2051
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Davey JW, Davey JL, Blaxter ML, Blaxter MW. RADSeq: next-generation population genetics. Brief Funct Genomics 2011; 9:416-23. [PMID: 21266344 DOI: 10.1093/bfgp/elq031] [Citation(s) in RCA: 397] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis of genetic diversity in populations. However, genome-scale population genetic studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promises to deliver high resolution population genomic data-thousands of sequenced markers across many individuals-for any organism at reasonable costs. It has found application in wild populations and non-traditional study species, and promises to become an important technology for ecological population genomics.
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Affiliation(s)
- John W Davey
- Institute of Evolutionary Biology, Edinburgh, UK.
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2052
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Grattapaglia D, Silva-Junior OB, Kirst M, de Lima BM, Faria DA, Pappas GJ. High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC PLANT BIOLOGY 2011; 11:65. [PMID: 21492434 PMCID: PMC3090336 DOI: 10.1186/1471-2229-11-65] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/14/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. RESULTS We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. CONCLUSIONS This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥ 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
- Genomic Sciences Program - Universidade Catolica de Brasília- SGAN, 916 modulo B, 70790-160 Brasília - DF, Brazil
| | - Orzenil B Silva-Junior
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
| | - Matias Kirst
- School of Forest Resources and Conservation, Genetics Institute, University of Florida, PO Box 110410, Gainesville, USA
| | - Bruno Marco de Lima
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
- Department of Genetics - Universidade de São Paulo - ESALQ/USP - Av. Pádua Dias, 11 - Caixa Postal 9 13418-900 Piracicaba, SP, Brazil
| | - Danielle A Faria
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
| | - Georgios J Pappas
- EMBRAPA Genetic Resources and Biotechnology - Estação Parque Biológico, final W5 norte, Brasilia, Brazil
- Genomic Sciences Program - Universidade Catolica de Brasília- SGAN, 916 modulo B, 70790-160 Brasília - DF, Brazil
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2053
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Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA. Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One 2011; 6:e18561. [PMID: 21541009 PMCID: PMC3076424 DOI: 10.1371/journal.pone.0018561] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 03/10/2011] [Indexed: 12/02/2022] Open
Abstract
Despite the power of massively parallel sequencing platforms, a drawback is the
short length of the sequence reads produced. We demonstrate that short reads can
be locally assembled into longer contigs using
paired-end sequencing of
restriction-site associated
DNA (RAD-PE) fragments. We use this RAD-PE contig
approach to identify single
nucleotide polymorphisms (SNPs)
and determine haplotype structure in threespine stickleback and to sequence
E. coli and stickleback genomic DNA with overlapping
contigs of several hundred nucleotides. We also demonstrate that adding a
circularization step allows the local assembly of contigs up to 5 kilobases (kb)
in length. The ease of assembly and accuracy of the individual contigs produced
from each RAD site sequence suggests RAD-PE sequencing is a useful way to
convert genome-wide short reads into individually-assembled sequences hundreds
or thousands of nucleotides long.
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Affiliation(s)
- Paul D. Etter
- Institute of Molecular Biology, University of
Oregon, Eugene, Oregon, United States of America
| | - Jessica L. Preston
- Institute of Molecular Biology, University of
Oregon, Eugene, Oregon, United States of America
| | - Susan Bassham
- Center for Ecology and Evolutionary Biology,
University of Oregon, Eugene, Oregon, United States of America
| | - William A. Cresko
- Center for Ecology and Evolutionary Biology,
University of Oregon, Eugene, Oregon, United States of America
| | - Eric A. Johnson
- Institute of Molecular Biology, University of
Oregon, Eugene, Oregon, United States of America
- * E-mail:
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2054
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Svensson O, Egger B, Gricar B, Woodhouse K, van Oosterhout C, Salzburger W, Seehausen O, Turner GF. Segregation of species-specific male attractiveness in f(2) hybrid lake Malawi cichlid fish. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:426179. [PMID: 21716739 PMCID: PMC3119475 DOI: 10.4061/2011/426179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 02/14/2011] [Indexed: 11/20/2022]
Abstract
Among the huge radiations of haplochromine cichlid fish in Lakes Malawi and Victoria, closely related species are often reproductively isolated via female mate choice although viable fertile hybrids can be produced when females are confined only with heterospecific males. We generated F2 hybrid males from a cross between a pair of closely related sympatric cichlid fish from Lake Malawi. Laboratory mate choice experiments using microsatellite paternity analysis demonstrated that F2 hybrid males differed significantly in their attractiveness to females of the two parental species, indicating heritable variation in traits involved in mate choice that may contribute to reproductive isolation between these species. We found no significant correlation between male mating success and any measurement of male colour pattern. A simple quantitative genetic model of reproductive isolation suggests that there may be as few as two chromosomal regions controlling species-specific attractiveness. We propose that adaptive radiation of Lake Malawi cichlids could be facilitated by the presence of genes with major effects on mate choice and reproductive isolation.
