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Wehrenberg G, Tokarska M, Cocchiararo B, Nowak C. A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison. Sci Rep 2024; 14:1875. [PMID: 38253649 PMCID: PMC10803807 DOI: 10.1038/s41598-024-51495-9] [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: 04/18/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The European bison was saved from the brink of extinction due to considerable conservation efforts since the early twentieth century. The current global population of > 9500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world's first studbook of a threatened species.
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Affiliation(s)
- Gerrit Wehrenberg
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany.
- Department of Ecology and Evolution, Biologicum, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 8000, 90014, Oulu, Finland.
| | | | - Berardino Cocchiararo
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Carsten Nowak
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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Korec E, Ungrová L, Hejnar J, Grieblová A, Zelená K. Three new genes associated with longevity in the European Bison. Vet Anim Sci 2022; 17:100266. [PMID: 35957660 PMCID: PMC9361326 DOI: 10.1016/j.vas.2022.100266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Evžen Korec
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
- Corresponding author.
| | - Lenka Ungrová
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Adéla Grieblová
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
| | - Kateřina Zelená
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
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3
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison ( Bison bonasus))-Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data. Animals (Basel) 2021; 11:ani11082226. [PMID: 34438684 PMCID: PMC8388393 DOI: 10.3390/ani11082226] [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: 06/09/2021] [Revised: 07/07/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.
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New data on the genetic diversity of European bison Bison bonasus (Linnaeus, 1758) in Belarus. THERIOLOGIA UKRAINICA 2020. [DOI: 10.15407/tu1905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The paper presents data on the assessment of the genetic diversity of five subpopulations of the European bison (Bison bonasus) in Belarus — from the National Park “Belovezhskaya Pushcha”, the National Park “Pripyatsky”, the Osipovichi district (Mogilev area), SEI “Berezinsky Biosphere Reserve” and the Grodno region. In general, the work includes 30 samples of muscle tissue from the collection of Gene bank of wild fauna in SSPA “SPC NAS of Belarus on Bioresources” (Minsk, Belarus). Microsatellites were used as markers to assess genetic diversity, structure, and search for signs of a sharp decline in the size of bison subpopulations in the past. A total of 11 microsatellite markers were used, recommended by the Food and Agriculture Organization of the United Nations for cattle research. The analysis of B. bonasus subpopulation from the NP “Pripyatsky” showed signs of passing through the genetic bottleneck. All studied subpopulations are characterized by a similarly low genetic diversity level in all analyzed indicators (mean number of alleles, allelic diversity, observed and expected heterozygosity). The expected heterozygosity (He) for the three subpopulations from the NP “Belovezhskaya Pushcha”, the NP “Pripyatsky” and from the Osipovichi district ranged from 0.37 to 0.39. For the studied subpopulations, the values of the fixation index were negative. The assessment of the presence of genetic structuring between the subpopulations of bison from the NP “Belovezhskaya Pushcha”, the NP “Pripyatsky” and from the Osipovichi district based on the values of such indexes as Fst and DJost which showed no signs of genetic differentiation, which is also confirmed by principal coordinates analysis (PCoA). The European bison conservation in Belarus has required tremendous efforts in the past. So far, even though the impressively large population size reached in Belarus, B. bonasus status still should not be considered as stable, which is closely linked to aspects of its overall low genetic diversity. Our research confirmed the low genetic variability of Belarusian subpopulations. Therefore, the more extensive research concentrated on identifying genetic diversity is necessary to ensure the beneficial control of gene flow and register a potential correlation of unfavorable gene variants with possible inbreeding depression. These attempts are required to lay the groundwork for the management and protection of the European bison in Belarus.
