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Journal ArticleDOI

The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat

01 Jan 2000-Euphytica (Kluwer Academic Publishers)-Vol. 113, Iss: 3, pp 163-185
TL;DR: The basic principles underlying different hybridization-based and PCR based approaches, making use of microsatellites, have been outlined and relevant literature on the subject has been reviewed and critically discussed.
Abstract: In recent years, a variety of molecular markers, based on microsatellites or simple sequence repeats (SSRs) have become the markers of choice, thus necessitating their development and use in a variety of plant systems. In this review, the basic principles underlying different hybridization-based (oligonucleotide fingerprinting) and PCR based approaches (STMS, MP-PCR, AMP-PCR/ ISSR/ ASSR, RAMPs/ dRAMPs, SAMPL), making use of microsatellites, have been outlined. Different methods for enrichment of genomic libraries for microsatellites have also been outlined. Relevant literature on the subject, giving a summary of results obtained using each approach, has been reviewed and critically discussed. The review also includes a discussion on literature, which deals with the use of microsatellites in genome mapping, gene tagging, DNA fingerprinting, characterization of germplasm and cytogenetics research. Special emphasis has been laid on the genome of bread wheat, where the work done in the authors' own laboratory has also been briefly reviewed.
Citations
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Journal ArticleDOI
TL;DR: This consensus map represents the highest-density public microsatellite map of wheat and is accompanied by an allele database showing the parent allele sizes for every marker mapped, which enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies.
Abstract: A microsatellite consensus map was constructed by joining four independent genetic maps of bread wheat. Three of the maps were F1-derived, doubled-haploid line populations and the fourth population was ‘Synthetic’ × ‘Opata’, an F6-derived, recombinant-inbred line population. Microsatellite markers from different research groups including the Wheat Microsatellite Consortium, GWM, GDM, CFA, CFD, and BARC were used in the mapping. A sufficient number of common loci between genetic maps, ranging from 52 to 232 loci, were mapped on different populations to facilitate joining the maps. Four genetic maps were developed using MapMaker V3.0 and JoinMap V3.0. The software CMap, a comparative map viewer, was used to align the four maps and identify potential errors based on consensus. JoinMap V3.0 was used to calculate marker order and recombination distances based on the consensus of the four maps. A total of 1,235 microsatellite loci were mapped, covering 2,569 cM, giving an average interval distance of 2.2 cM. This consensus map represents the highest-density public microsatellite map of wheat and is accompanied by an allele database showing the parent allele sizes for every marker mapped. This enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies.

1,761 citations


Cites background from "The development and use of microsat..."

  • ...The primary reason to shift toward PCR-based markers and particularly SSR marker maps is the potential to use the maps in plant breeding (Gupta and Varshney 2000)....

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Journal ArticleDOI
TL;DR: Applications and potential uses of EST-SSRs in plant genetics and breeding could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait.

1,750 citations


Cites background or methods from "The development and use of microsat..."

  • ...Comparative account on genic and genomic microsatellite markers A comparative analysis of genomic SSRs and genic SSRs reveals advantages to both; however, because of lower polymorphism, EST-SSRs are not as efficient as genomic SSRs for distinguishing the closely related genotypes (for references, see [ 4 ])....

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  • ...SSR markers have been useful for integratingthe genetic, physical and sequence-based physicalmapsinplantspecies,andsimultaneouslyhaveprovided breeders and geneticists with an efficient tool to link phenotypic and genotypic variation (for review, see [ 4 ])....

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  • ...common and has been reported earlier using genomic SSRs (for references, see [ 4 ])....

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  • ...In some earlier reports dealing with genomic SSRs, microsatellite markers were associated with repetitive DNA or retrotransposons [ 4 ,48]; however, recent reports indicated that they are predominately associated with nonrepetitive DNA (M. La Rota et al., unpublished) [16,49]....

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Journal ArticleDOI
TL;DR: An overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops and ways in which the potential of MAS can be realized are suggested.
Abstract: DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker–trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.

1,736 citations


Cites background from "The development and use of microsat..."

  • ...The most widely used markers in major cereals are called simple sequence repeats (SSRs) or microsatellites (Gupta et al. 1999; Gupta & Varshney 2000)....

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Journal ArticleDOI
TL;DR: An overview of the details of the ISSR-PCR technique and its application in genetics and plant breeding in a wide range of crop plants is provided.
Abstract: Summary Inter simple sequence repeat (ISSR)-PCR is a technique, which involves the use of microsatellite sequences as primers in a polymerase chain reaction to generate multilocus markers. It is a simple and quick method that combines most of the advantages of microsatellites (SSRs) and amplified fragment length polymorphism (AFLP) to the universality of random amplified polymorphic DNA (RAPD). ISSR markers are highly polymorphic and are useful in studies on genetic diversity, phylogeny, gene tagging, genome mapping and evolutionary biology. This review provides an overview of the details of the technique and its application in genetics and plant breeding in a wide range of crop plants.

