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Abstract
Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selection of core collections, determination of genetic distances, genome analysis, development of molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest, is cost-effective, and can be performed in a moderate laboratory for most of its applications. In addition, RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like arbitrarily primed polymerase chain reaction (AP-PCR), sequence characterized amplified region (SCAR), DNA amplification fingerprinting (DAF), sequence-related amplified polymorphism (SRAP), cleaved amplified polymorphic sequences (CAPS), random amplified microsatellite polymorphism (RAMPO), and random amplified hybridization microsatellites (RAHM) can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented along with the applications of RAPD in genetic diversity analysis, mapping, varietal identification, genetic fidelity testing, etc.
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Abstract
Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.
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Affiliation(s)
- Atul Grover
- a Biotechnology Division , Defence Institute of Bio Energy Research , Goraparao, P.O. Arjunpur , Haldwani , Uttarakhand , India and
| | - P C Sharma
- b University School of Biotechnology, Guru Gobind Singh Indraprastha University , Dwarka Sec. 16C , New Delhi , India
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Babu KN, Rajesh MK, Samsudeen K, Minoo D, Suraby EJ, Anupama K, Ritto P. Randomly amplified polymorphic DNA (RAPD) and derived techniques. Methods Mol Biol 2014; 1115:191-209. [PMID: 24415476 DOI: 10.1007/978-1-62703-767-9_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, developing molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest and cost-effective and can be performed in a moderate laboratory for most of its applications. In addition RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like AP-PCR, SCAR, DAF, SRAP, CAPS, RAMPO, and RAHM can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented.
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Isolation and characterization of polymorphic microsatellite loci from Metapenaeopsis barbata using PCR-Based Isolation of Microsatellite Arrays (PIMA). Int J Mol Sci 2012; 13:2763-2768. [PMID: 22489123 PMCID: PMC3317685 DOI: 10.3390/ijms13032763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/19/2012] [Accepted: 02/21/2012] [Indexed: 11/21/2022] Open
Abstract
The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species.
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Isolation and characterization of polymorphic microsatellite markers from Japanese grenadier anchovy (Coilia nasus). CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9532-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sun Y, Lin HD, Tang WQ, Ju YM, Liu ZZ, Liu D, Yang JQ. Polymorphic microsatellite loci isolated from the Squalidus argentatus using PCR-Based Isolation of Microsatellite Arrays (PIMA). Int J Mol Sci 2011; 12:5666-71. [PMID: 22016617 PMCID: PMC3189741 DOI: 10.3390/ijms12095666] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/28/2011] [Accepted: 08/30/2011] [Indexed: 11/17/2022] Open
Abstract
Squalidus argentatus (Sauvage and Dabry de Thiersant 1874) is a small-sized freshwater fish which is distributed in Mainland China, Hainan Island and Taiwan. The populations of S. argentatus have dropped sharply probably due to overharvesting and water pollution recently. Eleven polymorphic microsatellite markers were developed for the cyprinid fish S. argentatus. These new markers were tested on 43 individuals collected from Yangtze River and Qiantang River. The number of alleles, observed and expected heterozygosity per locus, in two populations ranged from 3 to 14, from 0.333 to 0.954 and from 0.480 to 0.928, respectively. Only two loci are significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency. No significant linkage disequilibrium was detected between the pairwise comparisons of these loci. These polymorphic microsatellite loci will enable us to study the genetic variation, population structure, and conservation genetics of this species in the future.
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Affiliation(s)
- Yang Sun
- Laboratory of Fishes, Shanghai Ocean University, Shanghai, 201306, China; E-Mails: (Y.S.); (W.-Q.T.); (Z.-Z.L); (D.L.)
