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Balog K, Mizeranschi AE, Wanjala G, Sipos B, Kusza S, Bagi Z. Application potential of chicken DNA chip in domestic pigeon species - Preliminary results. Saudi J Biol Sci 2023; 30:103594. [PMID: 36874200 PMCID: PMC9975693 DOI: 10.1016/j.sjbs.2023.103594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.
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Affiliation(s)
- Katalin Balog
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | | | - George Wanjala
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Bíborka Sipos
- University of Debrecen, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi út 138, 4032, Debrecen, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
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2
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Fountain ED, Zhou LC, Karklus A, Liu QX, Meyers J, Fontanilla IKC, Rafael EF, Yu JY, Zhang Q, Zhu XL, Pei EL, Yuan YH, Banes GL. Cross-Species Application of Illumina iScan Microarrays for Cost-Effective, High-Throughput SNP Discovery. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.629252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.
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3
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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4
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Coetzer WG, Grobler JP. Genetic variation among different springbok (Antidorcas marsupialis) colour variants. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Sacks BN, Lounsberry ZT, Statham MJ. Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range. J Hered 2019; 109:573-584. [PMID: 29889225 DOI: 10.1093/jhered/esy028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
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6
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More M, Gutiérrez G, Rothschild M, Bertolini F, Ponce de León FA. Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip. Front Genet 2019; 10:361. [PMID: 31105741 PMCID: PMC6492526 DOI: 10.3389/fgene.2019.00361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover alpaca SNPs by genotyping forty alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥0.70) and the GenTrain score ≥ 0.25 parameters were applied to all comparisons. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 alpaca SNPs have 100% similarity with dromedary.
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Affiliation(s)
- Manuel More
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Gustavo Gutiérrez
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Max Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Francesca Bertolini
- National Institute of Aquatic Resources, DTU-Aqua, Technical University of Denmark, Lyngby, Denmark
| | - F Abel Ponce de León
- Department of Animal Science, University of Minnesota, Minneapolis, MN, United States
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7
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Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019; 9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022] Open
Abstract
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA
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RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3-GENES GENOMES GENETICS 2018; 8:2709-2722. [PMID: 29954843 PMCID: PMC6071602 DOI: 10.1534/g3.118.200171] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.
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9
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Städele V, Vigilant L. Strategies for determining kinship in wild populations using genetic data. Ecol Evol 2016; 6:6107-20. [PMID: 27648229 PMCID: PMC5016635 DOI: 10.1002/ece3.2346] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 01/17/2023] Open
Abstract
Knowledge of kin relationships between members of wild animal populations has broad application in ecology and evolution research by allowing the investigation of dispersal dynamics, mating systems, inbreeding avoidance, kin recognition, and kin selection as well as aiding the management of endangered populations. However, the assessment of kinship among members of wild animal populations is difficult in the absence of detailed multigenerational pedigrees. Here, we first review the distinction between genetic relatedness and kinship derived from pedigrees and how this makes the identification of kin using genetic data inherently challenging. We then describe useful approaches to kinship classification, such as parentage analysis and sibship reconstruction, and explain how the combined use of marker systems with biparental and uniparental inheritance, demographic information, likelihood analyses, relatedness coefficients, and estimation of misclassification rates can yield reliable classifications of kinship in groups with complex kin structures. We outline alternative approaches for cases in which explicit knowledge of dyadic kinship is not necessary, but indirect inferences about kinship on a group- or population-wide scale suffice, such as whether more highly related dyads are in closer spatial proximity. Although analysis of highly variable microsatellite loci is still the dominant approach for studies on wild populations, we describe how the long-awaited use of large-scale single-nucleotide polymorphism and sequencing data derived from noninvasive low-quality samples may eventually lead to highly accurate assessments of varying degrees of kinship in wild populations.
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Affiliation(s)
- Veronika Städele
- Department of PrimatologyMax Planck Institute for Evolutionary AnthropologyDeutscher Platz 6D‐04103LeipzigGermany
| | - Linda Vigilant
- Department of PrimatologyMax Planck Institute for Evolutionary AnthropologyDeutscher Platz 6D‐04103LeipzigGermany
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10
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Ivy JA, Putnam AS, Navarro AY, Gurr J, Ryder OA. Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs. J Hered 2016; 107:403-12. [PMID: 27208150 DOI: 10.1093/jhered/esw029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/22/2016] [Indexed: 12/24/2022] Open
Abstract
Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84-0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (P << 0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs.