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Xiao G, Yang J, Zhu X, Wu J, Zhou B. Prevalence of Ineffective Haplotypes at the Rice Blast Resistance (R) Gene Loci in Chinese Elite Hybrid Rice Varieties Revealed by Sequence-Based Molecular Diagnosis. RICE (NEW YORK, N.Y.) 2020; 13:6. [PMID: 32002696 PMCID: PMC6990218 DOI: 10.1186/s12284-020-0367-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Multiple haplotypes at the same rice blast R-gene locus share extremely high sequence similarity, which makes the gene diagnostic method using molecular markers less effective in differentiation from one another. The composition and distribution pattern of deployed R genes/haplotypes in elite rice varieties has not been extensively analyzed. In this study, we employed PCR amplification and sequencing approach for the diagnosis of R-gene haplotypes in 54 Chinese elite rice varieties. A varied number of functional and nonfunctional haplotypes of 4 target major R-gene loci, i.e., Pi2/9, Pi5, Pik, and Pib, were deduced by referring to the reference sequences of known R genes. Functional haplotypes accounted for relatively low frequencies for the Pi2/9 (15%) and Pik (9%) loci but for relatively high frequencies for the Pi5 (50%) and Pib (54%) loci. Intriguingly, significant frequencies of 33%, 39%, 46% of non-functional haplotypes at the Pi2/9, Pik, and Pib loci, respectively, with traceable original donors were identified, suggesting that they were most likely unintentionally spread by using undesirable donors in various breeding programs. In the case of Pi5 locus, only a single haplotype, i.e., Pi5 was identified. The reactions of 54 rice varieties to the differential isolates were evaluated, which showed a good correlation to the frequency of cognate avirulence (Avr) genes or haplotypes in the differential isolates. Four R genes, i.e., Pi2, Piz-t, Pi50, and Pikm were found to contribute significantly to the resistance of the elite rice varieties. Other two genes, Pi9 and Pikh, which were not utilized in rice varieties, showed promising values in breeding durable resistance due to their high resistance frequencies to the contemporary rice blast population. The sequence-based molecular diagnosis provided a promising approach for the identification and verification of haplotypes in different R-gene loci and effective R genes valuable for breeding durable rice resistance to rice blast.
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Affiliation(s)
- Gui Xiao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan China
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jianyuan Yang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaoyuan Zhu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan China
| | - Bo Zhou
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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7
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Wecek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov G, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Zyla W, Szymura JM, Hofreiter M, Barlow A. Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild. Mol Biol Evol 2017; 34:598-612. [PMID: 28007976 PMCID: PMC5356474 DOI: 10.1093/molbev/msw254] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.
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Affiliation(s)
- Karolina Wecek
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Ulrike Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA.,University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, Petersberg, Russia
| | | | - Jennifer J Crees
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Roland Dobosz
- Upper Silesian Museum, Bytom, Poland.,Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Ninna Manaserian
- Institute of Zoology Armenian National Academy of Sciences, Yerevan, Armenia
| | - Henryk Okarma
- Institute of Nature Conservation Polish Academy of Sciences, Kraków, Poland
| | | | - Samuel T Turvey
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Jan M Wójcik
- Mammal Research Institute Polish Academy of Sciences, Bialowieza, Poland
| | | | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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8
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D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics 2016; 17:55. [PMID: 26763898 PMCID: PMC4712552 DOI: 10.1186/s12864-015-2194-9] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. Results We assembled 2 synthetic communities with an even (EM) and uneven (UM) distribution of archaeal and bacterial strains and species, as metagenomic control material, to assess performance of different experimental strategies. The 2 synthetic communities were used in this study, to highlight the limitations and the advantages of the leading sequencing platforms: MiSeq (Illumina), The Pacific Biosciences RSII, 454 GS-FLX/+ (Roche), and IonTorrent (Life Technologies). We describe an extensive survey based on synthetic communities using 3 experimental designs (fusion primers, universal tailed tag, ligated adaptors) across the 9 hypervariable 16S rDNA regions. We demonstrate that library preparation methodology can affect data interpretation due to different error and chimera rates generated during the procedure. The observed community composition was always biased, to a degree that depended on the platform, sequenced region and primer choice. However, crucially, our analysis suggests that 16S rRNA sequencing is still quantitative, in that relative changes in abundance of taxa between samples can be recovered, despite these biases. Conclusion We have assessed a range of experimental conditions across several next generation sequencing platforms using the most up-to-date configurations. We propose that the choice of sequencing platform and experimental design needs to be taken into consideration in the early stage of a project by running a small trial consisting of several hypervariable regions to quantify the discriminatory power of each region. We also suggest that the use of a synthetic community as a positive control would be beneficial to identify the potential biases and procedural drawbacks that may lead to data misinterpretation. The results of this study will serve as a guideline for making decisions on which experimental condition and sequencing platform to consider to achieve the best microbial profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2194-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosalinda D'Amore
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Melanie Schirmer
- School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK.
| | - John G Kenny
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Richard Gregory
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Migun Shakya
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755, USA.