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Affiliation(s)
- Ola Svensson
- Evolutionary Biology Group, Biological Sciences, University of Hull, Hull HU6 7RX, UK
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2055
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HIRD SARAHM, BRUMFIELD ROBBT, CARSTENS BRYANC. PRG
matic
: an efficient pipeline for collating genome‐enriched second‐generation sequencing data using a ‘provisional‐reference genome’. Mol Ecol Resour 2011; 11:743-8. [DOI: 10.1111/j.1755-0998.2011.03005.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- SARAH M. HIRD
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - ROBB T. BRUMFIELD
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - BRYAN C. CARSTENS
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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2056
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Abstract
The onset of flowering is an important adaptive trait in plants. The small ephemeral species Arabidopsis thaliana grows under a wide range of temperature and day-length conditions across much of the Northern hemisphere, and a number of flowering-time loci that vary between different accessions have been identified before. However, only few studies have addressed the species-wide genetic architecture of flowering-time control. We have taken advantage of a set of 18 distinct accessions that present much of the common genetic diversity of A. thaliana and mapped quantitative trait loci (QTL) for flowering time in 17 F₂ populations derived from these parents. We found that the majority of flowering-time QTL cluster in as few as five genomic regions, which include the locations of the entire FLC/MAF clade of transcription factor genes. By comparing effects across shared parents, we conclude that in several cases there might be an allelic series caused by rare alleles. While this finding parallels results obtained for maize, in contrast to maize much of the variation in flowering time in A. thaliana appears to be due to large-effect alleles.
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2057
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Storz JF, Wheat CW. Integrating evolutionary and functional approaches to infer adaptation at specific loci. Evolution 2011; 64:2489-509. [PMID: 20500215 DOI: 10.1111/j.1558-5646.2010.01044.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally,population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.
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2058
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HOHENLOHE PAULA, AMISH STEPHENJ, CATCHEN JULIANM, ALLENDORF FREDW, LUIKART GORDON. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Resour 2011; 11 Suppl 1:117-22. [DOI: 10.1111/j.1755-0998.2010.02967.x] [Citation(s) in RCA: 289] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2059
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OGDEN ROB. Unlocking the potential of genomic technologies for wildlife forensics. Mol Ecol Resour 2011; 11 Suppl 1:109-16. [DOI: 10.1111/j.1755-0998.2010.02954.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2060
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EVERETT MV, GRAU ED, SEEB JE. Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome. Mol Ecol Resour 2011; 11 Suppl 1:93-108. [DOI: 10.1111/j.1755-0998.2010.02969.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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2061
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van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJT, Prins M. Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Res 2011; 21:618-25. [PMID: 21324881 DOI: 10.1101/gr.112094.110] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present whole genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. WGP leverages short read sequences derived from restriction fragments of two-dimensionally pooled BAC clones to generate sequence tags. These sequence tags are assigned to individual BAC clones, followed by assembly of BAC contigs based on shared regions containing identical sequence tags. Following in silico analysis of WGP sequence tags and simulation of a map of Arabidopsis chromosome 4 and maize, a WGP map of Arabidopsis thaliana ecotype Columbia was constructed de novo using a six-genome equivalent BAC library. Validation of the WGP map using the Columbia reference sequence confirmed that 350 BAC contigs (98%) were assembled correctly, spanning 97% of the 102-Mb calculated genome coverage. We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data.