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan; E-Mail:
| | - Wen-Qiao Tang
- Laboratory of Fishes, Shanghai Ocean University, Shanghai, 201306, China; E-Mails: (Y.S.); (W.-Q.T.); (Z.-Z.L); (D.L.)
| | - Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung 900, Taiwan; E-Mail:
| | - Zhi-Zhi Liu
- Laboratory of Fishes, Shanghai Ocean University, Shanghai, 201306, China; E-Mails: (Y.S.); (W.-Q.T.); (Z.-Z.L); (D.L.)
| | - Dong Liu
- Laboratory of Fishes, Shanghai Ocean University, Shanghai, 201306, China; E-Mails: (Y.S.); (W.-Q.T.); (Z.-Z.L); (D.L.)
| | - Jin-Quan Yang
- Laboratory of Fishes, Shanghai Ocean University, Shanghai, 201306, China; E-Mails: (Y.S.); (W.-Q.T.); (Z.-Z.L); (D.L.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-021-6190-0425; Fax: +86-021-6190-0425
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Yang JQ, Zhou XD, Liu D, Liu ZZ, Tang WQ. Short Communication Isolation and characterization of microsatellite loci in the fish Coilia mystus (Clupeiformes: Engraulidae) using PCR-based isolation of microsatellite arrays. GENETICS AND MOLECULAR RESEARCH 2011; 10:1514-7. [DOI: 10.4238/vol10-3gmr1420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Isolation and characterization of microsatellite loci in the Indian false vampire bat Megaderma lyra. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9085-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hu CH, Huang CC, Hung KH, Hsu TW, Chiang TY. Isolation and characterization of polymorphic microsatellite loci from Areca catechu (Arecaceae) using PCR-based isolation of microsatellite arrays. Mol Ecol Resour 2009; 9:658-60. [PMID: 21564720 DOI: 10.1111/j.1755-0998.2008.02504.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Betel nut (Areca nut, Areca catechu L.) is a conspicuous and important cultivated plant of tropical and subtropical habitats throughout Southeast Asia and Oceania. As a significant cultural and social offering, the migration of betel nut associated with human dispersal is an important issue in ethnobotany and anthropology. In this study, we described the development of nine microsatellite loci from A. catechu. The number of alleles per locus ranged from 5 to 15. The expected and observed heterozygosities ranged from 0.71to 0.94 and from 0 to 0.88, respectively. All microsatellite loci, except for AC30, significantly deviated from Hardy-Weinberg equilibrium possibly due to artificially selected cultivation or the existence of excessive null alleles. No linkage disequilibrium was observed from pairwise comparisons of loci, except for AC06 and AC08.
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Affiliation(s)
- Cheng-Heng Hu
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan 300 Department of Life Sciences, Cheng Kung University, Tainan, Taiwan 701 Taiwan Endemic Species Research Institute, Nantou, Taiwan 552
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Chiang TY, Ju YM, Fang LS, Lin CJ. Isolation and characterization of polymorphic microsatellite loci in Candidia barbata (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9513-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Isolation and characterization of polymorphic microsatellite DNA makers for Euphrasia nankotaizanensis (Orobanchaceae) and cross amplification in another Euphrasia L. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9734-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Isolation and characterization of 15 microsatellite loci from Caridina gracilipes (Atyidae, Decapoda). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9689-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Isolation and characterization of microsatellite loci from a potential biofuel plant Miscanthus sinensis (Poaceae). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9699-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Huang CC, Chiang TY, Hsu TW, Hung CY, Chiang YC, Hung KH. Isolation and characterization of eight polymorphic microsatellite loci from Ludwigia polycarpa (Onagraceae), a threaten herb in North America. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9700-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Isolation and characterization of microsatellite loci in the endangered freshwater fish Varicorhinus alticorpus (Cyprinidae). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9508-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Development of 15 polymorphic microsatellite loci from Garrulax morrisonianus (Timaliidae), an endemic avian species of Taiwan. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9545-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Isolation and characterization of microsatellite loci in Pedicularis verticillata L. using PCR-based isolation of microsatellite arrays (PIMA). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9504-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Isolation and characterization of 11 polymorphic microsatellite loci from Fatsia polycarpa (Araliaceae), an element of evergreen forests in Taiwan. