Microsatellite DNA as shared genetic markers among conifer species

1999 ◽  
Vol 29 (3) ◽  
pp. 365-371 ◽  
Author(s):  
C S Echt ◽  
G G Vendramin ◽  
C D Nelson ◽  
P Marquardt
Keyword(s):  
Pinus Radiata ◽  
Picea Glauca ◽  
Ssr Marker ◽  
Allelic Variation ◽  
Conifer Species ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Shared Alleles ◽  
Simple Sequence ◽  
Shared Genetic

Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC)n loci that were polymorphic in P. strobus also amplified SSR loci in two other soft pines of the subgenus Strobus but not in seven hard pines of the subgenus Pinus, nor in Picea glauca (Moench) Voss or Pseudotsuga menziesii (Mirb.) Franco. The six P. strobus SSR primer pairs that did amplify loci from conifers other than soft pines were those that were specific to loci monomorphic within P. strobus. These six loci were also monomorphic within seven other species tested, but four of the loci were polymorphic among species. A comparison of allelic variation among the three soft pine species found only 25 shared alleles among a total of 122 alleles at eight loci. Primer pairs for dinucleotide SSR loci that were polymorphic in Pinus radiata also specifically amplified loci from various other hard pines but not from the soft pines or from the other conifers tested.

scholarly journals Using Simple Sequence Repeats (SSRs) for DNA Fingerprinting Germplasm Accessions of Grape (Vitis L.) Species

1998 ◽  
Vol 123 (2) ◽  
pp. 182-188 ◽  
Author(s):  
Warren F. Lamboy ◽  
Christopher G. Alpha
Keyword(s):  
Genetic Resources ◽  
Gene Diversity ◽  
Table Grape ◽  
Chain Reaction ◽  
Discrimination Power ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Effective Use ◽  
Simple Sequence ◽  
Germplasm Accessions

The USDA-ARS Vitis genetic resources collections in Geneva, N.Y., and Davis, Calif., contain ≈3600 accessions of >35 species. Accurate and unambiguous identification of these grapes is essential for efficient and effective use of this germplasm. Previous workers have successfully used polymerase chain reaction (PCR)-generated SSRs to fingerprint cultivars of the wine and table grape species, V. vinifera. Building on this work, we conducted a test of five previously characterized SSR loci on 110 accessions of 25 grape taxa (21 Vitis species and 4 hybrids) to determine if they would satisfy our need for identifying cultivars within the USDA-ARS grape collections. Scorable SSR fragments were produced with all 550 primer-accession combinations, with no null loci observed. The loci were highly polymorphic, with 16 to 38 different alleles found at a locus. Heterozygosity values ranged from 0.464 to 0.818, while gene diversity values ranged from 0.875 to 0.955. Discrimination power at a locus varied from a low of 0.947 to a high of 0.987. Combined discrimination power of all loci was effectively 1.000, with 2 chances in 100,000,000 that two sexually, independently derived grape accessions would not be distinguishable using this set of five SSR loci. Two plants in the study that had previously been classified as belonging to different grape species were shown to have identical SSR fingerprints, showing that they almost certainly possessed the same genotype. Because SSR markers are codominant and highly polymorphic and SSR loci are generally conserved across a range of related species, we strongly recommend SSRs for fingerprinting not only grape, but other clonal genetic resources collections as well.

scholarly journals Microsatellite Markers for Raspberry and Blackberry

2010 ◽  
Vol 135 (3) ◽  
pp. 271-278 ◽  
Author(s):  
Nina R.F. Castillo ◽  
Barbara M. Reed ◽  
Julie Graham ◽  
Felicidad Fernández-Fernández ◽  
Nahla Victor Bassil
Keyword(s):  
Rubus Idaeus ◽  
Reaction Products ◽  
Red Raspberry ◽  
Genomic Libraries ◽  
Crop Type ◽  
Ssr Loci ◽  
High Polymorphism Information Content ◽  
Polymerase Chain ◽  
Diversity Estimates ◽  
Simple Sequence