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2062
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Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 2011; 21:610-7. [PMID: 21233398 DOI: 10.1101/gr.115402.110] [Citation(s) in RCA: 273] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.
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Affiliation(s)
- Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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2063
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Pemberton JM, Beraldi D, Craig BH, Hopkins J. Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs. Mol Ecol 2011; 20:910-9. [PMID: 21324010 DOI: 10.1111/j.1365-294x.2010.04992.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Digital gene expression (DGE) analysis offers a route to gene discovery which by-passes the need to develop bespoke arrays for nonmodel species, and is therefore a potentially valuable tool for molecular ecologists. Scottish blackface sheep, which vary in resistance to the common abomasal parasitic nematode Teladorsagia circumcincta, were trickle-infected with L3 larvae over 3 months to mimic the natural progression of infection. DGE was performed on abomasal lymph node tissue after the resolution of infection in resistant animals. Susceptible (low resistance) animals showed a large number of differentially expressed genes associated with inflammation and cell activation, but generally few differentially regulated genes in either the susceptible or the resistant group were directly involved in the adaptive immune function. Our results are consistent with the hypothesis that both resistance and susceptibility are active responses to infection and that susceptibility is associated with dysfunction in T cell differentiation and regulation.
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Affiliation(s)
- J M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK.
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2064
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HELYAR SJ, HEMMER-HANSEN J, BEKKEVOLD D, TAYLOR MI, OGDEN R, LIMBORG MT, CARIANI A, MAES GE, DIOPERE E, CARVALHO GR, NIELSEN EE. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 2011; 11 Suppl 1:123-36. [DOI: 10.1111/j.1755-0998.2010.02943.x] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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2065
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Olsen MT, Volny VH, Bérubé M, Dietz R, Lydersen C, Kovacs KM, Dodd RS, Palsbøll PJ. A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida). Mol Ecol Resour 2011; 11 Suppl 1:9-19. [PMID: 21429159 DOI: 10.1111/j.1755-0998.2010.02941.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Morten Tange Olsen
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University, Sweden.
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2066
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HEMMER-HANSEN JAKOB, NIELSEN EINAREG, MELDRUP DORTE, MITTELHOLZER CHRISTIAN. Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod,Gadus morhua. Mol Ecol Resour 2011; 11 Suppl 1:71-80. [DOI: 10.1111/j.1755-0998.2010.02940.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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2067
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Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM. Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 2011; 12:4. [PMID: 21205322 PMCID: PMC3023751 DOI: 10.1186/1471-2164-12-4] [Citation(s) in RCA: 231] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 01/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL). RESULTS Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines--the "dominant" and "recessive" marker stocks--and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. CONCLUSIONS We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic maps and association mapping.
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Affiliation(s)
- Yada Chutimanitsakun
- Crop and Soil Science Department, Oregon State University, Corvallis, Oregon, USA
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2068
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Fu Y, Springer NM, Ying K, Yeh CT, Iniguez AL, Richmond T, Wu W, Barbazuk B, Nettleton D, Jeddeloh J, Schnable PS. High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. PLoS One 2010; 5:e14178. [PMID: 21152036 PMCID: PMC2996289 DOI: 10.1371/journal.pone.0014178] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 11/09/2010] [Indexed: 11/18/2022] Open
Abstract
To date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into genotyping assays. Here, we report a microarray-based genotyping technology for complex genomes (such as the 2.3 GB maize genome) that does not require genome complexity reduction prior to hybridization. Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to genotype two recombinant inbred lines. While multiple hybridization replicates provided ∼97% accuracy, even a single replicate provided ∼95% accuracy. Genotyping accuracy was further increased to >99% by utilizing information from adjacent probes. This microarray-based method provides a simple, high-density genotyping approach for large, complex genomes.