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9477-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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LIN CHUNGJIAN, WANG JIANGPING, LIN HUNGDU, CHIANG TZENYUH. Isolation and characterization of polymorphic microsatellite loci in Hemibarbus labeo (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA). ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01702.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hung CY, Wang KH, Huang CC, Gong X, Ge XJ, Chiang TY. Isolation and characterization of 11 microsatellite loci from Camellia sinensis in Taiwan using PCR-based isolation of microsatellite arrays (PIMA). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9391-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Isolation and characterization of microsatellite loci in the endangered freshwater fish Pararasbora moltrechti (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9365-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Huang CC, Chiang TY, Hsu TW. Isolation and characterization of microsatellite loci in Taxus sumatrana (Taxaceae) using PCR-based isolation of microsatellite arrays (PIMA). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9341-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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Chang A, Liew WC, Chuah A, Lim Z, Lin Q, Orban L. FluoMEP: a new genotyping method combining the advantages of randomly amplified polymorphic DNA and amplified fragment length polymorphism. Electrophoresis 2007; 28:525-34. [PMID: 17304486 DOI: 10.1002/elps.200600715] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
PCR-based identification of differences between two unknown genomes often requires complex manipulation of the templates prior to amplification and/or gel electrophoretic separation of a large number of samples with manual methods. Here, we describe a new genotyping method, called fluorescent motif enhanced polymorphism (fluoMEP). The fluoMEP method is based on random amplified polymorphic DNA (RAPD) assay, but combines the advantages of the large collection of unlabelled 10mer primers (ca. 5000) from commercial sources and the power of the automated CE devices used for the detection of amplified fragment length polymorphism (AFLP) patterns. The link between these two components is provided by a fluorescently labeled "common primer" that is used in a two-primer PCR together with an unlabeled RAPD primer. By using the same "common primer" and a series of RAPD primers, DNA templates can be screened quickly and effectively for polymorphisms. Our manuscript describes the optimization of the method and its characterization on different templates. We demonstrate by using several different approaches that the addition of the "common primer" to the PCR changes the profile of amplified fragments, allowing for screening various parts of the genome with the same set of unlabeled primers. We also present an in silico analysis of the genomic localization of fragments amplified by a RAPD primer with two different "common primers" and alone.
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Affiliation(s)
- Alex Chang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
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Usmani S, Tan SG, Siraj SS, Yusoff K. Isolation and characterization of microsatellites in the Southeast Asian river catfish Mystus nemurus. ACTA ACUST UNITED AC 2005. [DOI: 10.1046/j.1471-8278.2001.00101.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Acquadro A, Portis E, Lee D, Donini P, Lanteri S. Development and characterization of microsatellite markers in Cynara cardunculus L. Genome 2005; 48:217-25. [PMID: 15838543 DOI: 10.1139/g04-111] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cynara cardunculus L. is a species native to the Mediterranean basin that comprises 2 crops, globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC), as well as wild cardoon (var. sylvestris (Lamk) Fiori). Globe artichoke represents an important component of the South European agricultural economy but is also cultivated in North Africa, the Near East, South America, the United States, and China. Breeding activities and molecular marker studies have been, to date, extremely limited. Better knowledge of the genome of the species might be gained by developing a range of molecular markers. Here, we report on the development of 14 microsatellites (simple sequence repeats (SSRs)) through a novel approach that we have defined as the microsatellite amplified library (MAL). The approach represents a combination of amplified fragment length polymorphism and a primer extension based enriched library, is rapid, and requires no hybridization enrichment steps. The technique provided a ~40-fold increase in the efficiency of SSR identification compared with conventional library procedures. The developed SSRs were applied for genotyping 36 accessions of C. cardunculus, including a core of 27 varietal types of globe artichoke, 3 accessions of cultivated cardoon, and 6 Sicilian accessions of wild cardoon. Principal coordinates analysis made it possible to differentiate both cultivated and wild forms from each other.Key words: globe artichoke, wild and cultivated cardoon, molecular markers, AFLP, MAL (microsatellite amplified library).
