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Guo SS, Zhang GR, Guo XZ, Wei KJ, Ji W, Wei QW. Isolation and characterization of eighteen polymorphic microsatellite loci in Schizopygopsis younghusbandi Regan and cross-amplification in three other schizothoracinae species. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414010062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hou F, Zhang H, Wu B, Zhang X, Song Z. Characterization of microsatellite loci in Schizopygopsis chengi chengi and their utilization in assessment of the genetic diversity in Schizopygopsis chengi baoxingensis. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Saisug W, Ukoskit K. Comparative analysis of EST-derived markers for allelic variation in Jatropha curcas L. and cross transferability among economically important species of Euphorbiaceae. Genes Genomics 2013; 35:1-12. [DOI: 10.1007/s13258-013-0064-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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SUN DIANQIAO, XU TIANJUN, WANG RIXIN. Characterization of microsatellites in white croaker (Pennahia argentata) through cross species amplification of Miichthys miiuy. J Genet 2011. [DOI: 10.1007/s12041-011-0116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pfeiffer T, Roschanski AM, Pannell JR, Korbecka G, Schnittler M. Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae). ACTA ACUST UNITED AC 2011; 102:479-88. [PMID: 21576288 DOI: 10.1093/jhered/esr024] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as amplified fragment length polymorphisms (AFLPs). In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from 4 different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within 1 MLL, all analyses revealed the same 14 MLLs without conflicting with merigenet, sex, or plot assignment. For semiautomatic scoring, a combination of as few as 2 of the 4 most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.
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Affiliation(s)
- Tanja Pfeiffer
- Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt-University Greifswald, Grimmer Str. 88, 17487 Greifswald, Germany.
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Shikano T, Ramadevi J, Shimada Y, Merilä J. Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius). BMC Genomics 2010; 11:334. [PMID: 20507571 PMCID: PMC2891615 DOI: 10.1186/1471-2164-11-334] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 05/27/2010] [Indexed: 12/04/2022] Open
Abstract
Background Identification of genes involved in adaptation and speciation by targeting specific genes of interest has become a plausible strategy also for non-model organisms. We investigated the potential utility of available sequenced fish genomes to develop microsatellite (cf. simple sequence repeat, SSR) markers for functionally important genes in nine-spined sticklebacks (Pungitius pungitius), as well as cross-species transferability of SSR primers from three-spined (Gasterosteus aculeatus) to nine-spined sticklebacks. In addition, we examined the patterns and degree of SSR conservation between these species using their aligned sequences. Results Cross-species amplification success was lower for SSR markers located in or around functionally important genes (27 out of 158) than for those randomly derived from genomic (35 out of 101) and cDNA (35 out of 87) libraries. Polymorphism was observed at a large proportion (65%) of the cross-amplified loci independently of SSR type. To develop SSR markers for functionally important genes in nine-spined sticklebacks, SSR locations were surveyed in or around 67 target genes based on the three-spined stickleback genome and these regions were sequenced with primers designed from conserved sequences in sequenced fish genomes. Out of the 81 SSRs identified in the sequenced regions (44,084 bp), 57 exhibited the same motifs at the same locations as in the three-spined stickleback. Di- and trinucleotide SSRs appeared to be highly conserved whereas mononucleotide SSRs were less so. Species-specific primers were designed to amplify 58 SSRs using the sequences of nine-spined sticklebacks. Conclusions Our results demonstrated that a large proportion of SSRs are conserved in the species that have diverged more than 10 million years ago. Therefore, the three-spined stickleback genome can be used to predict SSR locations in the nine-spined stickleback genome. While cross-species utility of SSR primers is limited due to low amplification success, SSR markers can be developed for target genes and genomic regions using our approach, which should be also applicable to other non-model organisms. The SSR markers developed in this study should be useful for identification of genes responsible for phenotypic variation and adaptive divergence of nine-spined stickleback populations, as well as for constructing comparative gene maps of nine-spined and three-spined sticklebacks.