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Affiliation(s)
- Yan Fu
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Nathan M. Springer
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota, United States of America
| | - Kai Ying
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Cheng-Ting Yeh
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | | | - Todd Richmond
- Roche NimbleGen, Inc., Madison, Wisconsin, United States of America
| | - Wei Wu
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Brad Barbazuk
- Department of Biology and the Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Jeff Jeddeloh
- Roche NimbleGen, Inc., Madison, Wisconsin, United States of America
| | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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2069
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Rice AM, Rudh A, Ellegren H, Qvarnström A. A guide to the genomics of ecological speciation in natural animal populations. Ecol Lett 2010; 14:9-18. [PMID: 21070555 DOI: 10.1111/j.1461-0248.2010.01546.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interest in ecological speciation is growing, as evidence accumulates showing that natural selection can lead to rapid divergence between subpopulations. However, whether and how ecological divergence can lead to the buildup of reproductive isolation remains under debate. What is the relative importance of natural selection vs. neutral processes? How does adaptation generate reproductive isolation? Can ecological speciation occur despite homogenizing gene flow? These questions can be addressed using genomic approaches, and with the rapid development of genomic technology, will become more answerable in studies of wild populations than ever before. In this article, we identify open questions in ecological speciation theory and suggest useful genomic methods for addressing these questions in natural animal populations. We aim to provide a practical guide for ecologists interested in incorporating genomic methods into their research programs. An increased integration between ecological research and genomics has the potential to shed novel light on the origin of species.
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Affiliation(s)
- Amber M Rice
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
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2070
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Nadeau NJ, Jiggins CD. A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations. Trends Genet 2010; 26:484-92. [DOI: 10.1016/j.tig.2010.08.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/16/2010] [Accepted: 08/18/2010] [Indexed: 12/20/2022]
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2071
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Sarropoulou E, Fernandes JMO. Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 6:92-102. [PMID: 20961822 DOI: 10.1016/j.cbd.2010.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 12/14/2022]
Abstract
Comparative genomics is a powerful tool to transfer knowledge coming from model fish species to non-model fish species of economic or/and evolutionary interest. Such transfer is of importance as functional studies either are difficult to perform with most non-model species. The first comparative map constructed using the human and the chimpanzee genome allowed the identification of putative orthologues. Although comparative mapping in teleosts is still in its infancy, five model teleost genomes from different orders have been fully sequenced to date and the sequencing of several commercially important species are also underway or near completion. The accessibility of these whole genome sequences and rapid developments in genomics of fish species are paving the way towards new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of non-model, but economically, physiologically or evolutionary important species is now feasible. Furthermore, comparison of low coverage gene maps of non-model fish species against fully sequenced fish species will enhance the efficiency of candidate gene identification projected for quantitative trait loci (QTL) scans for traits of special interest.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, Crete, Greece.
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2072
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Allendorf FW, Hohenlohe PA, Luikart G. Genomics and the future of conservation genetics. Nat Rev Genet 2010; 11:697-709. [DOI: 10.1038/nrg2844] [Citation(s) in RCA: 939] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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2073
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Abstract
There are several different types of self-incompatibility in different flowering plant species, and there has recently been progress in understanding their molecular genetics by using combined molecular and evolutionary approaches. Questions include the mechanism of self-incompatibility (both the nature of the proteins encoded by the genes and whether incompatibility systems all have separate genes for the pollen and pistil recognition proteins, which is the focus of this mini-review) and whether these systems involve chromosome regions with suppressed recombination and, if so, the size of these regions.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratory King's Buildings, West Mains Road, Edinburgh, EH9 3JT UK
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2074
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Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci U S A 2010; 107:16196-200. [PMID: 20798348 DOI: 10.1073/pnas.1006538107] [Citation(s) in RCA: 291] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient technique to determine the fine-scale phylogenetic relationships among recently diverged populations in a species. This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii, from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000-19,000 B.P. The RAD tag method can be used to identify detailed patterns of phylogeography in any organism regardless of existing genomic data, and, more broadly, to identify incipient speciation and genome-wide variation in natural populations in general.
