| | - Azhati Zulipikaer
- Animal Science Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Hosblig
- Animal Husbandry Bureau of North Urad, Bayannuur, Inner Mongolia, China
| | - Erdemt
- Animal Husbandry Workstation of West Sunid, Xiliingol, Inner Mongolia, China
| | - Arkady Natyrov
- Agrarian Faculty, Kalmyk State University, Republic of Kalmykia, Russia
| | | | - Narenbatu
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Gendalai Meng
- Department of Pharmacy, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | | | - Orgodol Khongorzul
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Jing He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Le Hai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Weili Lin
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sirendalai
- Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Sarentuya
- Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Aiyisi
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. .,Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. .,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China. .,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China. .,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China. .,China-Mongolia Joint Laboratory for Biomacromolecule Research, Ulaanbaatar, Mongolia.
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28
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Ameen C, Feuerborn TR, Brown SK, Linderholm A, Hulme-Beaman A, Lebrasseur O, Sinding MHS, Lounsberry ZT, Lin AT, Appelt M, Bachmann L, Betts M, Britton K, Darwent J, Dietz R, Fredholm M, Gopalakrishnan S, Goriunova OI, Grønnow B, Haile J, Hallsson JH, Harrison R, Heide-Jørgensen MP, Knecht R, Losey RJ, Masson-MacLean E, McGovern TH, McManus-Fry E, Meldgaard M, Midtdal Å, Moss ML, Nikitin IG, Nomokonova T, Pálsdóttir AH, Perri A, Popov AN, Rankin L, Reuther JD, Sablin M, Schmidt AL, Shirar S, Smiarowski K, Sonne C, Stiner MC, Vasyukov M, West CF, Ween GB, Wennerberg SE, Wiig Ø, Woollett J, Dalén L, Hansen AJ, P Gilbert MT, Sacks BN, Frantz L, Larson G, Dobney K, Darwent CM, Evin A. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proc Biol Sci 2019; 286:20191929. [PMID: 31771471 PMCID: PMC6939252 DOI: 10.1098/rspb.2019.1929] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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Affiliation(s)
- Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, Devon, UK.,Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK
| | - Tatiana R Feuerborn
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Sarah K Brown
- Department of Anthropology, University of California Davis, Davis, CA, USA.,Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA.,Washington Department of Fish and Wildlife, Olympia, WA, USA
| | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, TX, USA.,The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK.,The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK.,The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,GCRF One Health Regional Network for the Horn of Africa (HORN) Project, Institute of Infection and Global Health, Liverpool, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Natural History Museum, University of Oslo, Oslo, Norway.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA
| | - Audrey T Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | | | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Matthew Betts
- Canadian Museum of History, Gatineau, Quebec, Canada.,Department of Anthropology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Kate Britton
- Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Sachsen, Germany
| | - John Darwent
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Rune Dietz
- Arctic Research Centre, Aarhus Universitet, Aarhus, Denmark.,Department of Bioscience Roskilde, Aarhus Universitet, Roskilde, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Oslo, Oslo, Norway
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Olga I Goriunova
- Laboratory of Archaeology and Paleoecology of the Institute of Archaeology and Ethnography (Siberian Branch of Russian Academy of Science), Irkutsk, Russian Federation
| | | | - James Haile
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Jón Hallsteinn Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Reykjavik, Iceland
| | - Ramona Harrison
- Department of Archaeology, History, Cultural Studies, and Religion, University of Bergen, Bergen, Hordaland, Norway
| | | | - Rick Knecht
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
| | - Robert J Losey
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Thomas H McGovern
- Department of Anthropology, Hunter College CUNY, New York, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | | | - Morten Meldgaard
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | | | - Madonna L Moss
- Department of Anthropology, University of Oregon, Eugene, OR, USA
| | - Iurii G Nikitin
- Museum of Archaeology and Ethnography at the Institute of History, Archaeology and Ethnography of the Peoples of the Far East (Far Eastern Branch of Russian Academy of Science), Vladivostok, Russian Federation
| | - Tatiana Nomokonova
- Department of Archaeology and Anthropology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albína Hulda Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences, University of Oslo, Oslo, Norway.,Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Reykjavik, Iceland
| | - Angela Perri
- Department of Archaeology, Durham University, Durham, UK
| | - Aleksandr N Popov
- Museum of Archaeology and Ethnography at the Institute of History, Archaeology and Ethnography of the Peoples of the Far East (Far Eastern Branch of Russian Academy of Science), Vladivostok, Russian Federation
