scholarly journals Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

2021 ◽  
Vol 12 ◽  
Author(s):  
Hanjing Liu ◽  
Yuli Zhang ◽  
Zhen Wang ◽  
Yingjuan Su ◽  
Ting Wang
Keyword(s):  
Ssr Markers ◽  
Genetic Information ◽  
Common Type ◽  
Trinucleotide Repeats ◽  
Biological Functions ◽  
Dinucleotide Repeats ◽  
Genetic Studies ◽  
Genetic Groups ◽  
Transcriptome Sequences ◽  
First Time

Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.

scholarly journals An Improved Method for Assessing Simple Sequence Repeat (SSR) Variation in Echinochloa crus-galli (L.) P. Beauv (Barnyardgrass)

Diversity ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 3
Author(s):  
Carlo Maria Cusaro ◽  
Carolina Grazioli ◽  
Francesco Zambuto ◽  
Enrica Capelli ◽  
Maura Brusoni
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Control Strategies ◽  
Intraspecific Variability ◽  
Rice Fields ◽  
Lombardy Region ◽  
Genetic Groups ◽  
Amplification Protocol ◽  
First Time ◽  
Simple Sequence

Echinochloa crus-galli (L.) P. Beauv. (barnyardgrass) is one of the most noxious weeds infesting Italian rice fields. It is characterized by high genetic intraspecific variability and has developed resistance to several classes of herbicides. The aim of our study was to assess, for the first time in Italy, the genetic diversity in E. crus-galli from differently managed rice fields in the Lombardy region (Northern Italy) using eight specific SSR markers. To this purpose, an amplification protocol was optimized, testing different DNA concentrations, PCR mixtures, and temperatures. A total of 48 alleles were identified in 144 samples. SSR fingerprint analysis using R 3.6.3 software (poppr, polysat, and StAMPP) allowed us to handle SSRs as codominant and polyploid data. The results suggested that genetic richness and diversity were high. The analysis of molecular variance (AMOVA) indicated that genetic variation exists mainly between agronomic managements (47.23%) and among populations (37.01%). Hierarchical clustering and PCoA were in concordance with the identification of four distinct genetic groups. Our results confirm that SSR markers represent a valuable and affordable tool for the assessment of E. crus-galli genetic diversity and would grant useful information to plan more targeted, effective, and sustainable control strategies against barnyardgrass. The improved methodology applied here allowed us to assess the genetic variability of an allo-hexaploid species without information loss and biased results.

scholarly journals Genetic diversity among asparagus species and cultivars using SSR markers

2018 ◽  
Vol 4 (2) ◽  
pp. 21-32
Author(s):  
M Idrees ◽  
M Irshad ◽  
ML Pathak ◽  
A Tariq ◽  
R Naeem
Keyword(s):  
Ssr Markers ◽  
Stop Codon ◽  
Curcuma Longa ◽  
Genetic Relationships ◽  
Trinucleotide Repeats ◽  
Asparagus Officinalis ◽  
Dinucleotide Repeats ◽  
Ssr Primers ◽  
Cluster A ◽  
Polymorphic Bands

The aim of the present study was used to develop SSR markers and to determine genetic relationships among Asparagus species and its cultivars. We mined 72953 Asparagus nucleotide sequences from NCBI and were analyzed. In total, 143 SSRs from 1943 SSRs containing sequences were identified. Of these, 13.6 % were dinucleotide repeats and 2.3 % were trinucleotide repeats. The most frequent dinucleotide repeat motif was AA/TT (73.9 %). The percentage of tri-nucleotide motifs was highest which coded for stop codon (36 %), whereas the Glycine was least present (4.5%). Among the total of 14 SSR primers used, 10 markers yielded 144 (92.3 %) polymorphic bands with an average of 14.4 alleles per primer. Cluster analysis based on UPGMA grouped the Asparagus species and its cultivars into two main clusters. Cluster A contained only A. grecilius which is more diverse than others, while cluster B was further clustered into two sub clusters. Cluster I was comprised of Asparagus officinalis cultivars and cluster II was comprised of Asparagus wild species. Furthermore, these primers (42.8%) were found to be transferable in other medicinal plants (Curcuma longa L. and Saussurea costus). The results suggest that SSR markers are sufficiently useful and powerful to assess genetic relationships and diversity analysis in Asparagus and A. officinalis cultivars. Furthermore, these markers will be particularly useful for evolutionary and genetic mapping studies in Asparagus. J. Biodivers. Conserv. Bioresour. Manag. 2018, 4(2): 21-32

scholarly journals Discovery of novel SSR markers from transcriptome data of Astronium fraxinifolium Schott, a threatened tree species in Brazil

