Microsatellite Markers in Plants and Insects. Part I: Applications of Biotechnology (original) (raw)
Related papers
Nucleotide sequence information available in searchable sequence databases and the free in silico software with which to extract and analyze microsatellite data continues to grow at a rapid rate across eukaryote taxa. The sheer amount of information available means that a comprehensive or exhaustive review of databases and free bioinformatic tools lies beyond the purview of any journal review. The purpose of this review is therefore to provide targeted information aimed at helping the insect and plant biologist effectively utilize in silico resources to find, navigate and analyze empirically derived data from sequence databases. The objectives are threefold. First, since the basic characteristics of microsatellites make them the markers of choice for studies of genetic structure that underlie adaptation and evolution, these will be delineated. Second, because sequence databases are increasingly mined for microsatellites, the major databases are discussed, as well as, available programs for in silico mining of sequence databases to retrieve microsatellites for a species of interest. Lastly, a general review is given of population genetics software for in silico genetic analyses of microsatellite data to determine population genetic structure, phylogenetic relationships, and genetic diversity in a species of interest.
Genic microsatellite markers in plants: features and applications
Trends in Biotechnology, 2005
Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.
Microsatellite markers: an overview of the recent progress in plants
Euphytica, 2010
EST-SSRs SSRs RFLPs RAPDs/AFLPs/ISSRs Need for sequence data Essential Essential Not required Not required Level of polymorphism Low High Low Low-moderate Dominance Co-dominant Co-dominant Co-dominant Dominant Interspecific transferability High Low-moderate Moderate-high Low-moderate Utility in Marker assisted selection High High Moderate Low-moderate Cost and labour involved in generation Low High High Low-moderate
2004
Abbreviations used: SSR -simple sequence repeats; ISSR -inter-simple sequence repeats; SAMPL -selective amplification of microsatellite polymorphic loci; STRshort tandem repeats; SSLP -simple sequence length polymorphism; VNTR -variable number of tandem repeats; EST -expressed sequence tags; RAPD -random amplified polymorphic DNA; RFLP -restriction fragment length polymorphisms; MAS -markerassisted selection; NIL -nearly isogenic lines; BSA -bulked segregant analysis; QTLquantitative trait loci; AFLP -amplified fragment-length polymorphism.
Microsatellite markers: An important fingerprinting tool for characterization of crop plants
2011
Microsatellites are simple sequence repeats (SSR) of 1-6 nucleotides. They appear to be ubiquitous in higher organisms, both in animal and plant genomes and involving repetitive as well as unique sequences, although the frequency of microsatellites varies between species. They are abundant, dispersed throughout the genome and show higher levels of polymorphism than do other genetic markers. These features coupled with their ease of detection have made them useful markers. Their potential for automation and their inheritance in a co-dominant manner are additional advantages when compared with other types of molecular markers. SSRs are highly polymorphic, genome specific, abundant and co-dominant, and have recently become important genetic markers in cereals including wheat and barley.
PMDBase: a database for studying microsatellite DNA and marker development in plants
Microsatellite DNAs (or SSRs) are important genomic components involved in many important biological functions. SSRs have been extensively exploited as molecular markers for diverse applications including genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection, variety identification and evolution analysis. However, a comprehensive database or web service for studying mi-crosatellite DNAs and marker development in plants is lacking. Here, we developed a database, PMD-Base, which integrates large amounts of microsatel-lite DNAs from genome sequenced plant species and includes a web service for microsatellite DNAs identification. In PMDBase, 26 230 099 microsatellite DNAs were identified spanning 110 plant species. Up to three pairs of primers were supplied for every microsatellite DNA. For 81 species, genomic features of the microsatellite DNAs (genic or non-genic) were supplied with the corresponding genes or transcripts from public databases. Microsatellite DNAs can be explored through browsing and searching modules with a user-friendly web interface and cus-tomized software. Furthermore, we developed MIS-Aweb and embedded Primer3web to help users to identify microsatellite DNAs and design corresponding primers in their own genomic sequences online. All datasets of microsatellite DNAs can be down-loaded conveniently. PMDBase will be updated regularly with new available genome data and can be accessed freely via the address http://www.sesame-bioinfo.org/PMDBase.
A High Through-put Procedure for Capturing Microsatellites from Complex Plant Genomes
1998
A method is outlined for large-scale isolation and characterization of microsatellite sequences from complex plant genomes. The method presented here differs from the previously published procedures in the use of randomly sheared (nebulized) genomic DNA for adapter-ligation, rigorous removal of biotinylated oligos, and high-density colony blots for constructing enriched libraries. Using this method we have constructed cotton microsatellite enriched libraries with over 20% (high stringency screening) or 75% (by random sequencing). Thus far we have identified and sequenced over 500 cotton microsatellites using this procedure. The procedure can be used to generate enriched SSR libraries from genomic DNA in about one week. High throughput screening and automated DNA sequencing can be accomplished in less than one month.
2014
Abstract: Microsatellites (SSR – simple sequence repeats, STR – short tandem repeats, SSLP – simple sequence length polymorphism, VNTR – variable number of tandem repeats) are the class of repetitive DNA sequences present in all living organisms. Particular characterstics of microsatellites, such as their presence in the genomes of all living organisms, high level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for a number of approaches like genotyping, mapping and positional clonig of genes. The three most popular types of markers containing microsatellite sequences that are presently used are: (1) SSR (simple sequence repeats), generated by amplifying in a PCR reaction with the use of primers complementary to flanking regions; (2) ISSR (inter-simple sequence repeats), based on the amplification of regions between inversely oriented closely spaced microsatellites; and (3) SAMPL (selective amplification of micro...
Interspecific evolution in plant microsatellite structure
Gene, 2000
Several intragenically linked microsatellites have been identified in the floral regulatory genes A. sandwicense APETALA1 (ASAP1) and A. sandwicense APETALA3/TM6 (ASAP3/TM6) in 17 species of the Hawaiian and North American Madiinae (Asteraceae). Thirty-nine microsatellite loci were observed in the introns of these two genes, suggesting that they are hotspots for microsatellite formation. The sequences of four of these microsatellites were mapped onto the phylogenies of these floral regulatory genes, and the structural evolution of these repeat loci was traced. Both nucleotide substitutions and insertion/deletion mutations may be responsible for the formation of perfect microsatellites from imperfect repeat regions (and vice versa).
Microsatellite markers discriminating accessions within collections of plant genetic resources
Cellular & molecular biology letters, 2002
The reliability of microsatellite analyses for discriminating between plant accessions maintained in collections of genetic resources was tested for 53 accessions of barley, 65 of soybean, 49 of chickpea, and 19 of alfalfa. The specific primer pairs used in this study were based on microsatellite DNA sequences surrounded by perfect dinucleotide and imperfect trinucleotide tandem repeat units. The evaluated polymorphic information content, diversity index, and probabilities of identity indicate that there is value in the application of SSR analyses in barley, soybean, and chickpea genetic resource management. Variation between alfalfa genotypes was not revealed at the five analyzed microsatellite loci.