| | - Lisa Rankin
- Department of Archaeology, Memorial University of Newfoundland, St John's, Canada
| | - Joshua D Reuther
- Department of Anthropology, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Mikhail Sablin
- Zoological Institute of Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | - Scott Shirar
- Department of Anthropology, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Konrad Smiarowski
- The Graduate Center, City University of New York, New York, NY, USA.,Section for Cultural Heritage Management, Department of Cultural History, University Museum of Bergen, Bergen, Norway
| | - Christian Sonne
- Arctic Research Centre, Aarhus Universitet, Aarhus, Denmark.,Department of Bioscience, Aarhus Universitet, Aarhus, Denmark.,School of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Mary C Stiner
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Mitya Vasyukov
- Department of Biological Diversity and Sustainable Use of Biological Resources, Russian Academy of Sciences, Moskow, Russian Federation
| | - Catherine F West
- Department of Anthropology and Archaeology Program, Boston University, Boston, MA, USA
| | | | | | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - James Woollett
- Département des Sciences Historiques, Université Laval, Quebec, Canada
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Anders J Hansen
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Benjamin N Sacks
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, USA.,Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Greger Larson
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Archaeology, University of Oxford, Oxford, UK
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, Merseyside, UK.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Allowen Evin
- Institut des Sciences de l'Evolution-Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, Occitanie, France
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29
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Yao YG, Shen H. From our roots, we grow. Zool Res 2019; 40:471-475. [PMID: 31631589 PMCID: PMC6822935 DOI: 10.24272/j.issn.2095-8137.2019.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/26/2019] [Indexed: 11/07/2022] Open
Abstract
Located at the head of the Indo-Burma biodiversity hotspot, the Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences (CAS), serves as China's main center for research into the diverse animal and ecological resources of southwestern China, Eastern Himalayas, and Southeast Asia. As of October 2019, it has been 60 years since the inception of KIZ. Since 1959, strong roots have been laid down by generations of researchers, allowing KIZ to grow and evolve into a comprehensive research institution renowned for its remarkable achievements in evolutionary mechanisms of animal biodiversity, animal resources protection, and sustainable utilization. It is now recognized as "a major powerhouse in evolutionary biology research in China" and is"establishing itself in the world stage" (Overseas Experts Review Committee, organized by the Bureau of Development Planning, CAS, during international evaluation in 2014).To celebrate the 60th anniversary of KIZ and the 70th anniversary of CAS, Zoological Research presents this commemorative issue, composed primarily of contributions from KIZ researchers. In addition, it is our great honor to provide here a brief retrospective of the pioneering work undertaken by the earlier scientists at KIZ and recent achievements, which will hopefully serve to motivate and inspire present and future successors.
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Affiliation(s)
- Yong-Gang Yao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Hua Shen
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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30
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Yang Q, Chen H, Ye J, Liu C, Wei R, Chen C, Huang L. Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs. Front Genet 2019; 10:1174. [PMID: 31803243 PMCID: PMC6872681 DOI: 10.3389/fgene.2019.01174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023] Open
Abstract
There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. Here, we systematically surveyed the genomes of 157 unrelated dogs that were from 15 diverse Chinese dog breeds. Canine 170K SNP chips were used to compare the genomic structures of Chinese and Western dogs. The genotyping data of 170K SNP chips in Western dogs were downloaded from the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Chinese indigenous and Western dog breeds were clearly differentiated into two separate clades revealed by the PCA and NJ-tree. We found evidence for historical introgression of Western dogs into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Papillon, and European Eurasier have Chinese dog lineages. Selection sweep analysis identified genome-wide selection signatures of each Chinese breed and three breed groups. We highlighted several genes including EPAS1 and DNAH9 that show signatures of natural selection in Qinghai-Tibetan plateau dogs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports suggested RBP7, NMNAT1, SLC2A5, and H6PD that exhibit signatures of natural selection in Chinese mountain hounds as promising candidate genes for the traits of endurance and night vision, and NOL8, KRT9, RORB, and CAMTA1 that show signals of selection in Xi dogs might be candidate genes influencing dog running speed. The results about genomic and population structures, and selection signatures of Chinese dog breeds reinforce the conclusion that Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.
