Characterization of microsatellite loci from Elymus alaskanus and length polymorphism in several Elymus species (Triticeae: Poaceae)

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 455-463 ◽  
Author(s):  
Gen-Lou Sun ◽  
Björn Salomon ◽  
Roland von Bothmer
Keyword(s):  
Genomic Library ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
Dinucleotide Repeats ◽  
Polymerase Chain ◽  
Elymus Species ◽  
Elymus Alaskanus ◽  
Simple Sequence

A size-selected genomic library from Elymus alaskanus was screened for the presence of (GA)n, (GT)n, (CAC)n, and (TCT)n microsatellite sequences. A total of 28 positive clones were found for the two dinucleotide repeats, whereas no positive clones were found for the trinucleotide repeats. Positive clones were sequenced to validate the presence of microsatellites and to generate polymerase chain reaction (PCR) primers, based on the sequences flanking the microsatellite. Primer pairs were designed and evaluated for 18 selected microsatellites. The resulting loci were analysed by PCR for their usefulness as molecular markers in an array of 18 accessions representing E. alaskanus and 10 other Elymus species. PCR amplification revealed alleles for the 18 loci, which varied in having 1-10 alleles in these accessions. In the 18 accessions tested, 7 of the 18 loci were polymorphic, with gene diversity values ranging from 0.54 to 0.80 among all species. Within E. alaskanus, gene diversity values ranged from 0.20 to 0.72, with a mean of 0.48. Polymorphism was also detected within accessions. No clear relationship between total repeat length and the degree of polymorphism was observed in this study. Primer pairs designed to amplify microsatellites in E. alaskanus can be used to generate polymorphism products in other species within the genus. Hence, microsatellites are useful markers for studying both inter- and intra-specific genetic variability within Elymus.Key words: Elymus alaskanus, Triticeae, microsatellites, simple sequence repeats, SSRs, polymorphism.

scholarly journals Characterization of a Suite of 40 EST-derived Microsatellite Markers For Use in Sitka Spruce (Picea sitchensis (Bong.) Carr)

2007 ◽  
Vol 56 (1-6) ◽  
pp. 138-141 ◽  
Author(s):  
S. W. A’Hara ◽  
J. E. Cottrell
Keyword(s):  
Pcr Amplification ◽  
Pcr Primers ◽  
Sitka Spruce ◽  
Mendelian Inheritance ◽  
Picea Sitchensis ◽  
Genetic Population ◽  
Genetic Studies ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract This paper describes 40 novel, data-mined, polymorphic microsatellite loci for use in a QTL association study in Sitka spruce. Publicly available EST sequences of Picea in Genbank were searched in silico for simple sequence repeat (SSR) motifs, principally dinucleotide microsatellites, and PCR primers were designed to flank these regions. PCR amplification was carried out in the progeny of a full-sib family to test simple Mendelian inheritance. For further characterization, the amplification products of Sitka spruce material from unrelated trees were assessed to determine the potential of these loci for population genetic studies. These polymorphic markers therefore represent a valuable tool-kit both for establishing a molecular map of this species and for Picea genetic population studies.

Characterization of a cDNA for Rhesus Monkey Protein C Inhibitor – Evidence for N-Terminal Involvement in Heparin Stimulation

1995 ◽  
Vol 74 (04) ◽  
pp. 1079-1087 ◽  
Author(s):  
Klaus-P Radtke ◽  
José A Fernández ◽  
Bruno O Villoutreix ◽  
Judith S Greengard ◽  
John H Griffin
Keyword(s):  
Rhesus Monkey ◽  
Protein C ◽  
Activated Protein C ◽  
Pcr Amplification ◽  
Amino Acid Sequences ◽  
Heparin Binding ◽  
Reactive Center ◽  
Protein C Inhibitor ◽  
Polymerase Chain

