scholarly journals Chloroplast microsatellites in barley: the reduction of variability spectrum in cultivated forms

2006 ◽  
Vol 4 (1) ◽  
pp. 17-21 ◽  
Author(s):  
Natalia V Lukhanina ◽  
Marina G Sinyavskaya ◽  
Inessa M Goloenko ◽  
Oleg G Davydenko
Keyword(s):  
Simple Sequence Repeat ◽  
Rare Variants ◽  
Chloroplast Microsatellites ◽  
Repeat Polymorphism ◽  
Hordeum Vulgare L ◽  
Chloroplast Genomes ◽  
Intergenic Regions ◽  
Ssr Loci ◽  
Cultivated Barley ◽  
Simple Sequence

The chloroplast genomes of 67 accessions of Hordeum vulgare L were surveyed for simple sequence repeat polymorphism. Seven SSR loci were investigated, trnL/trnF and psbI-trnS intergenic regions, as well as two regions 3' trnS genes were polymorphic. The rare variants of these loci were revealed and five rare accessions were found. Our results show an extremely low level of cpDNA polymorphism of cultivated barley.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

scholarly journals Evaluation of Genetic Diversity and Pedigree within Crapemyrtle Cultivars Using Simple Sequence Repeat Markers

2011 ◽  
Vol 136 (2) ◽  
pp. 116-128 ◽  
Author(s):  
Xinwang Wang ◽  
Phillip A. Wadl ◽  
Cecil Pounders ◽  
Robert N. Trigiano ◽  
Raul I. Cabrera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Interspecific Hybrids ◽  
Size Variation ◽  
Sequence Repeat ◽  
Allele Size ◽  
Low Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Estimates ◽  
Simple Sequence

Genetic diversity was estimated for 51 Lagerstroemia indica L. cultivars, five Lagerstroemia fauriei Koehne cultivars, and 37 interspecific hybrids using 78 simple sequence repeat (SSR) markers. SSR loci were highly variable among the cultivars, detecting an average of 6.6 alleles (amplicons) per locus. Each locus detected 13.6 genotypes on average. Cluster analysis identified three main groups that consisted of individual cultivars from L. indica, L. fauriei, and their interspecific hybrids. However, only 18.1% of the overall variation was the result of differences between these groups, which may be attributable to pedigree-based breeding strategies that use current cultivars as parents for future selections. Clustering within each group generally reflected breeding pedigrees but was not supported by bootstrap replicates. Low statistical support was likely the result of low genetic diversity estimates, which indicated that only 25.5% of the total allele size variation was attributable to differences between the species L. indica and L. fauriei. Most allele size variation, or 74.5%, was common to L. indica and L. fauriei. Thus, introgression of other Lagestroemia species such as Lagestroemia limii Merr. (L. chekiangensis Cheng), Lagestroemia speciosa (L.) Pers., and Lagestroemia subcostata Koehne may significantly expand crapemyrtle breeding programs. This study verified relationships between existing cultivars and identified potentially untapped sources of germplasm.

scholarly journals SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

2008 ◽  
Vol 2008 ◽  
pp. 1-9 ◽  
Author(s):  
Luciano Carlos da Maia ◽  
Dario Abel Palmieri ◽  
Velci Queiroz de Souza ◽  
Mauricio Marini Kopp ◽  
Fernando Irajá Félix de Carvalho ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Primer Design ◽  
Cdna Sequences ◽  
Additional Information ◽  
Ssr Loci ◽  
Eukaryotic Organisms ◽  
Simple Sequence ◽  
Rice Cdna ◽  
Tandem Duplications ◽  
Short Tandem

Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.

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

scholarly journals Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0127812 ◽  
Author(s):  
Jing Xiao ◽  
Jin Zhao ◽  
Mengjun Liu ◽  
Ping Liu ◽  
Li Dai ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Chinese Jujube ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.)

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 628-633 ◽  
Author(s):  
J. E. Bowers ◽  
G. S. Dangl ◽  
R. Vignani ◽  
C. P. Meredith
Keyword(s):  
Vitis Vinifera ◽  
Silver Staining ◽  
Simple Sequence Repeat ◽  
Pinot Noir ◽  
Sequence Repeat ◽  
Wine Grapes ◽  
Table Grapes ◽  
Isolation And Characterization ◽  
Ssr Loci ◽  
Simple Sequence

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.

scholarly journals Microsatellite DNA markers in Populus tremuloides

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 293-297 ◽  
Author(s):  
Muhammad H Rahman ◽  
S Dayanandan ◽  
Om P Rajora
Keyword(s):  
Populus Tremuloides ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
Simple Sequence Repeat ◽  
Mendelian Inheritance ◽  
Inheritance Pattern ◽  
Sequence Repeat ◽  
Microsatellite Dna Markers ◽  
Ssr Loci ◽  
Simple Sequence

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars. Key words: poplar, microsatellites, genetic mapping, simple sequence repeat (SSR) markers, DNA fingerprinting.

scholarly journals Multilocus Simple Sequence Repeat Markers for Differentiating Strains and Evaluating Genetic Diversity of Xylella fastidiosa

2005 ◽  
Vol 71 (8) ◽  
pp. 4888-4892 ◽  
Author(s):  
Hong Lin ◽  
Edwin L. Civerolo ◽  
Rong Hu ◽  
Samuel Barros ◽  
Marta Francis ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Xylella Fastidiosa ◽  
Sequence Repeat ◽  
Leaf Scorch ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Ssr Loci ◽  
Simple Sequence ◽  
Almond Leaf Scorch

ABSTRACT A genome-wide search was performed to identify simple sequence repeat (SSR) loci among the available sequence databases from four strains of Xylella fastidiosa (strains causing Pierce's disease, citrus variegated chlorosis, almond leaf scorch, and oleander leaf scorch). Thirty-four SSR loci were selected for SSR primer design and were validated in PCR experiments. These multilocus SSR primers, distributed across the X. fastidiosa genome, clearly differentiated and clustered X. fastidiosa strains collected from grape, almond, citrus, and oleander. They are well suited for differentiating strains and studying X. fastidiosa epidemiology and population genetics.

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