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.

scholarly journals Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

Forests ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 61 ◽  
Author(s):  
Chengcai Zhang ◽  
Xiaohua Yao ◽  
Huadong Ren ◽  
Jun Chang ◽  
Jun Wu ◽  
...  
Keyword(s):  
Genetic Study ◽  
Polymorphic Information Content ◽  
Genetic Research ◽  
Geographic Origin ◽  
Pcr Amplification ◽  
Genetic Studies ◽  
New Development ◽  
Ssr Loci ◽  
Simple Sequence

Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.

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 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.

scholarly journals Development and characterization of fifteen polymorphic microsatellite loci in Bryconamericus aff. iheringii (Teleostei: Characidae) and cross-amplification in related Characidae species

2018 ◽  
Vol 16 (1) ◽  
Author(s):  
Caroline Apolinário-Silva ◽  
Dhiego G. Ferreira ◽  
Analiza F. Cavenagh ◽  
Nícollas G. O. Aprígio ◽  
Bruno A. Galindo ◽  
...  
Keyword(s):  
Information Content ◽  
Microsatellite Loci ◽  
Polymorphic Information Content ◽  
Neotropical Fish ◽  
Genetic Studies ◽  
Cross Amplification ◽  
Abstract Data ◽  
Polymorphic Microsatellite

ABSTRACT Data on 15 novel microsatellite loci from the Neotropical fish Bryconamericus aff. iheringii are presented here. Analyses of 32 individuals from four different streams revealed 192 different alleles, ranging from four to 32 alleles per locus (mean of 12.8 per locus). Observed and expected heterozygosities ranged from 0.094 to 0.813 and 0.205 to 0.952, respectively. These loci showed high polymorphic information content and will be a resource for genetic studies of B. aff. iheringii. Furthermore, several loci also amplified other small Neotropical Characidae (Piabarchus stramineus and Piabina argentea) and should be useful for these species.

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.

scholarly journals Development and characterization of 24 polymorphic microsatellitelocifor the freshwater fishIchthyoelephas longirostris(Characiformes: Prochilodontidae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2419 ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Márquez
Keyword(s):  
Genetic Diversity ◽  
Migratory Species ◽  
Genetic Stock ◽  
Genetic Studies ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
First Time ◽  
Management And Conservation ◽  
Generation Sequencing

The Neotropical freshwater fishIchthyoelephas longirostris(Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellitelociby using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of theselociwere used to assess the genetic diversity and structure of 193I. longirostrisin three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally,I. longirostriswas genetically different among and across rivers. This first insight about the population genetic structure ofI. longirostrisis crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae.

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.

scholarly journals Molecular characterization of onion (Allium cepa) using RAPD markers

1970 ◽  
Vol 35 (2) ◽  
pp. 313-322 ◽  
Author(s):  
M Maniruzzaman ◽  
ME Haque ◽  
MM Haque ◽  
MA Sayem ◽  
M Al-Amin
Keyword(s):  
Allium Cepa ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Group Method ◽  
Genetic Studies ◽  
Pair Group ◽  
Genetic Level ◽  
Polymerase Chain

A polymerase chain reaction (PCR) based approach, namely random amplified polymorphic DNA (RAPD) analysis was applied to l0 varieties of onion (Allium cepa) in order to assess the degree of polymorphism within the genes and to investigate if this approach was suitable for genetic studies of onion. For this study, ten cultivars of onion were evaluated for variability using a set of 15 random l0-mer primers. The polymorphisms in PCR amplification products were subjected to the unweighed pair group method for arithmetic averages (UPGMA) and plotted in a phenogram. The dendogram constructed from the similarity data showed that all the cultivars analyzed were related. Among them, 12 of the primers revealed scorable (168 bands) polymorphisms between cultivars of A. cepa and the rest did not show polymorphism in their genetic level. In this study, it was found that Bermis and India-2 were more dissimilar and on the other hand, Faridpuri and Bhati were the most similar in their genetic level. Keywords: RAPD; onion; genetic diversity; polymorphism. DOI: 10.3329/bjar.v35i2.5894Bangladesh J. Agril. Res. 35(2) : 313-322, June 2010

scholarly journals MOLECULAR CHARACTERIZATION OF FIVE SELECTED BRINJAL (Solanum melongena L) GENOTYPES USING SSR MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 01-06 ◽  
Author(s):  
A. K. M. Khorsheduzzaman ◽  
M. Z. Alam ◽  
M. M. Rahman ◽  
M. A. K. Mian ◽  
M. I. H. Mian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Banding Pattern ◽  
Genomic Dna ◽  
Molecular Level ◽  
Narrow Range ◽  
Solanum Melongena ◽  
Pcr Amplification ◽  
Simple Sequence

Five brinjal (Solanum melongena L.) genotypes were selected for characterization using Simple Sequence Repeats (SSR) markers. All the genotypes showed considerable variation in respect of morphological, anatomical and biochemical aspects. For study of relatedness, plant genomic DNA was extracted by CTAB based method using 11 randomly selected primers produced from Calgene Inc. USA. The primers developed 22 bands through PCR amplification out of which 15 from 3 primers and were polymorphic. Genetic similarities of SSR profiles were estimated based on Jaccard’s coefficient value. The dendrogram generated two clusters and they were clearly distinct and separated from each other. Cluster-I consisted of genotypes TURBO and BL009; and cluster-II comprised of genotypes EG058, EG075 and ISD006. Genotype TURBO and BL009 were identified as the diverse genotype and showed a maximum of 17% dissimilarity from EG058, EG075 and ISD006. The similarity value ranged from 0.83 to 1.00 which indicated the presence of narrow range of genetic diversity at molecular level but have still a possibility of crossing among the genotypes of two clusters. The banding pattern of different genotypes could be utilized as reference for further comparisons.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17041

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