scholarly journals Variation and diversity of the breakpoint sequences on 4AL for the 4AL/5AL translocation in Triticum

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 635-641
Author(s):  
Wei Luo ◽  
Nana Qin ◽  
Yang Mu ◽  
Huaping Tang ◽  
Mei Deng ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Chromosomal Rearrangement ◽  
Evolutionary Relationships ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
Insertion And Deletion ◽  
Blast Analysis ◽  
Length Polymorphisms ◽  
Chromosomal Breakpoints

The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on their lengths, which ranged from 2009 to 2552 bp. Cluster analysis showed that they were further divided into three groups. Interesting evolutionary relationships among a few of the species were observed and discussed. Multiple sequence alignment of the 52 sequences made it possible to detect 13 insertion and deletion length polymorphisms (InDels) and 101 single nucleotide polymorphisms (SNPs). Furthermore, several species- or accession-specific SNPs or InDels were also identified. Based on BLAST analysis of the conserved sequences, the breakpoint was narrowed down to a 125 bp fragment. Taken together, the results obtained in this study enrich our understanding of chromosomal breakpoints and will be useful for the identification of other breakpoints in wheat.

scholarly journals Analysis of the genetic diversity of Phalaenopsis orchids with single nucleotide polymorphisms and snap markers derived from the Pto gene

2021 ◽  
Vol 53 (4) ◽  
pp. 620-631
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Functional Link ◽  
Single Nucleotide ◽  
Functional Changes ◽  
Interspecies Variability

The Pto gene is a plant gene that has been reported to be involved in resistance to bacterial pathogens. A partial genomic sequence corresponding to Pto (~449 bp) was isolated from 16 species and four hybrids of Phalaenopsis during 2017 at the Department of Agronomy and Horticulture, IPB University, Bogor, Indonesia. Multiple sequence analysis was performed to find putative single nucleotide polymorphisms (SNPs) and design the corresponding single nucleotide-amplified polymorphism (SNAP) markers, which were in turn used to estimate the genetic diversity of 25 Phalaenopsis species. In total, 20 SNPs, of which 14 were nonsynonymous, were identified from the partial Pto sequences. Eighteen SNAP primers were then developed based on these 14 nonsynonymous and four synonymous SNPs. Validation results showed that 15 SNAP primers showed a polymorphism information content exceeding 0.3, suggesting the existence of more than two alleles for this locus. Upon their use, the SNAP markers described 86% of all interspecies variability. The Pto 52, Pto 349, Pto 229, and Pto 380 SNAP markers were very informative in the determination of genetic diversity. Notably, the existence of these nonsynonymous SNPs implied the possibility of functional changes within the amino acid sequence of the putative PTO protein. Thus, the resulting differences in the activity of the PTO protein may be used to breed tolerance to pathogen infection. Further work may be required to establish a functional link between tolerance to pathogens and the presence of Pto-SNAP markers in Phalaenopsis properly.

scholarly journals DNA analyses and their applications in plant breeding

2012 ◽  
Vol 38 (No. 1) ◽  
pp. 29-40 ◽  
Author(s):  
J. Ovesná ◽  
K. Poláková ◽  
L. Leišová
Keyword(s):  
Molecular Markers ◽  
Fragment Length ◽  
Genome Mapping ◽  
Genome Structure ◽  
Detailed Knowledge ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Expressed Sequence

In recent years, molecular markers have been developed based on the more detailed knowledge of genome structure. Considerable emphasis has been laid on the use of molecular markers in practical breeding and genotype identification. This review attempts to give an account of different molecular markers currently available for genome mapping and for tagging different traits – restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs) and microsatellites. Other markers, expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also mentioned. The importance of structural, functional genomic and comparative mapping is also discussed.

scholarly journals The complete chloroplast genome of Glycyrrhiza uralensis Fisch. isolated in Korea (Fabaceae)

2021 ◽  
Vol 51 (4) ◽  
pp. 353-362
Author(s):  
Mi-Hee KIM ◽  
Suhyeon PARK ◽  
Junho LEE ◽  
Jinwook BAEK ◽  
Jongsun PARK ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Glycyrrhiza Uralensis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Glycyrrhiza Uralensis Fisch ◽  
Insertion And Deletion ◽  
Chloroplast Genomes ◽  
Intraspecific Variations