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2075
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MANEL STÉPHANIE, JOOST STÉPHANE, EPPERSON BRYANK, HOLDEREGGER ROLF, STORFER ANDREW, ROSENBERG MICHAELS, SCRIBNER KIMT, BONIN AURÉLIE, FORTIN MARIEJOSÉE. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol Ecol 2010; 19:3760-72. [DOI: 10.1111/j.1365-294x.2010.04717.x] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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2076
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Mammadov JA, Chen W, Ren R, Pai R, Marchione W, Yalçin F, Witsenboer H, Greene TW, Thompson SA, Kumpatla SP. Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:577-88. [PMID: 20401646 DOI: 10.1007/s00122-010-1331-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 03/26/2010] [Indexed: 05/20/2023]
Abstract
The duplicated and the highly repetitive nature of the maize genome has historically impeded the development of true single nucleotide polymorphism (SNP) markers in this crop. Recent advances in genome complexity reduction methods coupled with sequencing-by-synthesis technologies permit the implementation of efficient genome-wide SNP discovery in maize. In this study, we have applied Complexity Reduction of Polymorphic Sequences technology (Keygene N.V., Wageningen, The Netherlands) for the identification of informative SNPs between two genetically distinct maize inbred lines of North and South American origins. This approach resulted in the discovery of 1,123 putative SNPs representing low and single copy loci. In silico and experimental (Illumina GoldenGate (GG) assay) validation of putative SNPs resulted in mapping of 604 markers, out of which 188 SNPs represented 43 haplotype blocks distributed across all ten chromosomes. We have determined and clearly stated a specific combination of stringent criteria (>0.3 minor allele frequency, >0.8 GenTrainScore and >0.5 Chi_test100 score) necessary for the identification of highly polymorphic and genetically stable SNP markers. Due to these criteria, we identified a subset of 120 high-quality SNP markers to leverage in GG assay-based marker-assisted selection projects. A total of 32 high-quality SNPs represented 21 haplotypes out of 43 identified in this study. The information on the selection criteria of highly polymorphic SNPs in a complex genome such as maize and the public availability of these SNP assays will be of great value for the maize molecular genetics and breeding community.
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Affiliation(s)
- Jafar A Mammadov
- Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268-1054, USA.
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2077
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Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics 2010; 11:410. [PMID: 20591181 PMCID: PMC2996938 DOI: 10.1186/1471-2164-11-410] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/30/2010] [Indexed: 11/10/2022] Open
Abstract
Background Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the difficulty of ascertaining rare polymorphic ME insertions that occur against a large background of pre-existing fixed elements and then genotyping them in many individuals. Results Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%. Conclusions Mobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.
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Affiliation(s)
- David J Witherspoon
- Dept. of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA.
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2078
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The application of next generation sequencing in DNA methylation analysis. Genes (Basel) 2010; 1:85-101. [PMID: 24710012 PMCID: PMC3960863 DOI: 10.3390/genes1010085] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/01/2010] [Accepted: 06/03/2010] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states.
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2079
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Reed DH. Albatrosses, eagles and newts, Oh My!: exceptions to the prevailing paradigm concerning genetic diversity and population viability? Anim Conserv 2010. [DOI: 10.1111/j.1469-1795.2010.00353.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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2080
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Genome mapping in intensively studied wild vertebrate populations. Trends Genet 2010; 26:275-84. [DOI: 10.1016/j.tig.2010.03.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/26/2010] [Accepted: 03/29/2010] [Indexed: 11/18/2022]
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2081
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Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci U S A 2010; 107:10578-83. [PMID: 20498060 DOI: 10.1073/pnas.1005931107] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05x genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width (GW5) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.
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2082
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Reid DT, Peichel CL. Perspectives on the genetic architecture of divergence in body shape in sticklebacks. Integr Comp Biol 2010; 50:1057-66. [PMID: 21082067 DOI: 10.1093/icb/icq030] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The body shape of fishes encompasses a number of morphological traits that are intrinsically linked to functional systems and affect various measures of performance, including swimming, feeding, and avoiding predators. Changes in shape can allow a species to exploit a new ecological niche and can lead to ecological speciation. Body shape results from the integration of morphological, behavioral and physiological traits. It has been well established that functional interdependency among traits plays a large role in constraining the evolution of shape, affecting both the speed and the repeated evolution of particular body shapes. However, it is less clear what role genetic or developmental constraints might play in biasing the rate or direction of the evolution of body shape. Here, we suggest that the threespine stickleback (Gasterosteus aculeatus) is a powerful model system in which to address the extent to which genetic or developmental constraints play a role in the evolution of body shape in fishes. We review the existing data that begins to address these issues in sticklebacks and provide suggestions for future areas of research that will be particularly fruitful for illuminating the mechanisms that contribute to the evolution of body shape in fishes.