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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9
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Tokarska M, Bunevich AN, Demontis D, Sipko T, Perzanowski K, Baryshnikov G, Kowalczyk R, Voitukhovskaya Y, Wójcik JM, Marczuk B, Ruczyńska I, Pertoldi C. Genes of the extinct Caucasian bison still roam the Białowieża Forest and are the source of genetic discrepances between Polish and Belarusian populations of the European bison,Bison bonasus. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12470] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | | | - Ditte Demontis
- Department of Biomedicine; Aarhus University; Wilhelm Meyers Allé 4 8000Århus C Denmark
| | - Taras Sipko
- A.N. Severtsov Institute of Ecology and Evolution RAS; Leninsky pr. 33 Moscow 119071 Russia
| | - Kajetan Perzanowski
- Museum and Institute of Zoology; Polish Academy of Sciences; Wilcza 64 00-679 Warszawa Poland
- Applied Ecology; Catholic University of Lublin; Konstantynów 1H/402 20-708 Lublin Poland
| | - Gennady Baryshnikov
- Zoological Museum of the Zoological Institute RAS; Universitetskaya Naberezhnaya 1; St. Petersburg Russia
| | - Rafał Kowalczyk
- Mammal Research Institute PAS; Waszkiewicza 1 17-230 Białowieża Poland
| | - Yuliya Voitukhovskaya
- Institute of Genetics and Cytology at National Academy of Sciences of Belarus; Akademicheskaya st., 27 220072 Minsk Republic of Belarus
| | - Jan Marek Wójcik
- Mammal Research Institute PAS; Waszkiewicza 1 17-230 Białowieża Poland
| | - Barbara Marczuk
- Mammal Research Institute PAS; Waszkiewicza 1 17-230 Białowieża Poland
| | - Iwona Ruczyńska
- Mammal Research Institute PAS; Waszkiewicza 1 17-230 Białowieża Poland
| | - Cino Pertoldi
- Department 18/Section of Environmental Engineering; Aalborg University; Aalborg Denmark
- Aalborg Zoo; Aalborg Denmark
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Oleński K, Tokarska M, Hering D, Puckowska P, Ruść A, Pertoldi C, Kamiński S. Genome-wide association study for posthitis in the free-living population of European bison (Bison bonasus). Biol Direct 2015; 10:2. [PMID: 25585689 PMCID: PMC4302601 DOI: 10.1186/s13062-014-0033-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/16/2014] [Indexed: 11/24/2022] Open
Abstract
Background About 5–6% of the European bison (Bison bonasus) males are affected by posthitis (necrotic inflammation of the prepuce) and die in the wild forest. Despite many years of study, pathogenesis of this disease has not yet been determined. The main aim of the study was to find SNP markers significantly associated with the incidence of posthitis and mine the genome for candidate genes potentially involved in the development of the disease. Results It was shown that relatively small number of SNPs effects reached genome-wide significance after false discovery rate (FDR) correction. Among 25 significant markers, the highest effects were found for two SNPs (rs110456748 and rs136792896) located at the distance of 23846 bp and 37742 bp, respectively, from OR10A3 gene (olfactory receptor genes), known to be involved in atopic dermatitis in humans. It was also observed that five other significant SNP markers were located in the proximity of candidate genes involved in severe diseases of skin tissue and cancer/tumour development of epithelial or testicular germ cells, which suggest their potential participation in the posthitis. The 25 investigated SNPs showed marked differences in allelic and genotypic frequencies between the healthy and affected bison groups. Conclusions The 2 Mb region of the BTA15 chromosome is involved in genetic background of posthitis and should be closer examined to find causal mutations helpful in better understanding of the disease ethology and to control its incidence in the future. Reviewers This article was reviewed by Prof. Lev Klebanov and Dr. Fyodor Kondrashov.