The chloroplast genome of Glycyrrhiza uralensis Fisch was sequenced to investigate intraspecific variations on the chloroplast genome. Its length is 127,689 bp long (34.3% GC ratio) with atypical structure of chloroplast genome, which is congruent to those of Glycyrrhiza genus. It includes 110 genes (76 protein-coding genes, four rRNAs, and 30 tRNAs). Intronic region of ndhA presented the highest nucleotide diversity based on the six G. uralenesis chloroplast genomes. A total of 150 single nucleotide polymorphisms and 10 insertion and deletion (INDEL) regions were identified from the six G. uralensis chloroplast genomes. Phylogenetic trees show that the six chloroplast genomes of G. uralensis formed the two clades, requiring additional studies to understand it.

scholarly journals Single nucleotide polymorphism rs110861313 in the intergenic region of chromosome 23 is associated with the development of leukosis in the Russian Black Pied cattle

2020 ◽  
Vol 23 (8) ◽  
pp. 999-1005
Author(s):  
R. B. Aitnazarov ◽  
E. V. Ignatieva ◽  
T. A. Agarkova ◽  
N. G. Dvoeglazov ◽  
N. A. Osipova ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Genome Wide Association Study ◽  
Leukemia Virus ◽  
Bovine Chromosome ◽  
Nucleotide Polymorphisms ◽  
Persistent Lymphocytosis ◽  
Gwas Study ◽  
Single Nucleotide ◽  
Length Polymorphisms ◽  
A Genome

In recent years, using a genome-wide association study (GWAS), a number of single nucleotide polymorphisms (SNPs) have been suggested to be associated with susceptibility to leukemia in cattle. However, all studies have been done with purebred Holstein cows and their hybrids. In this regard, it is important to confirm the functional role of polymorphisms previously identified in a GWAS study in Russian cattle breeds. The aim of this study was to verify the association between rs110861313 in the intergenic region of bovine chromosome 23 and leukemia in the Russian Black Pied cattle. Based on the levels of bovine leukemia virus (BLV)-specific antibodies detected in serum using serodiagnostic techniques, animals were divided into three groups: healthy animals (n = 115), asymptomatic virus carriers (n = 145) and animals with leukemia (n = 107). Genotyping of rs110861313 was carried out using polymerase chain reaction followed by analysis of restriction fragment length polymorphisms. A significant decrease in the frequency of the A/A genotype (11.2 %) was revealed in animals with persistent lymphocytosis compared to virus carriers (27.6 %) (p < 0.002). At the same time, the frequency of animals with the C/C genotype in animals with persistent lymphocytosis (41.1 %) was significantly higher than that of virus carriers (21.4 %) (p < 0.001). In this case, asymptomatic virus carriers can be considered a more suitable control than healthy animals that have not been in contact with the virus. According to bioinformatics analysis, resistance to BLV can be due to the presence of the transcription factor FOXM1 binding site in the region of rs110861313. FOXM1 is expressed in immune cells and can potentially affect the expression of the neighboring genes (LY6G5B, GPANK1, ABHD16A, LY6G6F, LY6G6E, CSNK2B, ApoM). Thus, we found that SNP rs110861313 in the intergenic region of bovine chromosome 23 is associated with the development of leukemia following BLV infection in the Russian Black Pied cattle.

scholarly journals The Correlation between Phospholipase C Epsilon (PLCE1) Gene Polymorphisms and Risk of Gastric Adenocarcinoma in Iranian Population

2019 ◽  
Author(s):  
Ramin Shekarriz ◽  
Sahar Faghani ◽  
Alireza Tafazoli ◽  
Mohammad Bagher Hashemi-Soteh
Keyword(s):  
Gastric Cancer ◽  
Phospholipase C ◽  
Tumor Stage ◽  
Tumor Location ◽  
Iranian Population ◽  
Disease Stage ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Length Polymorphisms ◽  
Significant Difference