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Affiliation(s)
- Qianyong Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Provincial Key Laboratory for Police Dog Breeding and Behavioral Science, Nanchang Police Dog Base, Nanchang, China
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junhua Ye
- Jiangxi Provincial Key Laboratory for Police Dog Breeding and Behavioral Science, Nanchang Police Dog Base, Nanchang, China
| | - Chenlong Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Rongxing Wei
- Jiangxi Provincial Key Laboratory for Police Dog Breeding and Behavioral Science, Nanchang Police Dog Base, Nanchang, China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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31
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Luigi-Sierra MG, Cardoso TF, Martínez A, Pons A, Bermejo LA, Jordana J, Delgado JV, Adán S, Ugarte E, Arranz JJ, Casellas J, Amills M. Low genome-wide homozygosity in 11 Spanish ovine breeds. Anim Genet 2019; 50:501-511. [PMID: 31393638 DOI: 10.1111/age.12832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2019] [Indexed: 12/16/2022]
Abstract
The population of Spanish sheep has decreased from 24 to 15 million heads in the last 75 years due to multiple social and economic factors. Such a demographic reduction might have caused an increase in homozygosity and inbreeding, thus limiting the viability of local breeds with excellent adaptations to harsh ecosystems. The main goal of our study was to investigate the homozygosity patterns of 11 Spanish ovine breeds and to elucidate the relationship of these Spanish breeds with reference populations from Europe, Africa and the Near East. By using Ovine SNP50 BeadChip data retrieved from previous publications, we have found that the majority of studied Spanish ovine breeds have close genetic relatedness with other European populations; the one exception is the Canaria de Pelo breed, which is similar to North African breeds. Our analysis has also demonstrated that, with few exceptions, the genomes of Spanish sheep harbor fewer than 50 runs of homozygosity (ROH) with a total length of less than 350 Mb. Moreover, the frequencies of very long ROH (>30 Mb) are very low, and the inbreeding coefficients (FROH ) are generally small (FROH < 0.10), ranging from 0.008 (Rasa Aragonesa) to 0.086 (Canaria de Pelo). The low levels of homozygosity observed in the 11 Spanish sheep under analysis might be due to their extensive management and the high number of small to medium farms.
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Affiliation(s)
- M G Luigi-Sierra
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - T F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F, 70.040-020, Brazil
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - A Pons
- Unitat de Races Autòctones, Servei de Millora Agrària i Pesquera (SEMILLA), Son Ferriol, 07198, Spain
| | - L A Bermejo
- Departamento de Ingeniería, Producción y Economía Agrarias, Universidad de La Laguna, La Laguna, Tenerife, 38071, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - S Adán
- Pazo de Fontefiz, Federación de Razas Autóctonas de Galicia (BOAGA), 32152, Coles, Ourense, Spain
| | - E Ugarte
- Neiker-Tecnalia, Campus Agroalimentario de Arkaute, apdo 46 E-01080, Vitoria-Gazteiz (Araba), Spain
| | - J J Arranz
- Departamento de Producción Animal, Universidad de León, León, 24071, Spain
| | - J Casellas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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32
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Wang GD, Larson G, Kidd JM, vonHoldt BM, Ostrander EA, Zhang YP. Dog10K: the International Consortium of Canine Genome Sequencing. Natl Sci Rev 2019; 6:611-613. [PMID: 31598382 PMCID: PMC6776106 DOI: 10.1093/nsr/nwz068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, UK
| | - Jeffrey M Kidd
- Department of Human Genetics and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, USA
| | | | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
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33
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Jennings J, Sang Y. Porcine Interferon Complex and Co-Evolution with Increasing Viral Pressure after Domestication. Viruses 2019; 11:v11060555. [PMID: 31208045 PMCID: PMC6631851 DOI: 10.3390/v11060555] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/16/2022] Open
Abstract
Consisting of nearly 60 functional genes, porcine interferon (IFN)-complex represents an evolutionary surge of IFN evolution in domestic ungulate species. To compare with humans and mice, each of these species contains about 20 IFN functional genes, which are better characterized using the conventional IFN-α/β subtypes as examples. Porcine IFN-complex thus represents an optimal model for studying IFN evolution that resulted from increasing viral pressure during domestication and industrialization. We hypothesize and justify that porcine IFN-complex may extend its functionality in antiviral and immunomodulatory activity due to its superior molecular diversity. Furthermore, these unconventional IFNs could even confer some functional and signaling novelty beyond that of the well-studied IFN-α/β subtypes. Investigations into porcine IFN-complex will further our understanding of IFN biology and promote IFN-based therapeutic designs to confront swine viral diseases.