880 citations


Cites methods from "The development and use of microsat..."

  • ...The commonly used polymerase chain reaction (PCR)-based DNA marker systems are random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and more recently simple sequence repeats (SSRs) or microsatellites (Staub et al., 1996; Gupta & Varshney, 2000)....

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  • ...The commonly used polymerase chain reaction (PCR)-based DNA marker systems are random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and more recently simple sequence repeats (SSRs) or microsatellites (Staub et al., 1996; Gupta & Varshney, 2000 )....

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Journal ArticleDOI
TL;DR: The recent developments in plant genetics using SSR markers are discussed and a quantum of literature has accumulated regarding the applicability of SSR based techniques.
Abstract: In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4–5 years) made in plant genetics using SSR markers.

806 citations


Cites background from "The development and use of microsat..."

  • ...The sequences flanking the microsatellite motifs in the genome are conserved within the particular species and often across the species within a genus and even across related genera (Gupta and Varshney 2000)....

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References
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Journal ArticleDOI
TL;DR: A new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence is described, suggesting that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.
Abstract: Molecular genetic maps are commonly constructed by analyzing the segregation of restriction fragment length polymorphisms (RFLPs) among the progeny of a sexual cross. Here we describe a new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. These polymorphisms, simply detected as DNA segments which amplify from one parent but not the other, are inherited in a Mendelian fashion and can be used to construct genetic maps in a variety of species. We suggest that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.

13,764 citations


"The development and use of microsat..." refers methods in this paper

  • ...In this approach, genomic DNA is amplified with either a single arbitrary 10-mer primer (as in RAPD analysis; Williams et al., 1990) or with a microsatellite-complementary 15-mer or 10- mer primer (as in MP-PCR analysis; Gupta et al., 1994) and the PCR products are electrophoresed, blotted and…...

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Journal ArticleDOI
TL;DR: The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity that allows the specific co-amplification of high numbers of restriction fragments.
Abstract: A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50-100 restriction fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity.

12,960 citations

Journal Article
TL;DR: It is reported that specific human (dC-dA)n.(dG-dT)n blocks are polymorphic in length among individuals and therefore represent a vast new pool of potential genetic markers.
Abstract: Interspersed DNA elements of the form (dC-dA)n.(dG-dT)n constitute one of the most abundant human repetitive DNA families. We report that specific human (dC-dA)n.(dG-dT)n blocks are polymorphic in length among individuals and therefore represent a vast new pool of potential genetic markers. Comparison of sequences from the literature for (dC-dA)n.(dG-dT)n blocks cloned two or more times revealed length polymorphisms in seven of eight cases. Variations in the lengths of 10 (dC-dA)n.(dG-dT)n blocks were directly demonstrated by amplifying the DNA within and immediately flanking the repeat blocks by using the polymerase chain reaction and then resolving the amplified DNA on polyacrylamide DNA sequencing gels. Use of the polymerase chain reaction to detect DNA polymorphisms offers improved sensitivity and speed compared with standard blotting and hybridization.

3,457 citations

Journal ArticleDOI
15 Mar 1994-Genomics
TL;DR: The utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms.

3,292 citations

Journal ArticleDOI
14 Mar 1996-Nature
TL;DR: The last version of the Généthon human linkage map is reported, which consists of 5,264 short tandem repeat polymorphisms with a mean heterozygosity of 70%.
Abstract: The great increase in successful linkage studies in a number of higher eukaryotes during recent years has essentially resulted from major improvements in reference genetic linkage maps, which at present consist of short tandem repeat polymorphisms of simple sequences or microsatellites. We report here the last version of the Genethon human linkage map. This map consists of 5,264 short tandem (AC/TG)n repeat polymorphisms with a mean heterozygosity of 70%. The map spans a sex-averaged genetic distance of 3,699 cM and comprises 2,335 positions, of which 2,032 could be ordered with an odds ratio of at least 1,000:1 against alternative orders. The average interval size is 1.6 cM; 59% of the map is covered by intervals of 2 cM at most and 1% remains in intervals above 10 cM.

2,982 citations


"The development and use of microsat..." refers background in this paper

  • ...Consequently, microsatellite linkage maps have become available not only for the genome of some animal systems, including human (Weissenbach et al., 1992; Dib et al., 1996), rat (Jacob et al., 1995) and mouse (Dietrich et al., 1996), but also for a variety of plant genomes (Table 5)....

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