Background: Phospholipase C epsilon 1 (PLCE1) gene harbors different single nucleotide polymorphisms (SNPs), which can be correlated with the risk of different types of cancers. In this case-control study, the relationship between rs2274223 (A>G), a single nucleotide polymorphism in phospholipase C epsilon gene, (PLCE1) and gastric cancer was evaluated among Iranian patients. Materials and Methods: The PLCE1 rs2274223 polymorphism was genotyped in 60 patients with gastric cancer and 69 control subjects using polymerase chain reaction and restriction fragment length polymorphisms (PCR-RFLP) methods. Clinical and pathologic parameters such as tumor characteristics and disease stage were also recorded. Results: There were 48 (80%) male patients and 45 (65.5%) healthy male individuals (p=0.077). About 34 (56.6%) patients were smokers. A family history of gastric cancer was found in 21 (35%) cases. GG genotype was observed among 15% of patients and 8.7% of normals, respectively. There was no significant difference between the AA and AG genotypes. Also, there were no significant correlations between AA, AG or GG genotypes and the risk of gastric cancer, gender, tumor size, tumor stage, grade, as well as tumor location and metastasis. Conclusion: The PLCE1 rs2274223 polymorphism was not correlated with gastric cancer in Iranian population. However, a further comprehensive study with larger sample sizes is needed.

scholarly journals SNP-E: A New Method For Multiple Sequence Alignments Analysis And Accurate Single Nucleotide Polymorphism Evaluation

2017 ◽  
Vol 3 (1) ◽  
pp. 206-211
Author(s):  
Melody N. Hemmati-Sholeh ◽  
Larry A. Sholeh ◽  
David A. Lightfoot
Keyword(s):  
Computational Method ◽  
Genomic Research ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
Multiple Sequence Alignments ◽  
Microsoft Office ◽  
Change Identification ◽  
Identification Analysis

Identification of single nucleotide polymorphisms (SNPs) and insertion-deletion mutations are important for discovering the connection between the genetic mutations and complex diseases. The objective of this study was to develop a sensitive and accurate computational method for SNP detection among Multiple Sequence Alignments (MSAs) to be run on Microsoft Office SuiteTM and WindowsTM. The SNP-Evaluator, was designed to simulate the process of human eye visual change-identification. Analysis of three 82-Kbp genomic loci derived from Sanger sequencing and the corresponding SNPs from 31 genomes from IlluminaTM sequencing of soybean (Glycine max L. Merr.) demonstrated that the SNP-E was an effective method for medium-scale genomic research.

Use of the Coding Region of Leptospira Sp. LigB C-terminus as a Marker for Diagnostics of Animal Leptospirosis

2020 ◽  
Author(s):  
Vanina Saraullo ◽  
Sylvia Grune Loffler ◽  
Monica Florin Christensen ◽  
Olivia Watanabe ◽  
Micaela Hamer ◽  
...  
Keyword(s):  
Outer Membrane Proteins ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Analytical Sensitivity ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
C Terminus ◽  
High Degree

Abstract BackgroundThe causal agent of leptospirosis, pathogenic strains of the genus Leptospira spp., has Outer Membrane Proteins (OMPs) on its surface which play a fundamental role in infection and pathogenesis. Studies on the genome showed that the LigB protein gene is conserved in different pathogenic species. MethodsThe aim of this work was to propose a new end point PCR based on the amplification of the LigB C-Terminal coding region (ligb-ct), never used before and conserved among pathogenic Leptospira spp. Eighteen reference pathogenic, 2 intermediate and 2 no-pathogenic strains of Leptospira spp. were used. DNA from 10 other microorganism species were included in this study to determine the analytical specificity. ResultsWe obtained 100% positivity for pathogenic Leptospira strains. We found no cross-reaction with intermediate and non-pathogenic strains or with other microorganisms, highlighting a high analytical specificity. Analytical sensitivity estimated on clinical samples was higher on serum than blood and urine (6-9 x 102 lept/ml and 6-9 x 105 and 6-9 x 106 leptospires/ml, respectively). Multiple sequence alignment of this region in positive Leptospira species confirmed a high degree of conservation, with only a few single nucleotide polymorphisms. Conclusion To the best of our knowledge, the LigB C-Terminal coding region has not been previously used for molecular diagnostic and could be used for early diagnosis of leptospirosis.

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