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Affiliation(s)
- Jordan Jennings
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
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34
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Lye ZN, Purugganan MD. Copy Number Variation in Domestication. TRENDS IN PLANT SCIENCE 2019; 24:352-365. [PMID: 30745056 DOI: 10.1016/j.tplants.2019.01.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 05/22/2023]
Abstract
Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.
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Affiliation(s)
- Zoe N Lye
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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35
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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36
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Diversity of copy number variation in the worldwide goat population. Heredity (Edinb) 2018; 122:636-646. [PMID: 30401973 DOI: 10.1038/s41437-018-0150-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/09/2018] [Accepted: 09/18/2018] [Indexed: 11/08/2022] Open
Abstract
Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.
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Cornejo OE, Yee MC, Dominguez V, Andrews M, Sockell A, Strandberg E, Livingstone D, Stack C, Romero A, Umaharan P, Royaert S, Tawari NR, Ng P, Gutierrez O, Phillips W, Mockaitis K, Bustamante CD, Motamayor JC. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process. Commun Biol 2018; 1:167. [PMID: 30345393 PMCID: PMC6191438 DOI: 10.1038/s42003-018-0168-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/14/2018] [Indexed: 01/24/2023] Open
Abstract
Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time to our knowledge that a single population, the Criollo population, underwent strong domestication ~3600 years ago (95% CI: 2481-13,806 years ago). We also show that during the process of domestication, there was strong selection for genes involved in the metabolism of the colored protectants anthocyanins and the stimulant theobromine, as well as disease resistance genes. Our analyses show that domesticated populations of T. cacao (Criollo) maintain a higher proportion of high-frequency deleterious mutations. We also show for the first time the negative consequences of the increased accumulation of deleterious mutations during domestication on the fitness of individuals (significant reduction in kilograms of beans per hectare per year as Criollo ancestry increases, as estimated from a GLM, P = 0.000425).
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Affiliation(s)
- Omar E Cornejo
- School of Biological Sciences, Washington State University, PO Box 644236, Heald Hall 429B, Pullman, Washington, 99164, USA
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
| | - Muh-Ching Yee
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
- Stanford Functional Genomics Facility, Stanford, CA, 94305, USA
| | - Victor Dominguez
- Department of Biology, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Mary Andrews
- Department of Biology, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Alexandra Sockell
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
| | - Erika Strandberg
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
- Biomedical Informatics Training Program, 1265 Welch Road, MSOB, X-215, MC 5479, Stanford, CA, 94305-5479, USA
| | - Donald Livingstone
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Conrad Stack
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Alberto Romero
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Pathmanathan Umaharan
- Cocoa Research Centre, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Stefan Royaert
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Nilesh R Tawari
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Pauline Ng
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Osman Gutierrez
- SHRS, USDS-ARS, 13601 Old Cutler Road, Miami, FL, 33158, USA
| | - Wilbert Phillips
- Programa de Mejoramiento de Cacao, CATIE, 7170, Turrialba, Costa Rica
| | - Keithanne Mockaitis
- Department of Biology, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
- Pervasive Technology Institute, Indiana University, 2709 E. 10th St., Bloomington, IN, 47408, USA
| | - Carlos D Bustamante
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, CA, 94305, USA
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38
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Bertolini F, Schiavo G, Tinarelli S, Santoro L, Utzeri VJ, Dall'Olio S, Nanni Costa L, Gallo M, Fontanesi L. Exploiting phenotype diversity in a local animal genetic resource: Identification of a single nucleotide polymorphism associated with the tail shape phenotype in the autochthonous Casertana pig breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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39
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Kumar Jadav K, Pratap Singh A, Srivastav AB, Sarkhel BC. Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus). Anim Biotechnol 2018; 30:186-191. [DOI: 10.1080/10495398.2018.1469506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | | | - A. B. Srivastav
- School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, NDVSU, Jabalpur, India
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40
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Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA. Genes (Basel) 2018; 9:genes9070367. [PMID: 30037043 PMCID: PMC6070935 DOI: 10.3390/genes9070367] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022] Open
Abstract
The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th–18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.