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Affiliation(s)
- Duncan T Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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2083
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Pespeni MH, Oliver TA, Manier MK, Palumbi SR. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays. Genome Biol 2010; 11:R44. [PMID: 20403197 PMCID: PMC2884547 DOI: 10.1186/gb-2010-11-4-r44] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/07/2010] [Accepted: 04/19/2010] [Indexed: 12/28/2022] Open
Abstract
A method for the simultaneous identification of polymorphic loci and the quantitative genotyping of thousands of loci in individuals is presented. High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, Stanford University, Hopkins Marine Station, Oceanview Blvd Pacific Grove, CA 93950, USA.
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2084
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Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 2010; 6:e1000862. [PMID: 20195501 PMCID: PMC2829049 DOI: 10.1371/journal.pgen.1000862] [Citation(s) in RCA: 981] [Impact Index Per Article: 70.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 01/28/2010] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP-based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such regions in natural populations, and identifying new genomic regions and candidate genes of evolutionary significance.
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Affiliation(s)
- Paul A. Hohenlohe
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Susan Bassham
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Paul D. Etter
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Nicholas Stiffler
- Genomics Core Facility, University of Oregon, Eugene, Oregon, United States of America
| | - Eric A. Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - William A. Cresko
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America
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2085
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Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 2010. [PMID: 20195501 DOI: 10.1371/journal.pgen.1000862.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP-based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such regions in natural populations, and identifying new genomic regions and candidate genes of evolutionary significance.
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2086
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Abstract
New islands present the perfect opportunity for a species to get a fresh start and undergo adaptive radiation. For Galápagos land snails, both competition and resource diversity have together led to opportunity knocking twice.
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2087
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Pool JE, Hellmann I, Jensen JD, Nielsen R. Population genetic inference from genomic sequence variation. Genome Res 2010; 20:291-300. [PMID: 20067940 DOI: 10.1101/gr.079509.108] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are currently under way. And in light of the falling costs of next-generation sequencing technologies, such studies will soon become common in many other organisms as well. Here, we assess the challenges to analyzing whole-genome sequence polymorphism data, and we discuss the potential of these data to yield new insights concerning population history and the genomic prevalence of natural selection.
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Affiliation(s)
- John E Pool
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
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2088
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Hendry AP, Bolnick DI, Berner D, Peichel CL. Along the speciation continuum in sticklebacks. JOURNAL OF FISH BIOLOGY 2009; 75:2000-2036. [PMID: 20738669 DOI: 10.1111/j.1095-8649.2009.02419.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Speciation can be viewed as a continuum, potentially divisible into several states: (1) continuous variation within panmictic populations, (2) partially discontinuous variation with minor reproductive isolation, (3) strongly discontinuous variation with strong but reversible reproductive isolation and (4) complete and irreversible reproductive isolation. Research on sticklebacks (Gasterosteidae) reveals factors that influence progress back and forth along this continuum, as well as transitions between the states. Most populations exist in state 1, even though some of these show evidence of disruptive selection and positive assortative mating. Transitions to state 2 seem to usually involve strong divergent selection coupled with at least a bit of geographic separation, such as parapatry (e.g. lake and stream pairs and mud and lava pairs) or allopatry (e.g. different lakes). Transitions to state 3 can occur when allopatric or parapatric populations that evolved under strong divergent selection come into secondary contact (most obviously the sympatric benthic and limnetic pairs), but might also occur between populations that remained in parapatry or allopatry. Transitions to state 4 might be decoupled from these selective processes, because the known situations of complete, or nearly complete, reproductive isolation (Japan Sea and Pacific Ocean pair and the recognized gasterosteid species) are always associated with chromosomal rearrangements and environment-independent genetic incompatibilities. Research on sticklebacks has thus revealed complex and shifting interactions between selection, adaptation, mutation and geography during the course of speciation.
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Affiliation(s)
- A P Hendry
- Redpath Museum & Department of Biology, McGill University, 859 Sherbrooke St. W., Montréal, Québec, H3A 2K6 Canada.