SummarycDNAs for protein C inhibitor (PCI) were cloned from human and rhesus monkey 1 liver RNAs by reverse transcription and polymerase chain reaction (PCR) amplification. Sequencing showed that rhesus monkey and human PCI cDNAs were 93% identical. Predicted amino acid sequences differed at 26 of 387 residues. Pour of these differences (T352M, N359S, R362K, L3631) were in the reactive center loop that is important for inhibitory specificity, and two were in the N-terminal helix (M8T, E13K) that is implicated in glycosaminoglycan binding. PCI in human or rhesus monkey plasma showed comparable inhibitory activity towards human activated protein C in the presence of 10 U/ml heparin. However, maximal acceleration of the inhibition of activated protein C required 5-fold lower heparin concentration for rhesus monkey than for human plasma, consistent with the interpretation that the additional positive charge (E13K) in a putative-heparin binding region increased the affinity for heparin.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

scholarly journals Identification and Evolutionary Characterization of Papillomavirus Sequences in New World Monkeys (Genera Sapajus and Alouatta) from Argentina

2021 ◽  
Author(s):  
Candelaria Sanchez Fernandez ◽  
Elisa M Bolatti ◽  
Andres C.A. Culasso ◽  
Diego Chouhy ◽  
Martin M Kowalewski ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Pcr Primers ◽  
Host Tree ◽  
New World Monkeys ◽  
Alouatta Caraya ◽  
Captive Populations ◽  
L1 Protein ◽  
Viral Sequences ◽  
Northeastern Argentina

Abstract Objective: In this study, we investigated the occurrence of papillomavirus (PV) infection in non-human primates (NHP, Platyrrhine) of northeastern Argentina by using broad-spectrum PCR primers at the L1 gene. In addition, we conducted a phylogenetic and coalescence analysis of viral sequences to explore their evolutionary history and evaluate the co-speciation hypothesis in the context of primate evolution. Methods: We obtained samples of 57 individuals from wild and captive populations of Alouatta caraya, Sapajus nigritus and Sapajus cay. We assessed PV infection by PCR amplification with the CUT primer system and sequencing of 337 bp (112 amino acids) of the L1 protein. The viral sequences were analyzed by phylogenetic and Bayesian coalescence methods to estimate the age of the most common recent ancestor (tMCRA) with BEAST, v1.4.8 software. We evaluated viral/host tree congruence with TreeMap v3.0. Results: We identified two novel putative PV sequences of the genus Gamma- PV in Sapajus sp and Alouatta caraya (SPV1 and AcPV1, respectively). The tMRCA of SPV1 was estimated at 11,941,682 years before present (ybp) and that of AcPV1 at 46,638,071 ybp, both predating the coalescence times of their hosts: 6.4 million years (MYA) and 6.8 MYA, respectively. Based on the comparison of primate and viral phylogenies, we could not reject the null hypothesis that the PV tree is no more congruent with the host tree than a random tree would be (P>0.05). Thus, a model of virus-host coevolution was rejected. Conclusion: This study presents the first report of PV infection in Platyrrhine species from Argentina, expands the range of described hosts for these viruses, and proposes new scenarios for their origin and dispersal.

Characterization of nematode mitochondrial genomes.

2021 ◽  
pp. 250-264
Author(s):  
Danny A. Humphreys-Pereira ◽  
Taeho Kim ◽  
Joong-Ki Park
Keyword(s):  
Polymerase Chain Reaction ◽  
Mitochondrial Genome ◽  
Genome Annotation ◽  
Pcr Amplification ◽  
Gene Identification ◽  
Mitochondrial Genomes ◽  
Pcr Cloning ◽  
Chain Reaction ◽  
Polymerase Chain

Abstract This chapter presents procedures on polymerase chain reaction (PCR) amplification, protocols for PCR, cloning and sequencing, and mitochondrial genome annotation and gene identification for the characterization of nematodes.

Highly polymorphic microsatellite markers in Chamaecyparis obtusa

2001 ◽  
Vol 31 (12) ◽  
pp. 2248-2251 ◽  
Author(s):  
Y Nakao ◽  
H Iwata ◽  
A Matsumoto ◽  
Y Tsumura ◽  
N Tomaru
Keyword(s):  
Microsatellite Loci ◽  
Magnetic Beads ◽  
Genomic Library ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Chamaecyparis Obtusa ◽  
Mendelian Inheritance ◽  
Average Gene Diversity ◽  
Polymorphic Microsatellite ◽  
Average Gene