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41
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Marinov M, Teofanova D, Gadjev D, Radoslavov G, Hristov P. Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin. PeerJ 2018; 6:e5060. [PMID: 29967734 PMCID: PMC6026455 DOI: 10.7717/peerj.5060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak, n = 34; Bulgarian Scenthound Dog: Gonche, n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs.
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Affiliation(s)
- Miroslav Marinov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Denitsa Teofanova
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Dimitar Gadjev
- Agricultural and Stockbreeding Experimental Station, Agricultural Academy, Smolyan, Bulgaria
| | - Georgi Radoslavov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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42
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Xiang H, Liu X, Li M, Zhu Y, Wang L, Cui Y, Liu L, Fang G, Qian H, Xu A, Wang W, Zhan S. The evolutionary road from wild moth to domestic silkworm. Nat Ecol Evol 2018; 2:1268-1279. [PMID: 29967484 DOI: 10.1038/s41559-018-0593-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 05/29/2018] [Indexed: 12/22/2022]
Abstract
The Silk Road, which derives its name from the trade of silk produced by the domestic silkworm Bombyx mori, was an important episode in the development and interaction of human civilizations. However, the detailed history behind silkworm domestication remains ambiguous, and little is known about the underlying genetics with respect to important aspects of its domestication. Here, we reconstruct the domestication processes and identify selective sweeps by sequencing 137 representative silkworm strains. The results present an evolutionary scenario in which silkworms may have been initially domesticated in China as trimoulting lines, then subjected to independent spreads along the Silk Road that gave rise to the development of most local strains, and further improved for modern silk production in Japan and China, having descended from diverse ancestral sources. We find that genes with key roles in nitrogen and amino acid metabolism may have contributed to the promotion of silk production, and that circadian-related genes are generally selected for their adaptation. We additionally identify associations between several candidate genes and important breeding traits, thereby advancing the applicable value of our resources.
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Affiliation(s)
- Hui Xiang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaojing Liu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Muwang Li
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ya'nan Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lizhi Wang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yong Cui
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyuan Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Heying Qian
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Anying Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.
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43
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O’Brien CE, Roumbedakis K, Winkelmann IE. The Current State of Cephalopod Science and Perspectives on the Most Critical Challenges Ahead From Three Early-Career Researchers. Front Physiol 2018; 9:700. [PMID: 29962956 PMCID: PMC6014164 DOI: 10.3389/fphys.2018.00700] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/18/2018] [Indexed: 12/14/2022] Open
Abstract
Here, three researchers who have recently embarked on careers in cephalopod biology discuss the current state of the field and offer their hopes for the future. Seven major topics are explored: genetics, aquaculture, climate change, welfare, behavior, cognition, and neurobiology. Recent developments in each of these fields are reviewed and the potential of emerging technologies to address specific gaps in knowledge about cephalopods are discussed. Throughout, the authors highlight specific challenges that merit particular focus in the near-term. This review and prospectus is also intended to suggest some concrete near-term goals to cephalopod researchers and inspire those working outside the field to consider the revelatory potential of these remarkable creatures.
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Affiliation(s)
- Caitlin E. O’Brien
- Normandie Univ., UNICAEN, Rennes 1 Univ., UR1, CNRS, UMR 6552 ETHOS, Caen, France
- Association for Cephalopod Research – CephRes, Naples, Italy
| | - Katina Roumbedakis
- Association for Cephalopod Research – CephRes, Naples, Italy
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Benevento, Italy
| | - Inger E. Winkelmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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44
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Woo HJ, Reifman J. Collective interaction effects associated with mammalian behavioral traits reveal genetic factors connecting fear and hemostasis. BMC Psychiatry 2018; 18:175. [PMID: 29871603 PMCID: PMC5989392 DOI: 10.1186/s12888-018-1753-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/21/2018] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Investigation of the genetic architectures that influence the behavioral traits of animals can provide important insights into human neuropsychiatric phenotypes. These traits, however, are often highly polygenic, with individual loci contributing only small effects to the overall association. The polygenicity makes it challenging to explain, for example, the widely observed comorbidity between stress and cardiac disease. METHODS We present an algorithm for inferring the collective association of a large number of interacting gene variants with a quantitative trait. Using simulated data, we demonstrate that by taking into account the non-uniform distribution of genotypes within a cohort, we can achieve greater power than regression-based methods for high-dimensional inference. RESULTS We analyzed genome-wide data sets of outbred mice and pet dogs, and found neurobiological pathways whose associations with behavioral traits arose primarily from interaction effects: γ-carboxylated coagulation factors and downstream neuronal signaling were highly associated with conditioned fear, consistent with our previous finding in human post-traumatic stress disorder (PTSD) data. Prepulse inhibition in mice was associated with serotonin transporter and platelet homeostasis, and noise-induced fear in dogs with hemostasis. CONCLUSIONS Our findings suggest a novel explanation for the observed comorbidity between PTSD/anxiety and cardiovascular diseases: key coagulation factors modulating hemostasis also regulate synaptic plasticity affecting the learning and extinction of fear.