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Affiliation(s)
- Jamie A Ivy
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Andrea S Putnam
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Asako Y Navarro
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Jessica Gurr
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
| | - Oliver A Ryder
- From the Department of Life Sciences, San Diego Zoo Global, San Diego, CA 92112-0551 (Ivy and Putnam); Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027-7017 (Navarro and Ryder); and Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia (Gurr)
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11
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Kharzinova V, Sermyagin AA, Gladyr EA, Brem G, Zinovieva NA. Response to “Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity” by Shafer, Miller, and Kardos. J Hered 2016; 107:196-7. [DOI: 10.1093/jhered/esv139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/25/2015] [Indexed: 11/13/2022] Open
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12
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Shafer ABA, Miller JM, Kardos M. Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity. J Hered 2016; 107:193-5. [PMID: 26774056 PMCID: PMC5994971 DOI: 10.1093/jhered/esv137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/24/2015] [Accepted: 12/21/2015] [Indexed: 11/12/2022] Open
Abstract
Cross-species application of single-nucleotide polymorphism (SNP) chips is a valid, relatively cost-effective alternative to the high-throughput sequencing methods generally required to obtain a genome-wide sampling of polymorphisms. Kharzinova et al. (2015) examined the applicability of SNP chips developed in domestic bovids (cattle and sheep) to a semi-wild cervid (reindeer). The ancestors of bovids and cervids diverged between 20 and 30 million years ago (Hassanin and Douzery 2003; Bibi et al. 2013). Empirical work has shown that for a SNP chip developed in a bovid and applied to a cervid species, approximately 50% genotype success with 1% of the loci being polymorphic is expected (Miller et al. 2012). The genotyping of Kharzinova et al. (2015) follows this pattern; however, these data are not appropriate for identifying runs of homozygosity (ROH) and can be problematic for estimating linkage disequilibrium (LD) and we caution readers in this regard.
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Affiliation(s)
- Aaron B A Shafer
- From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller).
| | - Joshua M Miller
- From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller)
| | - Marty Kardos
- From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller)
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13
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Humble E, Martinez-Barrio A, Forcada J, Trathan PN, Thorne MAS, Hoffmann M, Wolf JBW, Hoffman JI. A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them. Mol Ecol Resour 2016; 16:909-21. [DOI: 10.1111/1755-0998.12502] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 01/19/2023]
Affiliation(s)
- E. Humble
- Department of Animal Behaviour; University of Bielefeld; Postfach 100131 33501 Bielefeld Germany
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - A. Martinez-Barrio
- Science of Life Laboratories and Department of Cell and Molecular Biology; Uppsala University; Husargatan 3 75124 Uppsala Sweden
| | - J. Forcada
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - P. N. Trathan
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - M. A. S. Thorne
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - M. Hoffmann
- Max Planck Institute for Developmental Biology; Spemannstrasse 35 72076 Tübingen Germany
| | - J. B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
| | - J. I. Hoffman
- Department of Animal Behaviour; University of Bielefeld; Postfach 100131 33501 Bielefeld Germany
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14
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Kharzinova VR, Sermyagin AA, Gladyr EA, Okhlopkov IM, Brem G, Zinovieva NA. A Study of Applicability of SNP Chips Developed for Bovine and Ovine Species to Whole-Genome Analysis of Reindeer Rangifer tarandus. J Hered 2015; 106:758-61. [PMID: 26447215 DOI: 10.1093/jhered/esv081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/14/2015] [Indexed: 12/20/2022] Open
Abstract
Two sets of commercially available single nucleotide polymorphisms (SNPs) developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50 BeadChip) have been trialed for whole-genome analysis of 4 female samples of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of them were respectively polymorphic. The scored and the polymorphic SNPs were identified on each bovine and each ovine chromosome, but their distribution was not unique. The maximal value of runs of homozygosity (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP chips developed for bovine and ovine species can be used as a powerful tool for genome analysis in reindeer R. tarandus.