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Affiliation(s)
- Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, P,O, Box 65, FI-00014, Helsinki, Finland.
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Chatrou LW, Escribano MP, Viruel MA, Maas JW, Richardson JE, Hormaza JI. Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics. Mol Phylogenet Evol 2009; 53:726-33. [DOI: 10.1016/j.ympev.2009.07.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 07/16/2009] [Accepted: 07/23/2009] [Indexed: 12/01/2022]
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Abstract
There is a lack of published microsatellite data which characterizes Ribes spp. To address this, an initial study of simple sequence repeat (SSR) variation was undertaken in 41 cultivars belonging to four species of the genus Ribes to evaluate its genetic variability. The cultivars were collected in Piedmont, northwest Italy, together with one cultivar from Switzerland. Twenty SSRs were screened for amplification and polymorphism. Seven failed to amplify, and therefore the remaining 13 were selected and used to fingerprint all the cultivars. Microsatellite analysis resulted in the identification of 38 genotypes, suggesting the existence of possible clonal genotypes and synonyms. Among the cultivars analyzed, two tetraploid accessions were found. The evaluation of genetic variability in Ribes is of fundamental importance for future nutritional breeding programs and to preserve genetic resources, as cultivar characterization permits better management of plant collections.
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Affiliation(s)
- M. Cavanna
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| | - D. Torello Marinoni
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| | - G. L. Beccaro
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| | - G. Bounous
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
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Moccia MD, Oger-Desfeux C, Marais GA, Widmer A. A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping. BMC Genomics 2009; 10:243. [PMID: 19467153 PMCID: PMC2689282 DOI: 10.1186/1471-2164-10-243] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 05/25/2009] [Indexed: 11/21/2022] Open
Abstract
Background Expressed sequence tag (EST) databases represent a valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. One class of markers derived from EST sequences are simple sequence repeat (SSR) markers, also known as EST-SSRs. These are useful in plant genetic and evolutionary studies because they are located in transcribed genes and a putative function can often be inferred from homology searches. Another important feature of EST-SSR markers is their expected high level of transferability to related species that makes them very promising for comparative mapping. In the present study we constructed a normalized EST library from floral tissue of Silene latifolia with the aim to identify expressed genes and to develop polymorphic molecular markers. Results We obtained a total of 3662 high quality sequences from a normalized Silene cDNA library. These represent 3105 unigenes, with 73% of unigenes matching genes in other species. We found 255 sequences containing one or more SSR motifs. More than 60% of these SSRs were trinucleotides. A total of 30 microsatellite loci were identified from 106 ESTs having sufficient flanking sequences for primer design. The inheritance of these loci was tested via segregation analyses and their usefulness for linkage mapping was assessed in an interspecific cross. Tests for crossamplification of the EST-SSR loci in other Silene species established their applicability to related species. Conclusion The newly characterized genes and gene-derived markers from our Silene EST library represent a valuable genetic resource for future studies on Silene latifolia and related species. The polymorphism and transferability of EST-SSR markers facilitate comparative linkage mapping and analyses of genetic diversity in the genus Silene.
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Affiliation(s)
- Maria Domenica Moccia
- ETH Zurich, Institute of Integrative Biology (IBZ), Universitaetstr, 16, 8092 Zürich, Switzerland.