Nine microsatellite loci in hinoki, Chamaecyparis obtusa (Sieb. et Zucc.) Endl., were identified and characterized. A genomic library, developed using enrichment with magnetic beads, was screened to identify microsatellite repeats (CT/AG). The microsatellite loci, where the alleles were segregated, displayed codominant Mendelian inheritance. Genetic analysis of 16 plus trees and two unrelated individuals of Chamaecyparis obtusa revealed that all loci were highly polymorphic, with an average of 10.3 alleles per locus, and an average gene diversity of 0.77. The applicability of these microsatellite loci was also tested in other species of the Cupressaceae and in Cryptomeria japonica (L.f.) D. Don (Taxodiaceae, a family closely related to Cupressaceae). Polymerase chain reaction (PCR) amplification was successful for about half of the loci of the species in the genus Chamaecyparis. However, the PCR amplification patterns of the 11 species of Cupressaceae showed no clear correlations with their molecular phylogeny. The highly polymorphic microsatellite loci in Chamaecyparis obtusa, identified here, will be useful in studies of hinoki breeding and population genetics.

Identifi cation of Species-Diagnostic Inter Simple Sequence Repeat Markers for Ten Phyllanthus Species

2011 ◽  
Vol 66 (3-4) ◽  
pp. 167-172 ◽  
Author(s):  
Sunil Kumar Senapati ◽  
Subhashree Aparajita ◽  
Gyana Ranjan Rout
Keyword(s):  
Simple Sequence Repeat ◽  
Viral Infections ◽  
Pcr Amplification ◽  
Inter Simple Sequence Repeat ◽  
Diagnostic Markers ◽  
Sequence Repeat ◽  
Botanical Drug ◽  
Polymerase Chain ◽  
Medicinal Plant Material ◽  
Simple Sequence

Phyllanthus has been widely used in traditional medicine as an antipyretic, a diuretic, and to treat liver diseases and viral infections. Correct genotype identification of medicinal plant material remains important for the botanical drug industry. Limitations of chemical and morphological approaches for authentication have generated the need for newer methods in quality control of botanicals. In the present study, attempts were made to identify species- diagnostic markers for ten Phyllanthus species using the inter simple sequence repeat-polymerase chain reaction (ISSR-PCR) fingerprinting method. PCR amplification using seven ISSR primers resulted in significant polymorphism among the populations from different species. P. angustifolius and P. urinaria showed monomorphic frequency of maximum (63.88%) and minimum (20.64%), respectively. Seventeen species-diagnostic markers were identified for seven species (P. acidus, P. emblica, P. fraternus, P. urinaria, P. rotundifolius, P. amarus, and P. angustifolius) while no marker was detected for P. reticulatus, P. nivosus, and P. virgulatus. A maximum of six species-diagnostic markers were identified for P. acidus and a minimum of only one of 755 bp was available for P. amarus. Among the seventeen markers, nine were present in all individuals of particular species. The speciesspecific differences in fragment numbers and sizes could be used as diagnostic markers to distinguish the Phyllanthus species quickly

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 Characterization of simple sequence repeat loci for Peltigera membranacea (lichenized Ascomycota) and its Nostoc photobiont

2021 ◽  
Vol 53 (6) ◽  
pp. 457-465
Author(s):  
Silke Werth ◽  
Stefán Þór Pálsson ◽  
Ólafur S. Andrésson
Keyword(s):  
Simple Sequence Repeat ◽  
Population Genetic ◽  
Common Ground ◽  
Gene Diversity ◽  
Similar Species ◽  
Sequence Repeat ◽  
Genetic Studies ◽  
Unbiased Gene ◽  
Simple Sequence

AbstractTo facilitate population-genetic studies, we developed simple sequence repeat (SSR) markers and a molecular species identification assay for Peltigera membranacea (Ascomycota, Peltigerales), a common ground-dwelling lichen of forest and tundra ecosystems. Additional markers were developed for its Nostoc photobiont. Twenty-one fungal markers for P. membranacea were found to be polymorphic, with the number of alleles ranging from 3–21. Nei's unbiased gene diversity ranged from 0.588 to 0.640 in four significantly structured (FST = 0.059) mycobiont populations. For the Nostoc photobiont, 14 polymorphic SSR were developed, yielding 4–14 alleles each, with gene diversity ranging from 0.062 to 0.771 in four populations showing substantial population structure (FST = 0.278). The new markers developed are suitable for population genetic studies of Peltigera membranacea and of its cyanobiont, and at the same time allowed us to distinguish 98.5% of P. membranacea specimens from morphologically similar species of Peltigera.

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