Twelve microsatellites were isolated from simple sequence repeat (SSR)-enriched genomic libraries of ‘Meeker’ red raspberry (Rubus idaeus) and ‘Marion’ blackberry (Rubus hybrid). These primer pairs plus one developed from a GenBank red raspberry sequence were evaluated in 48 raspberry and 48 blackberry genotypes. Only RhM031 did not generate a product in raspberry, whereas RiG001 failed to amplify in blackberry and hybrid accessions. The number of polymerase chain reaction products per primer pair in the 12 SSRs that successfully amplified was higher in blackberry genotypes and their hybrids than in raspberry, ranging from three to 29 in blackberry (average, 14.4) and from one to 15 in red raspberry (average, 7.5). Diversity estimates were determined for 10 of 12 SSRs that amplified up to two products in 44 red raspberry genotypes. The best SSR loci based on high observed and expected heterozygosities, high polymorphism information content, and low inbreeding coefficient were RiM019, RhM003, and RhM011. They mapped to three different linkage groups (5, 2, and 7, respectively) in red raspberry and differentiated the unique genotypes identified with the 12 SSRs in each crop type.

Simple Sequence Repeat (SSR) Polymorphisms and Population Genetics in Sichuan Wild Rhesus Macaques

2011 ◽  
Vol 343-344 ◽  
pp. 690-697
Author(s):  
Di Yan Li ◽  
Yong Fang Yao ◽  
Xiao Feng Huang ◽  
An Chun Cheng ◽  
Huai Liang Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Rhesus Macaques ◽  
Genetic Management ◽  
Future Studies ◽  
Ssr Loci ◽  
Different Populations ◽  
Polymerase Chain ◽  
High Level ◽  
Simple Sequence

Cross-species amplification of twenty-five SSR loci from the DNA of five rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Seven of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these five samples, were also used to amplify SSR loci for 111 Sichuan wild rhesus macaques of five different populations. The analysed microsatellite markers produced 109 alleles, varied from 4 to 16 alleles each locus. The number of alleles per population ranged from 6.79 to 11.38. Polymorphic information content showed that all seven loci were highly informative (mean = 0.9017±0.0166, >0.5). The average observed heterozygosity was less than the expected (mean = 0.6795 and mean = 0.8559, respectively). Genetic differentiation among the populations was considerably low with the overall and pairwise FST values (mean = 0.0375), and showed fairly low level of inbreeding (indicated by a mean FIS value of 0. 0.1991). Maintaining genetic diversity is a major issue in conservation biology. In comparison to other captive Macaca mulatta studies, these wild rhesus macaque populations showed a relatively high level of genetic diversity, and there was low gene flow among these populations. Careful genetic management is important for maintaining genetic variability levels. None of the seven informative loci are linked which screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.

scholarly journals SSR-Marker Analysis—A Method for S. cerevisiae Strain Characterization and Its Application for Wineries

Fermentation ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 101
Author(s):  
Friederike Rex ◽  
Adeline Hirschler ◽  
Maren Scharfenberger-Schmeer
Keyword(s):  
Ssr Marker ◽  
Yeast Genome ◽  
Strain Characterization ◽  
Spontaneous Fermentations ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Primer Sets ◽  
Ssrs Markers ◽  
Wine Flavor ◽  
Simple Sequence

Considering that many Saccharomyces cerevisiae strains exist and that they have different fermentation capacities, the challenge is to select the yeast strain that generates the most interesting wine character and wine flavor for the winemaker. A method based on simple sequence repeats (SSRs) markers, occurring in the yeast genome, was developed to differentiate the collected S.cerevisiae strains. For the amplification of the polymorphic SSR markers performed by polymerase chain reaction (PCR), two primer sets showing different size products for different S. cerevisiae strains were designed. The PCR-method with gel electrophoresis was validated using capillary sequencing and then used as a service for winegrowers combined with a sensory analysis via napping. This approach can be used for the preservation of the yeast diversity associated with given terroirs and as an option for an increased safety of fermentations. The application of S. cerevisiae strains collected in spontaneous fermentations and used for fermentation sustains the initial character of the wine and ensures a secure fermentation at the same time.