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2089
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Dettman JR, Anderson JB, Kohn LM. Genome-wide investigation of reproductive isolation in experimental lineages and natural species of Neurospora: identifying candidate regions by microarray-based genotyping and mapping. Evolution 2009; 64:694-709. [PMID: 19817850 DOI: 10.1111/j.1558-5646.2009.00863.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inherent incompatibilities between genetic components from genomes of different species may cause intrinsic reproductive isolation. In evolution experiments designed to instigate speciation in laboratory populations of the filamentous fungus Neurospora, we previously discovered a pair of incompatibility loci (dfe and dma) that interact negatively to cause severe defects in sexual reproduction. Here we show that the dfe-dma incompatibility also is a significant cause of genetic isolation between two naturally occurring species of Neurospora (N. crassa and N. intermedia). The strong incompatibility interaction has a simple genetic basis (two biallelic loci) and antagonistic epistasis occurs between heterospecific alleles only, consistent with the Dobzhansky-Muller model of genic incompatibility. We developed microarray-based, restriction-site associated DNA (RAD) markers that identified approximately 1500 polymorphisms between the genomes of the two species, and constructed the first interspecific physical map of Neurospora. With this new mapping resource, the approximate genomic locations of the incompatibility loci were determined using three different approaches: genome scanning, bulk-segregant analyses, and introgression. These population, quantitative, and classical genetics methods concordantly identified two candidate regions, narrowing the search for each incompatibility locus to only approximately 2% of the nuclear genome. This study demonstrates how advances in high-throughput, genome-wide genotyping can be applied to mapping reproductive isolation genes and speciation research.
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Affiliation(s)
- Jeremy R Dettman
- Department of Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, L5L 1C6, Canada.
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2090
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Abstract
Absolute barriers to dispersal are not common in marine systems, and the prevalence of planktonic larvae in marine taxa provides potential for gene flow across large geographic distances. These observations raise the fundamental question in marine evolutionary biology as to whether geographic and oceanographic barriers alone can account for the high levels of species diversity observed in marine environments such as coral reefs, or whether marine speciation also operates in the presence of gene flow between diverging populations. In this respect, the ecological hypothesis of speciation, in which reproductive isolation results from divergent or disruptive natural selection, is of particular interest because it may operate in the presence of gene flow. Although important insights into the process of ecological speciation in aquatic environments have been provided by the study of freshwater fishes, comparatively little is known about the possibility of ecological speciation in marine teleosts. In this study, the evidence consistent with different aspects of the ecological hypothesis of speciation is evaluated in marine fishes. Molecular approaches have played a critical role in the development of speciation hypotheses in marine fishes, with a role of ecology suggested by the occurrence of sister clades separated by ecological factors, rapid cladogenesis or the persistence of genetically and ecologically differentiated species in the presence of gene flow. Yet, ecological speciation research in marine fishes is still largely at an exploratory stage. Cases where the major ingredients of ecological speciation, namely a source of natural divergent or disruptive selection, a mechanism of reproductive isolation and a link between the two have been explicitly documented are few. Even in these cases, specific predictions of the ecological hypothesis of speciation remain largely untested. Recent developments in the study of freshwater fishes illustrate the potential for molecular approaches to address specific questions related to the ecological hypothesis of speciation such as the nature of the genes underlying key ecological traits, the magnitude of their effect on phenotype and the mechanisms underlying their differential expression in different ecological contexts. The potential provided by molecular studies is fully realized when they are complemented with alternative (e.g. ecological, theoretical) approaches.
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Affiliation(s)
- O Puebla
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancon, Republic of Panama.
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2091
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Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 2009; 7:287-96. [PMID: 19287448 DOI: 10.1038/nrmicro2122] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New sequencing methods generate data that can allow the assembly of microbial genome sequences in days. With such revolutionary advances in technology come new challenges in methodologies and informatics. In this article, we review the capabilities of high-throughput sequencing technologies and discuss the many options for getting useful information from the data.
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2092
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MacLean D, Jones JDG, Studholme DJ. Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 2009. [DOI: 10.1038/nrmicro2088] [Citation(s) in RCA: 243] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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