2020 ◽  
Author(s):  
Maiara Cornacini ◽  
Ricardo Oliveira Manoel ◽  
Marcelo Alcantara ◽  
Mário Moraes ◽  
Edvaldo Silva ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Tree Species ◽  
Natural Populations ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Endangered Tree ◽  
Genetic Studies ◽  
Endangered Tree Species ◽  
Ssr Loci ◽  
First Time

Abstract Background Astronium fraxinifolium is an endangered tree species from Brazil. Due to its high importance for environmental reforestation, as well as for the use of its wood, it is necessary to implement management programs for conservation of this species. Simple sequence repeats (SSR) or microsatellite markers have been widely used in population genetic studies across diverse organisms. In this study, we reported for the first time SSR markers for A. fraxinifolium as well as its frequency and distribution from transcriptome data. Results More than 125 thousand RNA-seq sequences derived microsatellites, with predominant distribution of trinucleotides repeats. From the initial screening, we selected 20 microsatellite loci, validated and evaluated genetic indexes in two natural populations. All loci were polymorphic, ranging from four to eleven alleles per locus. The observed and expected heterozygosities ranged from 0 to 1.0 and from 0.533 to 1.0, respectively. Genetic differentiation between populations (= 0.363) showed higher diversity within than among populations. Conclusions The developed SSR loci from RNA-seq consists in a base for future studies of genetic diversity and population structure, mating system and gene flow in A. fraxinifolium populations as well as related species, aiming the conservation and management of the species.

scholarly journals Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 481 ◽  
Author(s):  
Chen ◽  
Lin ◽  
Xie ◽  
Zhong ◽  
Zhang ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Single Molecule ◽  
Functional Categories ◽  
Genetic Studies ◽  
Sequencing Technologies ◽  
Clusters Of Orthologous Groups ◽  
Long Read ◽  
Main Gene ◽  
First Time ◽  
Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

History of Headache Research in Denmark

Cephalalgia ◽  
2001 ◽  
Vol 21 (7) ◽  
pp. 748-752 ◽  
Author(s):  
P Tfelt-Hansen
Keyword(s):  
Migraine With Aura ◽  
Tension Type Headache ◽  
Regional Cerebral Blood ◽  
Danish Population ◽  
Genetic Studies ◽  
History Of ◽  
Headache Clinic ◽  
Type Headache ◽  
Acute Headache ◽  
First Time

Headache research in Denmark started with the description in 1949 by Dalsgaard-Nielsen of the percutaneous nitroglycerin test. In 1976 Jes Olesen started The Copenhagen Acute Headache Clinic and from that time modern headache research began in Denmark. Specific changes in regional cerebral blood flow during attacks of migraine with aura, spreading oligaemia, were described for the first time in 1980. The first headache classification with operational diagnostic criteria was published in 1988 and used in a Danish population study from 1989. The lifetime prevalence of migraine was 8% in men and 25% in women. An intravenous nitroglycerin test was introduced in 1989 and has been developed as an experimental headache model. In 1993 it was suggested by Jes Olesen et al. that NO supersensitivity could be a possible molecular mechanism of migraine pain. Recent genetic studies have supported the distinction between migraine with aura and migraine without aura. From the middle of the 1980s the pathophysiology of tension-type headache has been investigated and recent results indicate central sensitization in patients with chronic tension-type headache.

scholarly journals Nucleic Acids Chemistry and Engineering: Special Issue on Nucleic Acid Conjugates for Biotechnological Applications

2021 ◽  
Vol 11 (8) ◽  
pp. 3594
Author(s):  
Tamaki Endoh ◽  
Eriks Rozners ◽  
Takashi Ohtsuki
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Genetic Information ◽  
Biotechnological Applications ◽  
Biological Functions ◽  
Primary Sequence ◽  
Special Issue

Nucleic acids not only store genetic information in their primary sequence but also exhibit biological functions through the formation of their unique structures [...]

scholarly journals Genetic and Antigenic Characterization of Avian Avulavirus Type 6 (AAvV-6) Circulating in Canadian Wild Birds (2005–2017)

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 543
Author(s):  
Tamiko Hisanaga ◽  
Catherine Soos ◽  
Nicola Lewis ◽  
Oliver Lung ◽  
Matthew Suderman ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Fusion Gene ◽  
Full Genome ◽  
Genome Sequences ◽  
Viral Shedding ◽  
Genetic Groups ◽  
Antigenic Characterization ◽  
Specific Pathogen ◽  
First Time