scholarly journals Genetic Diversity of Fig (Ficus Carica L.) Germplasm From The Mediterranean Basin As Revealed by SSR Markers

2021 ◽  
Author(s):  
Athanasios Sclavounos ◽  
Petros Roussos ◽  
Sotiria Milla ◽  
Panagiotis Kostas ◽  
Yiannis Samaras ◽  
...  
Keyword(s):  
Geographical Origin ◽  
Allelic Variation ◽  
Principal Coordinate Analysis ◽  
Ficus Carica ◽  
Ex Situ ◽  
Mediterranean Countries ◽  
Ssr Loci ◽  
Genetic Makeup ◽  
Simple Sequence ◽  
The Mediterranean Basin

Abstract Fig (Ficus carica L.) tree is cultivated worldwide and is highly appreciated for its fruit, which is consumed fresh or dried, having high nutritional and pharmaceutical value and for these reasons there is an increasing interest for its cultivation. In the present study, an ex situ collection of 60 fig accessions (41 indigenous Greek and 19 from other Mediterranean countries) was established and its diversity was analyzed using eight simple sequence repeat (SSR) loci. Greek fig genotypes showed relatively low allelic variation (average number of SSR alleles per locus was 3.3), an excess of heterozygosity (mean He = 0.449 and Ho = 0.537), and extensive outbreeding (mean F index -0.184). Cluster analysis showed that the established fig population exhibited weak genetic structure with the majority of the genetic variation (69%) being present within individual members of the clusters. Both cluster and principal coordinate analysis confirmed that there is no correlation between genetic makeup and geographical origin of the fig accessions. Polymorphism information content (PIC) with an average of 0.398 was reasonably informative. An identification key scheme for fig cultivars that will be useful in cultivar discrimination and intellectual property protection was developed. This work will contribute to a sustainable fig production regionally and worldwide, through the establishment and conservation of a reference fig collection, providing germplasm for future breeding efforts.

scholarly journals An Optimised Protocol for Fluorescent-dUTP Based SSR Genotyping and its Application to Genetic Mapping in Eucalyptus

2011 ◽  
Vol 60 (1-6) ◽  
pp. 18-25 ◽  
Author(s):  
F. Li ◽  
S. Gan
Keyword(s):  
Genetic Mapping ◽  
Biological Applications ◽  
Fluorescent Intensity ◽  
Wide Range ◽  
Ssr Loci ◽  
Touchdown Pcr ◽  
Polymerase Chain ◽  
Ssr Genotyping ◽  
Simple Sequence

AbstractIntegration of fluorescent-dUTP in polymerase chain reaction (PCR) appears to be a sound method for fluorescence labelling of amplicons in genotyping with simple sequence repeats (SSRs) using an automated sequence analyser. However, the method has not been explored in terms of performance optimisation and cost control. In this paper, we optimised the protocol for fluorescent-dUTP based SSR genotyping in a case study withEucalyptus. A combination of low dNTP concentration (25 μM each) in PCR reaction and a touchdown PCR programme contributed to increase dramatically the fluorescent intensity of SSR amplicons, thereby facilitating accurate and multiplexed scoring of SSR alleles. The usefulness of the optimised protocol was demonstrated in its application to genetic mapping of SSR loci ontoE. urophyllaandE. tereticornislinkage maps constructed previously. The protocol optimised here would provide a reliable and economical assay for sequencer-based SSR genotyping in a wide range of biological applications.

scholarly journals Transfer of Cornus florida and C. kousa Simple Sequence Repeats to Selected Cornus (Cornaceae) Species