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11
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Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol 2011; 3:1312-23. [PMID: 22002916 PMCID: PMC3236605 DOI: 10.1093/gbe/evr106] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2011] [Indexed: 12/03/2022] Open
Abstract
Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.
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Affiliation(s)
- Seth M Bybee
- Department of Biology, Brigham Young University, USA.
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12
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Bybee SM, Bracken-Grissom HD, Hermansen RA, Clement MJ, Crandall KA, Felder DL. Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea). ZOOL ANZ 2011. [DOI: 10.1016/j.jcz.2011.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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TOKARSKA M, PERTOLDI C, KOWALCZYK R, PERZANOWSKI K. Genetic status of the European bison Bison bonasus after extinction in the wild and subsequent recovery. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2010.00178.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics. Genome Biol Evol 2011. [DOI: 10.evr106[pii]10.1093/gbe/evr106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | | | | | - Russell A. Hermansen
- Department of Biology, Brigham Young University
- Department of Molecular Biology, University of Wyoming
| | - Robert L. Byers
- Department of Plant and Wildlife Sciences, Brigham Young University
| | | | - Joshua A. Udall
- Department of Plant and Wildlife Sciences, Brigham Young University
| | - Edward R. Wilcox
- Department of Biology, Brigham Young University
- DNA Sequencing Center, Brigham Young University
| | - Keith A. Crandall
- Department of Biology, Brigham Young University
- Monte L. Bean Life Science Museum, Brigham Young University
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15
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Michelizzi VN, Wu X, Dodson MV, Michal JJ, Zambrano-Varon J, McLean DJ, Jiang Z. A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo. Int J Biol Sci 2010; 7:18-27. [PMID: 21209788 PMCID: PMC3014552 DOI: 10.7150/ijbs.7.18] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 12/25/2010] [Indexed: 01/17/2023] Open
Abstract
The Illumina BovineSNP50 BeadChip features 54,001 informative single nucleotide polymorphisms (SNPs) that uniformly span the entire bovine genome. Among them, 52,255 SNPs have locations assigned in the current genome assembly (Btau_4.0), including 19,294 (37%) intragenic SNPs (i.e., located within genes) and 32,961 (63%) intergenic SNPs (i.e., located between genes). While the SNPs represented on the Illumina Bovine50K BeadChip are evenly distributed along each bovine chromosome, there are over 14,000 genes that have no SNPs placed on the current BeadChip. Kernel density estimation, a non-parametric method, was used in the present study to identify SNP-poor and SNP-rich regions on each bovine chromosome. With bandwidth = 0.05 Mb, we observed that most regions have SNP densities within 2 standard deviations of the chromosome SNP density mean. The SNP density on chromosome X was the most dynamic, with more than 30 SNP-rich regions and at least 20 regions with no SNPs. Genotyping ten water buffalo using the Illumina BovineSNP50 BeadChip revealed that 41,870 of the 54,001 SNPs are fully scored on all ten water buffalo, but 6,771 SNPs are partially scored on one to nine animals. Both fully scored and partially/no scored SNPs are clearly clustered with various sizes on each chromosome. However, among 43,687 bovine SNPs that were successfully genotyped on nine and ten water buffalo, only 1,159 were polymorphic in the species. These results indicate that the SNPs sites, but not the polymorphisms, are conserved between two species. Overall, our present study provides a solid foundation to further characterize the SNP evolutionary process, thus improving understanding of within- and between-species biodiversity, phylogenetics and adaption to environmental changes.
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Affiliation(s)
- Vanessa N. Michelizzi
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | - Xiaolin Wu
- 2. Department of Dairy Science, University of Wisconsin-Madison, Madison, WI 53706-1284, USA
| | - Michael V. Dodson
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | - Jennifer J. Michal
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | - Jorge Zambrano-Varon
- 3. Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Derek J. McLean
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | - Zhihua Jiang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
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