Hybridization of microsatellites to RAPD: a new source of polymorphic markers

Richardson, Thomas E.; Cato, S. A.; Ramser, Juliane; Kahl, Günter; Weising, Kurt

doi:10.1093/nar/23.18.3798

Cited by 62 publications

(35 citation statements)

References 7 publications

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“…To avoid library construction and screening, some authors proposed modifications of the RAPD approach for the amplification of unknown microsatellites, by either using repeat-anchored random primers (Wu et al 1994) or using RAPD primers and subsequent southern hybridization of polymerase chain reaction (PCR) bands with microsatellite probes (Cifarelli et al 1995;Richardson et al 1995). Although not useful for single-locus analyses as no information on microsatellite flanking regions is obtained, these methods inspired alternative strategies for the identification of single microsatellite loci.…”

Section: Development Of Microsatellites Through Screening Of Rapd Ampmentioning

confidence: 99%

Microsatellite markers: an overview of the recent progress in plants

et al. 2010

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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.

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Section: Development Of Microsatellites Through Screening Of Rapd Ampmentioning

confidence: 99%

Microsatellite markers: an overview of the recent progress in plants

et al. 2010

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“…The hybridization signals resulted from the PCR products and were not from unamplified genomic DNA. The occurrence of new bands in hybridization is usually explained as follows: the RAPD reactions probably create thousands of different products of various abundance, and staining visualizes only the most abundant amplicons, whereas the majority of the minor fragments remain undetected or form a background smear (Ramser et al, 1997;Richardson et al, 1995).…”

Section: Identification Of Ecorace-specific Rapd Markers and Their Hymentioning

confidence: 99%

Molecular Identification of Tropical Tasar Silkworm (Antheraea mylitta) Ecoraces with RAPD and SCAR Markers

Saha

Kundu

2006

Biochem Genet

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The tropical tasar silkworm, Antheraea mylitta, has several ecoraces, 10 of which are commercially exploited for the production of tasar silk. These ecoraces are identified by morphological markers that are greatly influenced by photoperiod, humidity, altitude, and host plants. The DNA markers, random amplification of polymorphic DNA (RAPD), and sequence-characterized amplified region (SCAR) are identified to complement the existing morphological markers. Seven RAPD bands are selected that identify 8 of the 10 ecoraces. These identified RAPD fragments are sequenced and primers are designed for SCAR markers. Of the seven sets of primers, a single primer pair produced polymorphic SCAR bands that diagnose 5 of the 10 ecoraces. All 10 ecoraces are identified by the use of RAPD and SCAR markers together.

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“…Subsequent autoradiography reveals reproducible, probe dependent fingerprints, polymorphic at the intraspecific level. This provides for speed of the assay along with high sensitivity, so that high level of polymorphism is detected (Richardson et al, 1995;Cifarelli et al, 1995;Ender et al, 1996). The method was variously termed as RAMPO (random amplified microsatellite polymorphism; Richardson et al, 1995), RAHM (random amplified hybridization microsatellites; Cifarelli et al., 1995) or RAMS (randomly amplified microsatellites; Ender et al, 1996).…”

Section: Oligonucleotide Fingerprinting Using Rapd/mp-pcr Fragments Amentioning

confidence: 99%