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Affiliation(s)
- Alberto Acquadro
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
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He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS. Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2003; 3:3. [PMID: 12713672 PMCID: PMC155651 DOI: 10.1186/1471-2229-3-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Accepted: 04/24/2003] [Indexed: 05/18/2023]
Abstract
BACKGROUND Genomic research of cultivated peanut has lagged behind other crop species because of the paucity of polymorphic DNA markers found in this crop. It is necessary to identify additional DNA markers for further genetic research in peanut. RESULTS Microsatellite markers in cultivated peanut were developed using the SSR enrichment procedure. The results showed that the GA/CT repeat was the most frequently dispersed microsatellite in peanut. The primer pairs were designed for fifty-six different microsatellites, 19 of which showed a polymorphism among the genotypes studied. The average number of alleles per locus was 4.25, and up to 14 alleles were found at one locus. This suggests that microsatellite DNA markers produce a higher level of DNA polymorphism than other DNA markers in cultivated peanut. CONCLUSIONS It is desirable to isolate and characterize more DNA markers in cultivated peanut for more productive genomic studies, such as genetic mapping, marker-assisted selection, and gene discovery. The development of microsatellite markers holds a promise for such studies.
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Affiliation(s)
- Guohao He
- Tuskegee University, Tuskegee, AL 36088, USA
| | | | - Melanie Newman
- USDA-ARS, Plant Genetic Resources Conservation Unit, Griffin, GA 30223, USA
| | - Guoqing Gao
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Roy N Pittman
- USDA-ARS, Plant Genetic Resources Conservation Unit, Griffin, GA 30223, USA
| | - CS Prakash
- Tuskegee University, Tuskegee, AL 36088, USA
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Mace ES, Godwin ID. Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta). Genome 2002; 45:823-32. [PMID: 12416614 DOI: 10.1139/g02-045] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.
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Affiliation(s)
- Emma S Mace
- M.S. Swaminathan Applied Genomics Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India.
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Abstract
In the last few years microsatellites have become one of the most popular molecular markers used with applications in many different fields. High polymorphism and the relative ease of scoring represent the two major features that make microsatellites of large interest for many genetic studies. The major drawback of microsatellites is that they need to be isolated de novo from species that are being examined for the first time. The aim of the present paper is to review the various methods of microsatellite isolation described in the literature with the purpose of providing useful guidelines in making appropriate choices among the large number of currently available options. In addition, we propose a fast and easy protocol which is a combination of different published methods.
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Affiliation(s)
- L Zane
- Dipartimento di Biologia, Università di Padova Via Ugo Bassi 58/B, 35121, Padova, Italy
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Englbrecht CC, Largiadèr CR, Hänfling B, Tautz D. Isolation and characterization of polymorphic microsatellite loci in the European bullhead Cottus gobio L. (Osteichthyes) and their applicability to related taxa. Mol Ecol 1999; 8:1966-9. [PMID: 10620244 DOI: 10.1046/j.1365-294x.1999.00778-6.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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D'Amato ME, Lunt DH, Carvalho GR. Microsatellite markers for the hake Macruronus magellanicus amplify other gadoid fish. Mol Ecol 1999. [DOI: 10.1046/j.1365-294x.1999.00655_7.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Ujino T, Kawahara T, Tsumura Y, Nagamitsu T, Yoshimaru H, Ratnam W. Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species. Heredity (Edinb) 1998; 81 ( Pt 4):422-8. [PMID: 9839438 DOI: 10.1046/j.1365-2540.1998.00423.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nine simple sequence repeat (SSR) markers were developed from Shorea curtisii using two different methods. One SSR locus was isolated by the commonly used method of screening by colony hybridization, and the other eight loci were isolated by a vectorette PCR method. Primer pairs were designed based on the sequences of all these SSR loci. Analysis of 40 individuals of S. curtisii from natural forest in Malaysia revealed that all SSR loci were polymorphic. Four SSR markers, Shc01, Shc04, Shc07 and Shc09, were highly polymorphic. We have also tested the applicability of these SSR printers to other species of Dipterocarpaceae using PCR amplification. Because the flanking region sequences of the S. curtisii SSRs were well conserved within this family, the SSR primers for S. curtisii can be applied to almost all species of Dipterocarpaceae.