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Hilario E, Fraser LG, McNeilage M. Trinucleotide repeats as bait for vectorette PCR: a tool for developing genetic mapping markers. Mol Biotechnol 2009; 42:320-6. [PMID: 19277911 DOI: 10.1007/s12033-009-9157-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/16/2009] [Indexed: 10/21/2022]
Abstract
Trinucleotide repeats are common within gene coding regions and could serve as beacons to locate genes. Five of the most common trinucleotide repeats in an Actinidia (kiwifruit) expressed sequence tag (EST) database were found to be (ACC)(4), (CAC)(4), (CCA)(4), (CTC)(4), and (TGG)(4). These repeats, with or without an artificial 5'-end tail, were tested by vectorette PCR against genomic DNA from Actinidia chinensis. Eighty-nine randomly selected clones showed an average insert size of 383 bp, with a maximum of 1,151 bp and a minimum of 78 bp. Two-thirds of the clones contained the artificial tail attached to the trinucleotide, showing a slight advantage of possessing such a tail during annealing and amplification. The sequences were searched against the Actinidia EST database and GenBank. Of the 89 clones, 33 had a significant hit (expect value < e(-15)). Twenty-four of those clones matched an Actinidia EST. Twenty-one clones contained one or more simple sequence repeats. This methodology can be applied by conventional cloning and sequencing methods or by high throughput pyrosequencing technologies to develop genetic markers and also for gene mining in species with little or no genetic/genomic resources.
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Affiliation(s)
- Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.
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Kim C, Jang CS, Kamps TL, Robertson JS, Feltus FA, Paterson AH. Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cDNA library. Funct Plant Biol 2008; 35:585-594. [PMID: 32688814 DOI: 10.1071/fp08133] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 06/03/2008] [Indexed: 06/11/2023]
Abstract
A normalised cDNA library was constructed from Bermudagrass to gain insight into the transcriptome of Cynodon dactylon L. A total of 15 588 high-quality expressed sequence tags (ESTs) from the cDNA library were subjected to The Institute for Genomic Research Gene Indices clustering tools to produce a unigene set. A total of 9414 unigenes were obtained from the high-quality ESTs and only 39.6% of the high-quality ESTs were redundant, indicating that the normalisation procedure was effective. A large-scale comparative genomic analysis of the unigenes was carried out using publicly available tools, such as BLAST, InterProScan and Gene Ontology. The unigenes were also subjected to a search for EST-derived simple sequence repeats (EST-SSRs) and conserved-intron scanning primers (CISPs), which are useful as DNA markers. Although the candidate EST-SSRs and CISPs found in the present study need to be empirically tested, they are expected to be useful as DNA markers for many purposes, including comparative genomic studies of grass species, by virtue of their significant similarities to EST sequences from other grasses. Thus, knowledge of Cynodon ESTs will empower turfgrass research by providing homologues for genes that are thought to confer important functions in other plants.
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Affiliation(s)
- Changsoo Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Cheol Seong Jang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Terry L Kamps
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Jon S Robertson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Frank A Feltus
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Andrew H Paterson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
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Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL, Bulley SM, Chagne D, Marsh KB, Matich AJ, Montefiori M, Newcomb RD, Schaffer RJ, Usadel B, Allan AC, Boldingh HL, Bowen JH, Davy MW, Eckloff R, Ferguson AR, Fraser LG, Gera E, Hellens RP, Janssen BJ, Klages K, Lo KR, MacDiarmid RM, Nain B, McNeilage MA, Rassam M, Richardson AC, Rikkerink EH, Ross GS, Schröder R, Snowden KC, Souleyre EJF, Templeton MD, Walton EF, Wang D, Wang MY, Wang YY, Wood M, Wu R, Yauk YK, Laing WA. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 2008; 9:351. [PMID: 18655731 PMCID: PMC2515324 DOI: 10.1186/1471-2164-9-351] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 07/27/2008] [Indexed: 11/13/2022] Open
Abstract
Background Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs). Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.
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Affiliation(s)
- Ross N Crowhurst
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, New Zealand.
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Abstract
Genomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene space of almost any organism. We review how ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome-wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for studies of gene family and genome evolution. Given the tremendous recent advances in inexpensive sequencing technologies, we predict that molecular ecologists will increasingly be developing and using EST collections in the years to come. With this in mind, we close our review by discussing aspects of EST resource development of particular relevance for molecular ecologists.
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Affiliation(s)
- Amy Bouck
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA.
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