Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome

Powell, W.; Morgante, Michèle; Andre, Chaz; McNicol, James W.; Machray, Gordon C.; Doyle, Jeff J.; Tingey, Scott V.; Rafalski, J. Antoni

doi:10.1016/s0960-9822(95)00206-5

Cited by 192 publications

(142 citation statements)

References 17 publications

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“…Simple sequence repeats (so-called SSRs) such as mono-or di-nucleotide repeats have been reported in cpDNA (Powell et al, 1995a;Powell et al, 1995b;Palmer, 1987). However, to the best of our knowledge, tandem repeats that consist of such a long motif (so-called VNTR or minisatellite in Hartl, 2000) have not been detected previously in cpDNA.…”

Section: Discussionmentioning

confidence: 92%

Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers.

Kamiya

Harada

Clyde³

et al. 2002

Genes Genet. Syst.

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The genetic variation of Trigonobalanus verticillata , the most recently described genus of Fagaceae, was studied using chloroplast DNA sequences and AFLP fingerprinting. This species has a restricted distribution that is known to include seven localities in tropical lower montane forests in Malaysia and Indonesia. A total of 75 individuals were collected from Bario, Kinabalu, and Fraser's Hill in Malaysia. The sequences of rbc L , mat K, and three non-coding regions ( atp B -rbc L spacer, trn L intron, and trn L -trn F spacer) were determined for 19 individuals from these populations. We found a total of 30 nucleotide substitutions and four length variations, which allowed identification of three haplotypes characterizing each population. No substitutions were detected within populations, while the tandem repeats in the trn L -trn F spacer had a variable repeat number of a 20-bp motif only in Kinabalu. The differentiation of the populations inferred from the cp DNA molecular clock calibrated with paleontological data was estimated to be 8.3 MYA between Bario and Kinabalu, and 16.7 MYA between Fraser's Hill and the other populations. In AFLP analysis, four selective primer pairs yielded a total of 431 loci, of which 340 (78.9%) were polymorphic. The results showed relatively high gene diversity ( H S = 0.153 and H T = 0.198) and nucleotide diversity ( π S = 0.0132 and π T = 0.0168) both within and among the populations. Although the cp DNA data suggest that little or no gene flow occurred between the populations via seeds, the fixation index estimated from AFLP data ( F ST = 0.153 and N ST = 0.214) implies that some gene flow occurs between populations, possibly through pollen transfer.

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Section: Discussionmentioning

confidence: 92%

Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers.

Kamiya

Harada

Clyde³

et al. 2002

Genes Genet. Syst.

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“…Powell et al (1995) provided experimental evidence of length variation in the mononucleotide repeats of the chloroplast genome of angiosperms, and polymorphisms within these regions might be used to study both intraspecific and interspecific variability. Soranzo et al (1999) was the first to show length variation at a mitochondrial SSR locus in conifers.…”

Section: Identification and Featuresmentioning

confidence: 99%

Microsatellites as Tools for Genetic Diversity Analysis

Hoshino¹,

Bravo²,

Nóbile³

et al. 2012

Genetic Diversity in Microorganisms

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“…The relevance of assays based on nuclear microsatellites for genetic analysis is well established. The principle has been extended to the chloroplast genome in a variety of species [18,22]. The chloroplast genome is a useful source of markers for genetic studies of plants because of conserved gene order and general lack of heteroplasmy and recombination.…”

Section: Introductionmentioning

confidence: 99%

Use of chloroplast microsatellites to differentiate oak populations

2004

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-The possibility to use chloroplast microsatellites (cpSSRs) instead of restriction analysis of PCR-amplified DNA fragments to differentiate oak populations was tested in two economically important tree species: Quercus petraea and Quercus robur. The level and pattern of inter-and intraspecific cpDNA variation were studied over 48 French populations using a total of 24 cpSSR loci. The same pattern of low intrapopulation diversity and high population differentiation was noted with both types of markers, since there was an almost total redundancy of haplotypes identified with both techniques. Overall, our results indicate that chloroplast microsatellites can be used for haplotype discrimination in many contexts including certification or traceability of oak material. microsatellites / cpSSR / PCR-RFLP / haplotypic diversity / population geneticsRésumé -Utilisation des microsatellites chloroplastiques pour différencier des populations de chênes. Nous avons cherché à comparer l'efficacité de deux types de marqueurs chloroplastiques, les marqueurs microsatellites (cpSSR) et marqueurs PCR-RFLP (cpRFLP), à différencier des populations de chênes sessiles et pédonculés, deux espèces d'arbres forestiers économiquement importantes. Le niveau et la structuration de la diversité inter et intra-spécifique ont été mesurés au sein de 48 populations françaises au travers de l'analyse de 24 microsatellites chloroplastiques. Une faible diversité intra-population, ainsi qu'une forte différenciation des populations de chênes ont pu être mesurées à l'aide des deux types de marqueurs, du fait d'une redondance quasi-complète des haplotypes identifiés par les deux techniques. Nos résultats indiquent donc que les marqueurs microsatellites chloroplastiques peuvent être utilisés pour la distinction d'haplotypes et de populations de chênes dans le cadre de la certification ou de la traçabilité de matériel forestier (graines, plants, bois). microsatellites / cpSSR / PCR-RFLP / diversité haplotypique / génétique des populations

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Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome

Cited by 192 publications

References 17 publications

Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers.

Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers.

Microsatellites as Tools for Genetic Diversity Analysis

Use of chloroplast microsatellites to differentiate oak populations

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