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Affiliation(s)
- T Ujino
- Bio-technology Division, Forestry and Forest Products Research Institute, Ibaraki, Japan
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van Belkum A, Scherer S, van Alphen L, Verbrugh H. Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 1998; 62:275-93. [PMID: 9618442 PMCID: PMC98915 DOI: 10.1128/mmbr.62.2.275-293.1998] [Citation(s) in RCA: 452] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10(-4) per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.
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Affiliation(s)
- A van Belkum
- Department of Medical Microbiology & Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
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Ramser J, Weising K, Terauchi R, Kahl G, Lopez-Peralta C, Terhalle W. Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata–D.cayenensis). Genome 1997; 40:903-15. [DOI: 10.1139/g97-117] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Four different molecular techniques were used to assess relationships among 21 accessions of Guinea yam (Dioscorea rotundata and Dioscorea cayenensis) and 21 accessions belonging to seven putative progenitor species. Random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) analysis yielded 246 informative characters that were transformed into a matrix of pairwise distances and analyzed by neighbor joining or split decomposition. Both methods gave congruent results. Well-separated groups were formed that corresponded to their species designation. Dioscorea rotundata and D. cayenensis accessions were clearly separated from each other, supporting the concept that both are distinct species. Two morphological intermediates grouped together with D. rotundata. All investigated species fell into two main clusters, one comprising D. rotundata, D. cayenensis, Dioscorea abyssinica, Dioscorea liebrechtsiana, and Dioscorea praehensilis, the other comprising Dioscorea smilacifolia, Dioscorea minutiflora, Dioscorea burkilliana, and Dioscorea togoensis. The same grouping was also obtained by comparative sequence analysis of chloroplast DNA, which supports earlier studies of nuclear rDNA variation and chloroplast restriction fragment length polymorphisms. We also analyzed the same set of Dioscorea samples with the recently developed random amplified microsatellite polymorphism (RAMPO) technique. A series of diagnostic RAMPO bands was identified that clearly distinguished between D. rotundata and D. cayenensis. Some of these bands could also be traced back to the putative progenitors of both species. The evolutionary origin of Guinea yam is discussed in light of the present results.Key words: random amplified polymorphic DNA, RAPD, random amplified microsatellite polymorphisms, RAMPO, chloroplast DNA, genetic relatedness.
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Dean JF, LaFayette PR, Eriksson KE, Merkle SA. Forest tree biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1997; 57:1-44. [PMID: 9204750 DOI: 10.1007/bfb0102071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium.
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Affiliation(s)
- J F Dean
- Daniel B. Warnell School of Forest Resources, University of Georgia, Athens 30602, USA
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Caetano-Anollés G. Scanning of nucleic acids by in vitro amplification: new developments and applications. Nat Biotechnol 1996; 14:1668-74. [PMID: 9634849 DOI: 10.1038/nbt1296-1668] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleic acids can be characterized using a variety of "fingerprinting" techniques usually based on nucleic acid hybridization or enzymatic amplification. The scanning of nucleic acids by amplification with arbitrary oligonucleotide primers has become popular because it can generate simple-to-complex patterns from anonymous DNA or RNA templates without requiring prior knowledge of nucleic acid sequence or cloned or characterized probes. Discrete loci are amplified within genomic DNA, DNA complementary to mRNA populations (cDNA), cloned DNA fragments, and even PCR products. The potential and limitations of the various genome scanning techniques, novel improvements, and their recent use in comparative and experimental biology applications, including the analysis of plant and bacterial genomes are discussed.
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Affiliation(s)
- G Caetano-Anollés
- Department of Ornamental Horticulture and Landscape Design, University of Tennessee, Knoxville 37901-1071, USA
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