2010 ◽  
Vol 135 (3) ◽  
pp. 279-288 ◽  
Author(s):  
Phillip A. Wadl ◽  
Xinwang Wang ◽  
John K. Moulton ◽  
Stan C. Hokanson ◽  
John A. Skinner ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Related Species ◽  
Breeding Population ◽  
Reaction Products ◽  
Closely Related Species ◽  
Genetic Studies ◽  
Ssr Loci ◽  
Internal Transcribed Spacer Sequences ◽  
Polymerase Chain ◽  
Simple Sequence

Cross-species transferability of simple sequence repeats (SSRs) is common and allows SSRs isolated from one species to be applied to closely related species, increasing the use of previously isolated SSRs. The genus Cornus consists of 58 species that are ecologically and economically important. SSRs have previously been isolated from C. florida and C. kousa. In this study, 36 SSRs were tested on taxa from 18 Cornus species and hybrids for cross-species transferability and genetic diversity was calculated for each locus using polymorphism information content (PIC). Cross-species transferability of SSR loci was higher in more closely related species and PIC values were high. Evidence was found for conserved primer sites as determined by the amplification of SSR loci in the taxa examined. Polymerase chain reaction products were cloned and sequenced for three SSR loci (CF48, CF59, and CF124) and all individuals sequenced contained the appropriate repeat. Phylogenetic relationships of 14 Cornus species were inferred using nucleotide sequences of SSR locus CF48. The most parsimonious tree resulting from this analysis was in concordance with phylogenies based on matK and internal transcribed spacer sequences. The SSR loci tested in this study will be useful in future breeding, population, and genetic studies within Cornus.

scholarly journals Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen

2017 ◽  
Vol 107 (3) ◽  
pp. 322-328 ◽  
Author(s):  
Friederike Busse ◽  
Annette Bartkiewicz ◽  
Diro Terefe-Ayana ◽  
Frank Niepold ◽  
Yvonne Schleusner ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Synchytrium Endobioticum ◽  
Sequence Characterized Amplified Region ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Low Levels ◽  
Taxonomic Studies ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Open Access Article

Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host–pathogen interactions in this difficult pathosystem. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The SUSPECT SYMPTOMS OF INBREEDING DEPRESSION AND THE HOMOZYGOSITY LEVEL OF FOURTH GENERATION OF SP450T AND FIFTH GENERATION OF DURA DELI OIL PALM SELFING POPULATION

2018 ◽  
Vol 24 (2) ◽  
pp. 55-66
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Hernawan Yuli Rahmadi ◽  
Abdul Razak Purba
Keyword(s):  
Inbreeding Depression ◽  
Oil Palm ◽  
Recurrent Selection ◽  
Fourth Generation ◽  
Depression Symptoms ◽  
Reciprocal Recurrent Selection ◽  
Chain Reaction ◽  
Fifth Generation ◽  
Polymerase Chain ◽  
Simple Sequence

Inbreeding is a common method used to reproduce candidate mother plant from selected parental lines for commercial seeds in Reciprocal Recurrent Selection (RRS) oil palm breeding program. However this practice may increased homozigosity level of selected population. This study concerned the level of homozygosity of SP540T fourth generations and Dura Deli Dolok Sinumbah fifth generations (3 crosses respectively) and their correlation with inbreeding depression symptoms. Polymerase Chain Reaction-Simple Sequence Repeat (PCR-SSR) with 16 markers developed for oil palm was used to analyze 327 samples. The result shows that the levels of homozigosity of SP540T fourth selfing generation were ranged between 0.44-0.84 or 0.61 in average. While the levels of homozygosity of Dura Deli fifth selfing generations were ranged between 0.60-0.93 or 0.78 in average. The homozygosity level in Dura Deli was 1.27% higher than SP540T populations. Correlation analysis showed that the higher the level of homozygosity, the higher of the inbreeding symptoms 2 observed (R =0.95).

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.

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