We describe for the first time the genetic and antigenic characterization of 18 avian avulavirus type-6 viruses (AAvV-6) that were isolated from wild waterfowl in the Americas over the span of 12 years. Only one of the AAvV-6 viruses isolated failed to hemagglutinate chicken red blood cells. We were able to obtain full genome sequences of 16 and 2 fusion gene sequences from the remaining 2 isolates. This is more than double the number of full genome sequences available at the NCBI database. These AAvV-6 viruses phylogenetically grouped into the 2 existing AAvV-6 genotype subgroups indicating the existence of an intercontinental epidemiological link with other AAvV-6 viruses isolated from migratory waterfowl from different Eurasian countries. Antigenic maps made using HI assay data for these isolates showed that the two genetic groups were also antigenically distinct. An isolate representing each genotype was inoculated in specific pathogen free (SPF) chickens, however, no clinical symptoms were observed. A duplex fusion gene based real-time assay for the detection and genotyping of AAvV-6 to genotype 1 and 2 was developed. Using the developed assay, the viral shedding pattern in the infected chickens was examined. The chickens infected with both genotypes were able to shed the virus orally for about a week, however, no significant cloacal shedding was detected in chickens of both groups. Chickens in both groups developed detectable levels of anti-hemagglutinin antibodies 7 days after infection.

scholarly journals Quantifying the prevalence of assortative mating in a human population

2019 ◽  
Author(s):  
Klaus Jaffe
Keyword(s):  
Assortative Mating ◽  
Genetic Relatedness ◽  
Random Mating ◽  
Human Populations ◽  
Genetic Composition ◽  
Genetic Studies ◽  
Maintenance Of Sex ◽  
Animal Populations ◽  
The Uk ◽  
First Time

AbstractFor the first time, empirical evidence allowed to construct the frequency distribution of a genetic relatedness index between the parents of about half a million individuals living in the UK. The results suggest that over 30% of the population is the product of parents mating assortatively. The rest is probably the offspring of parents matching the genetic composition of their partners randomly. High degrees of genetic relatedness between parents, i.e. extreme inbreeding, was rare. This result shows that assortative mating is likely to be highly prevalent in human populations. Thus, assuming only random mating among humans, as widely done in ecology and population genetic studies, is not an appropriate approximation to reality. The existence of assortative mating has to be accounted for. The results suggest the conclusion that both, assortative and random mating, are evolutionary stable strategies. This improved insight allows to better understand complex evolutionary phenomena, such as the emergence and maintenance of sex, the speed of adaptation, runaway adaptation, maintenance of cooperation, and many others in human and animal populations.

scholarly journals aS1-Casein Lineage Assessed by RFLP in the Endangered Goat Breed “Retinta Extremeña”

2015 ◽  
Vol 5 (1) ◽  
pp. 32
Author(s):  
José L. Fernández-García ◽  
María P. Vivas Cedillo
Keyword(s):  
Fatty Acid Content ◽  
Raw Milk ◽  
Allelic Frequency ◽  
Null Alleles ◽  
Goat Breed ◽  
Genetic Studies ◽  
Animal Genetic Resources ◽  
Pcr Rflp ◽  
Conservation Plans ◽  
First Time

<p class="1Body">The Retinta Extremeña goat is a well-adapted breed to "Dehesa" environment. Traditionally their raw milk is used to make artisan cheese. However, crosses with specialized breeds are occurring since the eighties, this goat breed has been declared of special protection by the Spanish Agriculture Ministry (R.D. 1682/1997 and R.D. 229/2008). Genetic studies about casein variants have been mainly performed on Spanish goats of high milk yields because the caseins are a relevant fraction of milk. But recent studies claimed to study the caseins in all breeds, including threatened goat breeds to decide about its conservation value. This study was focused on the aS1-casein in the endangered “Retinta Extremeña” goat for the first time to enhance its conservation interest. Genomic DNA of seventy five pureblood goats was studied. A PCR-RFLP assay was designed to find a B<em>my</em>I target that distinguishing A versus B2 lineages (including recombinant variant M and B1, respectively) of the aS1-casein locus. The allelic frequency of variants related to A lineage (CAG triplet) was 14.0% similar to other southwestern Spanish breeds. It is suggested that individuals or families carrying A lineage should be more studied to detect less allergen null alleles while the opposite allele pools of the B2 lineages should be tested for alleles associated to unsaturated fatty acid content. Therefore, the priorities for conservation plans of animal genetic resources as threatened goat breeds; more investigation is claimed in the aim to study for proved useful alleles of certain genes, as casein variants.</p>

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