Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci

Depeiges, Annie; Goubely, Chantal; Lenoir, Alain; Cocherel, Sylvie; Picard, Georges; Raynal, Monique; Grellet, Françoise; Delseny, Michel

doi:10.1007/bf00220873

Cited by 74 publications

(50 citation statements)

References 32 publications

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“…The majority of the microsatellites detected contained GA-repeats, which were variable in length and composition, some having up to 19 perfect repeats. Microsatellites containing GA-repeats are common in many plants (Lagercrantz et al 1993;Terauchi 1994;Wang et al 1994;Depeiges et al 1995), which may also be the case for cassava. The isolation of other types of microsatellites may require the screening of libraries enriched for specific repeats.…”

Section: Resultsmentioning

confidence: 99%

Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability

et al. 1998

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Fourteen microsatellites containing GArepeats were isolated and characterized in cassava (Manihot esculenta Crantz, Euphorbiaceae). Microsatellite heterozygosity (h) was estimated in 48 accessions using (P)-end-labeled primers and in more than 500 accessions using fluorescence-based genotyping. Heterozygosity values ranged from 0.00 to 0.88 and the number of alleles detected varied from 1 to 15. The reproducibility of allele sizing was also assessed using fluorescence-based genotyping. The average inter-gel size difference was 1.03 nucleotides. Chi-square tests ( ) were performed to analyse segregation distortion and the linkage between alleles segregating from either or both parents in an F mapping population. Most microsatellite loci segregated in the expected 1 : 1, 1 : 2 : 1 or 1 : 1 : 1 : 1 ratio. Linkage was detected between loci segregating from either parent, and segregation distortion from the male parent was detected for locus GA-131. Approximately 80% of the microsatellites detected one or two alleles per accession, suggesting a low degree of microsatellite locus duplication, an unexpected finding for a putative allopolyploid, highly

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Section: Resultsmentioning

confidence: 99%

Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability

et al. 1998

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“…Dinucleotide microsatellites were reported to occur in a higher frequency than tri-and tetra-nucleotide microsatellites in plants (Depeiges et al 1995, Diwan et al 1997, Plieske and Struss 2001. Furthermore, Smith et al (1997) and Senior et al (1998) reported that the average PIC value for dinucleotide repeats was higher than that for tri-and tetranucleotide repeats.…”

Section: Development Of Microsatellite Markersmentioning

confidence: 99%

Development of Microsatellite Markers in Melon (Cucumis melo L.) and Their Application to Major Cucurbit Crops.

et al. 2003

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We developed 31 sets of melon (Cucumis melo L.) microsatellite markers in this study. Primers for these markers were designed from clones containing simple sequence repeats (SSRs) of (GA/CT)n or (GT/CA)n isolated from a melon genomic library. These microsatellite loci were examined for the detection of alleles among twelve lines and cultivars from six varieties of C. melo. A total of 28 marker loci showed polymorphism by 2.0 % agarose TBE gel separation. And these markers were also examined for cross-species amplification applicable to nine other species in Cucurbitaceae. Among them, 13 marker loci were commonly detected within the major cucurbit crops, cucumber, pumpkin and watermelon using the present primer sets. The species to which the melon microsatellite markers would be most applicable was Momordica charantia (24 markers), followed by Cucumis sativus (20 markers) and Cucurbita maxima (18 markers). These conserved microsatellite loci could be used as anchor markers in studies on synteny in Cucurbitaceae.

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“…The discriminatory potential for ISSR markers depends on the variety and frequency of microsatellites, which change with species and the SSR motifs that are targeted. The sequence of repeats and anchored nucleotides were selected in a way to allowed analysis of multiple loci in a single, multiplexed reaction (Depeiges et al 1995). The reproducibility of the fragments generated by ISSR primers exceeds that of primers of arbitrary sequences typically used for RAPD analysis as described previously (Ajibade et al 2000).…”

Section: Genetic Classificationmentioning

confidence: 99%

Morphological and molecular diversity within Algerian cowpea (Vigna unguiculata (L.) Walp.) landraces

Ghalmi

Malice

Jacquemin

et al. 2009

Genet Resour Crop Evol

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Twenty landraces of cowpea (Vigna unguiculata (L.) Walp.) scattered throughout Algeria were compared through morphological and genetic characterization. At the morphological level, for qualitative characters there was no intra-landrace variation and for quantitative characters the variations were low except for landrace NAG2 Three different cultigroups were located in Algeria: Biflora that was dominant in the Sahara, Melanophtalmus in the North and Unguiculata including one landrace in Kabylia and two in Sahara. The AMOVA analysis indicated that the genetic variation was lower within than among agro-ecological regions. A Mantel test, revealed a correlation between the qualitative morphological data and the geographical data (R = 0.28; P \ 0.01), indicating that the degree of morphological change among landraces was roughly proportional to the geographical distances separating them.Genetic diversity was analyzed by using 11 random amplified polymorphic DNA (RAPD) and 12 intersimple sequence repeat (ISSR) markers. No intralandrace variability was found. The eleven RAPD primers yielded 77 bands, of which 45 (58.44%) were polymorphic; the genetic similarity ranged from 66.0 to 96.7%. The twelve ISSR primers provided a total of 104 bands, of which 65 (62.5%) were polymorphic; the genetic similarity ranged from 62.8 to 97.8%. cluster analysis showed a good match between genetic background and geographical distribution, which was confirmed by the results of the Mantel test. In particular, geographical data and genetic data were found to be correlated: (R = 0.33; P \ 0.01) for RAPD, (R = 0.37; P \ 0.01) for ISSR, and (R = 0.33; P \ 0.01) for a combined RAPD-ISSR dataset. Moreover, despite the absence of significant correlation between morphological and RAPD data (R = 0.14; P = 0.14), significant correlations between morphological data and both ISSR (R = 0.27, P \ 0.05) and a combined RAPD-ISSR dataset (R = 0.22, P \ 0.05) were noted. ISSR markers were better linked to morphological variation than were RAPD markers. However, despite this, genetic distances among these landraces were found to be essentially the same no matter which markers were used.

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Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci

Cited by 74 publications

References 32 publications

Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability

Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability

Development of Microsatellite Markers in Melon (Cucumis melo L.) and Their Application to Major Cucurbit Crops.

Morphological and molecular diversity within Algerian cowpea (Vigna unguiculata (L.) Walp.) landraces

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