Characterisation and inheritance of polymorphic plastid microsatellites in Abies

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 857-864 ◽  
Author(s):  
G. G. Vendramin ◽  
B. Ziegenhagen
Keyword(s):  
Population Genetics ◽  
Simple Sequence Repeats ◽  
Natural Populations ◽  
Abies Alba ◽  
Chloroplast Microsatellites ◽  
Length Variation ◽  
Pcr Products ◽  
Considerable Length ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Two polymorphic microsatellite loci were identified and sequenced in the genus Abies, using primer pairs derived from chloroplast simple sequence repeats (SSRs) of Pinus thunbergii. PCR products exhibited considerable length variation among six different Abies species and within Abies alba. F1 progeny of both an interspecific and an intraspecific reciprocal cross confirmed that the two SSRs were predominantly paternally inherited. The maternal size variant predominantly occurred in the megagametophytes analysed. First analysis of the two chloroplast microsatellites in seven natural populations of A. alba revealed 36 different haplotypes. The use of these highly polymorphic SSRs as potential markers in population genetics is discussed.Key words: Abies, chloroplast simple sequence repeats, sequences, inheritance, intraspecific variation, population genetics.

Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 786-798 ◽  
Author(s):  
T Kyndt ◽  
B Van Droogenbroeck ◽  
A Haegeman ◽  
I Roldán-Ruiz ◽  
G Gheysen
Keyword(s):  
Population Genetics ◽  
Chloroplast Microsatellites ◽  
Microsatellite Data ◽  
Chloroplast Microsatellite ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Polymorphism Rate ◽  
Nuclear Ssr ◽  
Simple Sequence ◽  
Future Population

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea × heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.Key words: Carica, Jacaratia, Vasconcellea, simple sequence repeats, cross-species amplification, classification, interspecific hybrids.

Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses

2003 ◽  
Vol 81 (8) ◽  
pp. 814-832 ◽  
Author(s):  
Sang-Min Chung ◽  
Deena S Decker-Walters ◽  
Jack E Staub
Keyword(s):  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Morphological Data ◽  
Insertion And Deletion ◽  
Nicotiana Tabacum L ◽  
The Family ◽  
Pcr Products ◽  
Species Comparisons ◽  
Sequence Substitution ◽  
Simple Sequence

To investigate genetic relationships in Benincaseae (19 accessions), Cucurbiteae (1), Joliffieae (2), Melothrieae (2), and Sicyeae (3) tribes of the family Cucurbitaceae, consensus chloroplast simple sequence repeats (ccSSR) primer pairs obtained from tobacco (Nicotiana tabacum L.) chloroplast DNA were used. Variation in the length and putative sequence substitution events of polymerase chain reaction (PCR) products were analyzed. Sequencing of four fragments (ccSSR-1, -7, -8, and -19) revealed that convergence in fragment length occurs in more distant species comparisons. In ccSSR-1 and -8, the same fragment lengths occurred as the result of different insertion and deletion events. Nevertheless, the examination of a large number of ccSSR fragments suggested that this apparent homoplasy could be overshadowed by evolutionary relationships among taxa. This hypothesis is supported by the relative degree of positive congruence of taxon groupings after cluster and principal components analyses performed on both base pair length and sequence substitution data. Moreover, these analyses support previous biochemical and morphological data indicating that distinct lineages exist within the Benincaseae. Likewise, data support the hypotheses that the genus Benincasa is descended from an ancient African ancestor and that the progenitor of the New World Sicyeae tribe shares a common ancestor with the genus Luffa of the Old World Benincaseae.Key words: Benincaseae, chloroplast, consensus, homoplasy, microsatellite, simple sequence repeats.

A Low Mutation Rate For Chloroplast Microsatellites

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 943-947
Author(s):  
Jim Provan ◽  
Nicole Soranzo ◽  
Neil J Wilson ◽  
David B Goldstein ◽  
Wayne Powell
Keyword(s):  
Chloroplast Genome ◽  
Mutation Rate ◽  
Simple Sequence Repeats ◽  
Mutation Rates ◽  
Chloroplast Microsatellites ◽  
Ssr Loci ◽  
Nuclear Ssr ◽  
Monomorphic Population ◽  
Simple Sequence ◽  
Pinus Torreyana

Abstract We used chloroplast simple sequence repeats (cpSSRs) to examine whether there is any variation present in the chloroplast genome of Pinus torreyana (Parry ex Carrière) that may previously not have been detected using RFLPs. Analysis of 17 cpSSR loci showed no variation, which is consistent with previous cpRFLP work and confirms that the species is descended from an original, highly monomorphic population following a bottleneck. This lack of biological variation in the chloroplast genome of P. torreyana allowed us to estimate the mutation rates at cpSSR loci as between 3.2 × 10-5 and 7.9 × 10-5. This estimate is lower than published mutation rates at nuclear SSR loci but higher than substitution rates elsewhere in the chloroplast genome.

Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 884-889 ◽  
Author(s):  
M. Lynn Senior ◽  
Manfred Heun
Keyword(s):  
Polymerase Chain Reaction ◽  
Simple Sequence Repeats ◽  
Genome Mapping ◽  
Pcr Amplification ◽  
Chain Reaction ◽  
Expected Size Range ◽  
Pcr Products ◽  
Mammalian Genomes ◽  
Polymerase Chain ◽  
Simple Sequence

Microsatellites, also called simple sequence repeats (SSRs), have yielded an important class of DNA markers most notable for mapping mammalian genomes. To study the occurrence of microsatellites and their inheritance in maize, a search was made of 280 maize GenBank® sequences. Six SSRs were chosen and unique flanking primers were designed for polymerase chain reaction (PCR) amplification. Eight different maize inbreds were studied with these six primer pairs and a mean of 3.5 polymorphic patterns occurred within the expected size range. For five of these putative microsatellites, the segregation in a maize restriction fragment length polymorphism mapping population was analyzed. Four of the microsatellites cosegregated with the Adh1, Gpc1, Pdk1, and Tpi genes from which the primer sequences were derived. The fifth primer pair (MZEGPA1) showed segregating polymorphisms, but the products were larger than expected. To verify the existence of the original SSRs in the segregating PCR products, a CT primer, containing a CT SSR and an arbitrary leader sequence, was used to reamplify these products. The four microsatellites that cosegregated with the original gene were reamplified as anticipated, whereas a suspicious 230-bp product obtained when using the MZEGPA1 primers could not be reamplified. Based on these results it is concluded that microsatellites can be a valuable tool for maize mapping.Key words: maize, microsatellites, simple sequence repeats, genome mapping.

scholarly journals 054 Characterization of Malus hupehensis (Tea Crabapple) with DNA Simple Sequence Repeats

HortScience ◽  
1999 ◽  
Vol 34 (3) ◽  
pp. 450D-450
Author(s):  
Laura L. Benson ◽  
Warren F. Lamboy ◽  
Richard H. Zimmerman
Keyword(s):  
Fragment Length ◽  
Simple Sequence Repeats ◽  
Plant Introduction ◽  
Length Variation ◽  
Clonal Lineage ◽  
Malus Hupehensis ◽  
National Plant Germplasm System ◽  
The City ◽  
Simple Sequence

Simple sequence repeats (SSRs) are highly polymorphic regions of DNA that can be used for the molecular characterization of apple (Malus) germplasm. SSR markers are sufficiently variable to distinguish between individual plants in wild Malus species. In this study, accessions of Malus hupehensis were screened for fragment length variation in PCR amplified simple sequence repeat regions of DNA. The fragment length phenotype produced by five SSR primer pairs showed no variation between two lineages of M. hupehensis collected in the Changjiang (Yangtse) River valley. One lineage was collected by E.H. Wilson in 1908 near the city of Ichang, Hubei Province. The second lineage was collected by cooperators at China's Southwest Agricultural University (SWAU) in 1997 near the city of Chongqing (Chungking). M. hupehensis Plant Introduction No. 588760 from the National Plant Germplasm System lacks provenance, but displays a fragment length phenotype identical to both the Wilson and SWAU lineages. The spread of a clone may be aided by asexual reproduction through seed, which is not uncommon in polyploid apples. Two seedlings each of 15 maternal trees from the SWAU lineage were assayed for ploidy level by flow cytometry. The DNA content per nucleus for all SWAU progeny fell within the range for triploids, 2.19 to 2.68 pg DNA/nucleus. It appears that plant explorers in China separated by almost 90 years have succeeded in sampling a single clonal lineage of M. hupehensis.

scholarly journals Length variation of chloroplast simple sequence repeats in the genus Eucalyptus L'Hér.

2020 ◽  
Vol 7 (3) ◽  
pp. 353
Author(s):  
Sonu Kumar ◽  
Asheesh Shanker
Keyword(s):  
Simple Sequence Repeats ◽  
Molecular Breeding ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Sufficient Information ◽  
Length Variation ◽  
The Common ◽  
Diversity Studies ◽  
Simple Sequence ◽  
Genus Eucalyptus

Eucalyptus L'Hér. is an economically important genus of plants with several environmental significances and great industrial advantages. To accelerate breeding and conservation studies, efforts on molecular breeding and molecular genetic analysis are underway in the genus Eucalyptus. Despite these efforts, no sufficient information is available about common, polymorphic and unique chloroplast simple sequence repeats (cpSSRs) in the genus Eucalyptus. . These repeats consist of 1-6 nucleotides and play important role in the development of molecular markers, genetic mapping and plant breeding. In the present study, a total of 920 cpSSRs were detected and length variation of cpSSRs analysed between each pair of species among 31 chloroplast genome sequences of the genus Eucalyptus. Additionally, cross species transferability of common and polymorphic cpSSRs were also observed. The common, unique and putative polymorphic cpSSRs analysed in this study can be used for species identification and genetic diversity studies of Eucalyptus.

Polymorphism revealed by simple sequence repeats

1996 ◽  
Vol 1 (7) ◽  
pp. 215-222 ◽  
Author(s):  
W POWELL ◽  
G MACHRAY ◽  
J PROVAN
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence
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