Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 104-110 ◽  
Author(s):  
J. Provan ◽  
G. Corbett ◽  
W. Powell ◽  
J. W. McNicol
Keyword(s):  
Simple Sequence Repeats ◽  
Wild Rice ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Cultivated Rice ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Wild Accessions ◽  
Simple Sequence

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.Key words: rice, chloroplast, simple sequence repeat, microsatellites.

Mapping of digested and undigested random amplified microsatellite polymorphisms in barley

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 991-998 ◽  
Author(s):  
Jörg Becker ◽  
Manfred Heun
Keyword(s):  
Simple Sequence Repeats ◽  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Sequence Data ◽  
Linkage Maps ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Alternative Approach ◽  
Microsatellite Mapping ◽  
Simple Sequence

The broad use of microsatellites as a tool for constructing linkage maps in plants has been limited by the need for sequence data to detect the underlying simple sequence repeats. Therefore, random amplified microsatellite polymorphisms (RAMPs) were studied as an alternative approach for barley mapping. Labelled (GA)n simple sequence repeat primers were combined with RAPD primers of different length and sequence to generate RAMPs. To get additional polymorphisms (called dRAMPs), the obtained products were also analysed after digestion with MseI. There were 0–11 polymorphisms found per primer combination. Sixty RAMPs/dRAMPs identifying 40 new loci were mapped onto a barley RFLP map. The new DNA markers are found on all chromosomes and they increased the length of the barley map by 174 cM to a total of 1270 cM. Interestingly, the RAMPs/dRAMPs caused stretching effects in genome areas where stretching was also observed for AFLPs.Key words: barley, microsatellite, mapping, RAMP, RFLP.

Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants

1999 ◽  
Vol 99 (5) ◽  
pp. 859-867 ◽  
Author(s):  
G. J. Bryan ◽  
J. McNicoll ◽  
G. Ramsay ◽  
R. C. Meyer ◽  
W. S. De Jong
Keyword(s):  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Chloroplast Genomes ◽  
Solanaceous Plants ◽  
Simple Sequence

A taxonomic appraisal of the Chatham Islands flax (Phormium tenax) using morphological and DNA fingerprint data

2010 ◽  
Vol 23 (5) ◽  
pp. 371 ◽  
Author(s):  
R. D. Smissen ◽  
P. B. Heenan
Keyword(s):  
New Zealand ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
The Other ◽  
Dna Fingerprint ◽  
Sequence Repeat ◽  
In The Wild ◽  
The 19Th Century ◽  
Simple Sequence ◽  
Fingerprint Data

A range of leaf forms of Phormium tenax J.R.Forst. & G.Forst. can be observed in the wild on the Chatham Island archipelago. At one extreme are plants with more or less upright leaves, similar to those observed in New Zealand P. tenax, and at the other extreme there are plants with floppy leaves. The upright-leaved form is found more or less throughout the archipelago, whereas the floppy-leaved form is concentrated in the southern part of Chatham Island, Pitt Island, and on the other southern islands (e.g. South East and Mangere islands). Analysis of amplified fragment length polymorphism (AFLP) and simple-sequence-repeat (SSR) variation, and comparison with a diverse sampling of New Zealand Phormium suggested that both Chatham Islands forms are indigenous and part of a common gene pool. We found no evidence of hybridism with Phormium introduced from New Zealand. Floppy-leaved forms are therefore linked to typical upright leaved P. tenax through upright-leaved plants with bent tips, and do not require taxonomic recognition. AFLP and SSR data both support the view that a plant collected from Ranui Cove, Auckland Island, is descended from Chatham Islands material, and was most likely introduced there by Ngāti Mutunga and Moriori settlers during the 19th century.

scholarly journals New Insight into Wild Red Raspberry Populations using Simple Sequence Repeat Markers

2009 ◽  
Vol 134 (1) ◽  
pp. 109-119 ◽  
Author(s):  
Julie Graham ◽  
Mary Woodhead ◽  
Kay Smith ◽  
Joanne Russell ◽  
Bruce Marshall ◽  
...  
Keyword(s):  
Population Differentiation ◽  
Simple Sequence Repeat ◽  
Rubus Idaeus ◽  
Small Scale ◽  
Climate Change Scenarios ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
In The Wild ◽  
Simple Sequence ◽  
Significant Population Differentiation

Scottish wild red raspberry (Rubus idaeus) plants at 12 sites were re-examined 10 years after initial studies had been carried out to examine the decline in population size and to address an earlier finding that demonstrated significant population differentiation over a small scale. Ten simple sequence repeat (SSR) loci were screened on the plants and a total of 80 alleles were detected, half of which were unique to a particular population, with all populations containing unique SSR alleles. Only 18 of the 80 alleles present in the wild were found in cultivated raspberries, highlighting the genetic diversity available for future breeding. This finding makes the decline in population number observed a concern, as this unique diversity is being eroded, primarily due to human impact. An additional 17 unique alleles were identified in the cultivars that were not present in the wild individuals studied. Gene flow into one lowland site was identified by the gain of one new allele into progeny at the site, but three alleles were also lost from parents to progeny. SSR markers were used to estimate the levels of outcrossing in wild red raspberry for the first time, and confirmed that the populations studied were outcrossing, intermating populations. The nonsignificant global F IS value indicates that red raspberry is an outbreeder (global F IS = −0.117), but significant population differentiation was observed [global F ST = 0.348 (P < 0.001)]. Diversity in this crop's wild relative and the population differentiation observed may have use in the future for breeding aimed at addressing climate change scenarios, and consideration should be given to means of conserving the diversity revealed by these studies.

Genetic mapping and variability of seven soybean simple sequence repeat loci

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 763-769 ◽  
Author(s):  
M. Morgante ◽  
A. Rafalski ◽  
P. Biddle ◽  
S. Tingey ◽  
A. M. Olivieri
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Rflp Markers ◽  
Sequence Motifs ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Simple Sequence

Microsatellites or simple sequence repeats are stretches of short tandemly repeated DNA sequence motifs, dispersed throughout the genomes of most eukaryotes. Simple sequence repeat polymorphisms (SSRPs) have recently been reported in plants. Here we present the genetic map position of seven different soybean (Glycine max (L.) Merr. and Glycine soja Sieb. and Zucc.) SSRPs contained in sequenced genes, four of which represent newly mapped positions for these genes. The other three SSRPs coincided with independently established RFLP map positions for the corresponding genes. When a set of 61 soybean accessions was screened at four of these loci by using agarose gels, the average number of alleles per locus was 7.75, the effective number of alleles (ne) was 2.57, and the level of allele differentiation (δT) was 0.62. Allelic variation decreased sharply with increasing levels of domestication, with the level of differentiation going from 84% in the wild soybean to 43% in the elite germplasm. Variation levels observed on a subset made of 19 of the 61 lines were always higher for SSRPs than for RFLP markers, with the average number of alleles per locus going from 4.25 to 2.15. In comparison with RFLP markers, SSRPs are more informative and are easier to analyse but require more effort to develop.Key words: simple sequence repeats, soybean, variability, mapping, domestication, microsatellites.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence

Mapping Unequal Crossing over Hotspot Region of Simple Sequence Repeat in Maize

2009 ◽  
Vol 35 (5) ◽  
pp. 958-961
Author(s):  
Ji-Hua TANG ◽  
Xi-Qing MA ◽  
Wen-Tao TENG ◽  
Jian-Bing YAN ◽  
Jing-Rui DAI ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Crossing Over ◽  
Sequence Repeat ◽  
Unequal Crossing Over ◽  
Simple Sequence
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