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Affiliation(s)
- Veronika R Kharzinova
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem).
| | - Alexander A Sermyagin
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Elena A Gladyr
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Innokentiy M Okhlopkov
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Gottfried Brem
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Natalia A Zinovieva
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
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15
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Silva-Junior OB, Faria DA, Grattapaglia D. A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species. THE NEW PHYTOLOGIST 2015; 206:1527-40. [PMID: 25684350 DOI: 10.1111/nph.13322] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/02/2015] [Indexed: 05/23/2023]
Abstract
We used whole genome resequencing of pooled individuals to develop a high-density single-nucleotide polymorphism (SNP) chip for Eucalyptus. Genomes of 240 trees of 12 species were sequenced at 3.5× each, and 46 997 586 raw SNP variants were subject to multivariable filtering metrics toward a multispecies, genome-wide distributed chip content. Of the 60 904 SNPs on the chip, 59 222 were genotyped and 51 204 were polymorphic across 14 Eucalyptus species, providing a 96% genome-wide coverage with 1 SNP/12-20 kb, and 47 069 SNPs at ≤ 10 kb from 30 444 of the 33 917 genes in the Eucalyptus genome. Given the EUChip60K multi-species genotyping flexibility, we show that both the sample size and taxonomic composition of cluster files impact heterozygous call specificity and sensitivity by benchmarking against 'gold standard' genotypes derived from deeply sequenced individual tree genomes. Thousands of SNPs were shared across species, likely representing ancient variants arisen before the split of these taxa, hinting to a recent eucalypt radiation. We show that the variable SNP filtering constraints allowed coverage of the entire site frequency spectrum, mitigating SNP ascertainment bias. The EUChip60K represents an outstanding tool with which to address population genomics questions in Eucalyptus and to empower genomic selection, GWAS and the broader study of complex trait variation in eucalypts.
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Affiliation(s)
- Orzenil B Silva-Junior
- Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, 70790-160, Brasilia, DF, Brazil
| | - Danielle A Faria
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
| | - Dario Grattapaglia
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, 70790-160, Brasilia, DF, Brazil
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
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16
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Kasarda R, Moravčíková N, Židek R, Mészáros G, Kadlečík O, Trakovická A, Pokorádi J. Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip. Arch Anim Breed 2015. [DOI: 10.5194/aab-58-57-2015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. This study presents the application of BovineSNP50 BeadChip for genome-wide screening of two taurine breeds (Bos primigenius taurus) and Zebu (Bos primigenius indicus), and two species from the family Cervidae: red deer (Cervus elaphus) and fallow deer (Dama dama). The aim of the paper was to evaluate the use of bovine array for cross-species genotyping and analyse single nucleotide polymorphism (SNP) distribution, diversity within groups of animals and genetic distance among analysed species. The number of polymorphic SNPs decreased with the increase of phylogenetic distance between species, which also reflected a decrease in call rate (from 99.54 to 61.19%). The minor allele frequency (MAF) values were significantly different between species and ranged from 0.18 ± 15 (Zebu) to 0.26 ± 0.14 (Pinzgau). The subsequent analyses of genetic diversity were based on the polymorphic loci detected in cervids. Differences in the expected heterozygosity was low (0.06), on average 0.34. In analysed groups the FIS values were close to zero, which suggested low SNP variance within them. The value of FIT indicated homozygote excess in evaluated individuals. Analysis of molecular variance revealed that most of the variability was distributed within all individuals. Observed genetic distances within and across groups of animals suggested that taurine cattle and cervids were more distant. The study results showed that genotyping array prepared for model species can be applied not only to organisms for which was developed, but can be also successfully used in closely related and more phylogenetically divergent species.
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17
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Kraus RHS, vonHoldt B, Cocchiararo B, Harms V, Bayerl H, Kühn R, Förster DW, Fickel J, Roos C, Nowak C. A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples. Mol Ecol Resour 2014; 15:295-305. [DOI: 10.1111/1755-0998.12307] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 07/11/2014] [Accepted: 07/16/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Robert H. S. Kraus
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544 USA
| | - Berardino Cocchiararo
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
| | - Verena Harms
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Senckenberg Museum of Natural History Görlitz; PF 300154 02806 Görlitz Germany
| | - Helmut Bayerl
- Molecular Zoology Unit; Research Department Animal Sciences; Technische Universität München; Hans-Carl-von-Carlowitz-Platz 2 D-85354 Freising Germany
| | - Ralph Kühn
- Molecular Zoology Unit; Research Department Animal Sciences; Technische Universität München; Hans-Carl-von-Carlowitz-Platz 2 D-85354 Freising Germany
- Wildlife and Conservation Ecology and Molecular Biology Program; Department of Fish; New Mexico State University; Box 30003 MSC 4901 Las Cruces NM 88003-8003 USA
| | - Daniel W. Förster
- Department of Evolutionary Genetics; Leibniz-Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 D-10315 Berlin Germany
| | - Jörns Fickel
- Department of Evolutionary Genetics; Leibniz-Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 D-10315 Berlin Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory; German Primate Center; Leibniz Institute for Primate Research; Kellnerweg 4 D-37077 Göttingen Germany
| | - Carsten Nowak
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
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