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Affiliation(s)
- Hyung Jun Woo
- 0000 0001 0036 4726grid.420210.5Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD USA
| | - Jaques Reifman
- Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, USA.
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45
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Abstract
In this article, we attempt to integrate recent advances in our understanding of the relations between culture and genes into an emerging field—cultural genomics—and discuss its promises and theoretical and methodological challenges. We first provide a brief review of previous conceptualizations about the relations between culture and genes and then argue that recent advances in molecular evolution research has allowed us to reframe the discussion away from parallel genetic and cultural evolution to focus on the interactions between the two. After outlining the key issues involved in cultural genomics (unit of analysis, timescale, mechanisms, and direction of influence), we provide examples of research for the different levels of interactions between culture and genes. We then discuss ideological, theoretical, and methodological challenges in cultural genomics and propose tentative solutions.
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46
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Ni P, Bhuiyan AA, Chen JH, Li J, Zhang C, Zhao S, Du X, Li H, Yu H, Liu X, Li K. De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs. Genetica 2018; 146:277-285. [PMID: 29748765 DOI: 10.1007/s10709-018-0018-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 04/21/2018] [Indexed: 11/29/2022]
Abstract
Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.
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Affiliation(s)
- Pan Ni
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ali Akbar Bhuiyan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Bangladesh Livestock Research Institute, Savar, Dhaka, 1341, Bangladesh
| | - Jian-Hai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Cheng Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiaoyong Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hua Li
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China
| | - Hui Yu
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China
| | - Xiangdong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Kui Li
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China.
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47
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Yang L, Xu L, Zhou Y, Liu M, Wang L, Kijas JW, Zhang H, Li L, Liu GE. Diversity of copy number variation in a worldwide population of sheep. Genomics 2018; 110:143-148. [DOI: 10.1016/j.ygeno.2017.09.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/24/2017] [Accepted: 09/11/2017] [Indexed: 01/14/2023]
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48
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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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Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB. Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. Cell 2017; 171:470-480.e8. [PMID: 28919077 DOI: 10.1016/j.cell.2017.08.030] [Citation(s) in RCA: 552] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/30/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022]
Abstract
Major advances in crop yields are needed in the coming decades. However, plant breeding is currently limited by incremental improvements in quantitative traits that often rely on laborious selection of rare naturally occurring mutations in gene-regulatory regions. Here, we demonstrate that CRISPR/Cas9 genome editing of promoters generates diverse cis-regulatory alleles that provide beneficial quantitative variation for breeding. We devised a simple genetic scheme, which exploits trans-generational heritability of Cas9 activity in heterozygous loss-of-function mutant backgrounds, to rapidly evaluate the phenotypic impact of numerous promoter variants for genes regulating three major productivity traits in tomato: fruit size, inflorescence branching, and plant architecture. Our approach allows immediate selection and fixation of novel alleles in transgene-free plants and fine manipulation of yield components. Beyond a platform to enhance variation for diverse agricultural traits, our findings provide a foundation for dissecting complex relationships between gene-regulatory changes and control of quantitative traits.
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Affiliation(s)
| | - Zachary H Lemmon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jarrett Man
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
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Moyers BT, Morrell PL, McKay JK. Genetic Costs of Domestication and Improvement. J Hered 2017; 109:103-116. [DOI: 10.1093/jhered/esx069] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Brook T Moyers
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN (Morrell)
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
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