Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants

Bryan, Glenn J.; McNicoll, Jean; Ramsay, Gavin; Meyer, Rhonda C.; Jong, Walter S. De

doi:10.1007/s001220051306

Cited by 199 publications

(133 citation statements)

References 13 publications

Supporting

Mentioning

124

Contrasting

Unclassified

Order By: Relevance

“…Chloroplast microsatellite method A total of 10 universal microsatellite primers (Ccmp1 to Ccmp10) described by Weising and Gardner (1999), six rice microsatellite primers (Rtc3, Rtc4, Rtc5, Rtc6, Rtc9, Rtc10) described by Ishii and McCouch (2000) and five tobacco microsatellites (Ntcp7, Ntcp9, Ntcp19, Ntcp23, Ntcp28) described by Bryan et al (1999) were tested over a subset of the total population. Among the 21 primer pairs tested on a sample of eight individuals, 10 amplified and only four (Ccmp3, Ccmp5, Ntcp8, Ntcp9) were polymorphic.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers

Fontaine

Lovett²,

Sanou

et al. 2004

Heredity

View full text Add to dashboard Cite

RAPDs and chloroplast microsatellites were used to quantify the genetic variation of Vitellaria paradoxa (an economically important tree species in sub-Saharan Africa, north of the equator) and to analyse the geographic distribution of diversity in relation to the refuge theory. A total of 13 locations were sampled in eight countries, covering most of the natural range from Senegal to Uganda. A total of 67 polymorphic and 15 monomorphic RAPD loci were detected in 179 individuals. No relationship was identified between diversity and longitude or latitude. An unrooted neighbourjoining tree suggested a western group and an eastern group, representing 7% (P ¼ 0.000) of the total variation. A Mantel test suggested that genetic distances between populations were correlated to geographic distances (R ¼ 0.88, P ¼ 0.001). The three-chloroplast microsatellite primers, assayed in 116 individuals, revealed 10 different alleles and seven chlorotypes. Most of the populations comprised a single haplotype. It is proposed from these results that the difference between western and eastern populations results from putative refugia separated by the current 'Dahomey Gap' (a semiarid zone that meets the coast around the Ghana-Togo-Benin-Nigeria borders), an area that may have been exceptionally dry during glacial periods. In addition, it is suggested that the haplotype distribution and frequency in the western populations could be due to the more recent impact of humans, particularly shea tree selection and dispersal during traditional agroforestry.

show abstract

Section: Methodsmentioning

confidence: 99%

Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers

Fontaine

Lovett²,

Sanou

et al. 2004

Heredity

View full text Add to dashboard Cite

show abstract

“…Eleven of the SSR loci in the IGS region and five SSR loci in the CDSs are also found in the Panax cp genome. With the exception of these conserved SSR loci, length variation in SSR loci provide useful markers for identifying varieties of plant species and understanding population genetics (Bryan et al, 1999;Garris et al, 2005;Powell et al, 1995b;Xu et al, 2002). The variable SSR loci in Eleutherococcus will be useful for elucidating the genetic structures and the genetic variability of this rare and endangered plant species, and will be useful tools for the identification of cultivars and determination of the geographical origin of the medicinally important E. senticosus.…”

Section: Evolution Of Repeated Sequencesmentioning

confidence: 99%

The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

Lee

Sun

et al. 2012

Molecules and Cells

View full text Add to dashboard Cite

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

show abstract

“…Its generally uniparental mode of inheritance makes it a powerful tool to elucidate relative contributions of seed and pollen flow to the genetic structure of natural populations by comparison with nuclear markers. Whilst nuclear microsatellites are the marker system of choice for genetic diversity, genome mapping, DNA fingerprinting and parentage analysis, chloroplast microsatellites (cpSSRs) revealed to be of special value in studies of plant population geographic structure and differentiation [2,7,20] and for paternity analysis in the specific case of conifers [30]. However, as for nuclear microsatellites, a high level of homoplasy (alleles identical in size but not necessarily identical by descent due to convergent mutations) is expected [11].…”

Section: Introductionmentioning

confidence: 99%

Use of chloroplast microsatellites to differentiate oak populations

2004

View full text Add to dashboard Cite

-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

show abstract

Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants

Cited by 199 publications

References 13 publications

Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers

Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers

The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

Use of chloroplast microsatellites to differentiate oak populations

Contact Info

Product

Resources

About