Analysis of genetic diversity inCitrus

2011 ◽  
Vol 9 (2) ◽  
pp. 218-221 ◽  
Author(s):  
François Luro ◽  
Julia Gatto ◽  
Gilles Costantino ◽  
Olivier Pailly
Keyword(s):  
Genetic Diversity ◽  
Organic Acids ◽  
Metabolic Pathways ◽  
Single Strand Conformation Polymorphism ◽  
Strongly Correlated ◽  
Cultivation Conditions ◽  
Citrus Pulp ◽  
Genes Encoding ◽  
Citrus Juices ◽  
Conformation Polymorphism

Sugar and acidity levels are the main criteria of general fruit quality and for citrus juices pulp, in particular. The constituents of the acidity (organic acids) and the sweetness (glucose, fructose and sucrose) and the genes involved in their regulation have seldom been used to exploreCitrusgenetic diversity. We evaluated the juice composition of primary metabolic components for 87 varieties belonging to the eight majorCitrusspecies grown under the same environmental and cultivation conditions by HPLC. We investigated the sequence polymorphism of nine candidate genes encoding for key enzymes of sugars and organic acids metabolic pathways by single strand conformation polymorphism (SSCP). Whatever the biochemical or molecular analyses, the observed structure ofCitrusdiversity was organized around three groups corresponding to the ancestral species (mandarin, pummelo and citron). As expected, the secondary species were closely related to their putative ancestors except forCitrus aurantium. Biochemical diversity was strongly correlated to molecular SSCP diversity at the genus level but not at the intraspecific level. Compared with other molecular marker types, higher diversity has been observed with SSCP technology, which makes it suitable for future quantitative trait loci mapping approach on gene polymorphism in citrus pulp acidity and sweetness regulation.

Genetic diversity in a remnant population of lake trout (Salvelinus namaycush)

2009 ◽  
Vol 87 (7) ◽  
pp. 642-647 ◽  
Author(s):  
Tina M.J. Giroux ◽  
Douglas P. Chivers ◽  
Michael J. Fitzsimmons ◽  
Neil B. Chilton
Keyword(s):  
Genetic Diversity ◽  
National Park ◽  
Sequence Variation ◽  
Lake Trout ◽  
Single Strand Conformation Polymorphism ◽  
Salvelinus Namaycush ◽  
Nucleotide Variation ◽  
Prince Albert National Park ◽  
Conformation Polymorphism ◽  
Remnant Population

Genetic diversity of the remnant population of lake trout ( Salvelinus namaycush (Walbaum in Artedi, 1792)) in Crean Lake was compared with that for two other populations in the Prince Albert National Park (PANP) using single-strand conformation polymorphism (SSCP) and DNA sequencing analyses of two mtDNA genes. Although there was no sequence variation among individuals for nad5, six different nad2 haplotypes were detected. The Crean Lake population had the least number of haplotypes and lowest nucleotide variation. Also, one common nad2 haplotype in Crean Lake was not detected in the other populations. The results suggest that introductions of lake trout from Wassegam Lake into Crean Lake were unsuccessful with respect to the establishment and (or) reproduction of the stocked fish. Conservation of the remnant population of lake trout in Crean Lake is important because it is genetically distinct from other populations within PANP and in adjacent areas.

scholarly journals Detection of Genetic Diversity in Four Candidate Genes by Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) Analysis of Goats in Sri Lanka

2016 ◽  
Vol 4 (1) ◽  
pp. 133-138
Author(s):  
H.B.P.C. Ariyarathne ◽  
LGS Lokugalappatti ◽  
H.B.S. Ariyaratne ◽  
D.M.S. Munasinghe
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Candidate Genes ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sri Lankan ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Phenotypic Groups ◽  
Conformation Polymorphism

Genetic diversity of Sri Lankan goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymophism in four candidate genes (LALBA, k-CSN3, GnRHR and BMP4) in a sample of 219 goats representing three phenotypic groups. All studied loci were polymorphic, having three morphs for BMP4, LALBA and two morphs for k-CSN3 and GnRHR in the study population. A significant difference between genotypic frequencies for BMP4 and GnRHR genes was found while PIC criterion revealed an intermediate polymorphism for all analyzed phenotypic groups except for k-CSN3 and GnRHR genes. Cross-bred animals for BMP4 gene and nondescript animals for LALBA gene were comparatively more polymorphic according to the effective allele number criterion. This study provides insight into the genetic diversity of Sri Lankan goats, which can be utilized to develop single nucleotide polymorphism markers to be used in association studies, and marker assisted selection.Int J Appl Sci Biotechnol, Vol 4(1): 133-138

scholarly journals Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids

2021 ◽  
Vol 12 ◽  
Author(s):  
Phongthana Pasookhush ◽  
Asmatullah Usmani ◽  
Kowit Suwannahong ◽  
Prasit Palittapongarnpim ◽  
Kamolchanok Rukseree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Single Strand Conformation Polymorphism ◽  
Ssu Rdna ◽  
Single Strand ◽  
Biological Research ◽  
Gene Sequences ◽  
Genetic Diversity Study ◽  
Conformation Polymorphism ◽  
Diversity Study

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the SSU rDNA gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR–single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the SSU rDNA gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the SSU rDNA gene sequences.

scholarly journals Discriminatory Detection of Inhibitor-Resistant β-Lactamases in Escherichia coli by Single-Strand Conformation Polymorphism-PCR

1998 ◽  
Vol 42 (4) ◽  
pp. 879-884 ◽  
Author(s):  
Valérie Speldooren ◽  
Beate Heym ◽  
Roger Labia ◽  
Marie-Hélène Nicolas-Chanoine
Keyword(s):  
Escherichia Coli ◽  
Clavulanic Acid ◽  
Consensus Sequence ◽  
Acid Resistance ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Genes Encoding ◽  
Amoxicillin Clavulanic Acid ◽  
Pcr Method ◽  
Conformation Polymorphism

ABSTRACT Plasmid-mediated mechanisms, comprising TEM hyperproduction, TEM derivative production, and OXA production, lead to amoxicillin-clavulanic acid resistance in enterobacteria. The ability of the single-strand conformation polymorphism (SSCP)-PCR method to differentiate the genes encoding inhibitor-resistant β-lactamases was evaluated with three bla TEM primer pairs. Thebla TEM genes, which were known to be different on the basis of their nucleotide sequences (bla TEM-1A, bla TEM-1B,bla TEM-2, bla TEM-30,bla TEM-32, andbla TEM-35), were identified as different by their electrophoretic mobilities. Thebla TEM-33, bla TEM-34,bla TEM-36, bla TEM-37,bla TEM-38, andbla TEM-39 genes, whose sequence differences have been established by oligotyping, displayed different SSCP profiles for different fragments, suggesting genetic differences in addition to those defined by oligotyping. Confirmed by sequencing, these additional genetic events concerned silent mutations at certain positions and, notably, a G→T transversion at position 1 of the −10 consensus sequence in bla TEM-34,bla TEM-36, bla TEM-37, and bla TEM-39. Applied to eight clinical isolates of Escherichia coli resistant to amoxicillin-clavulanic acid, the SSCP method detected TEM-1 in three strains and TEM-30, TEM-32, and TEM-35 in three other strains, respectively. A novel TEM derivative (TEM-58) was detected in another strain, and the deduced amino acid sequence showed two substitutions: Arg244Ser, which is known to confer amoxicillin-clavulanic acid resistance in TEM-30, and Val261Ile, which has not been described previously. The eighth strain produced an OXA β-lactamase. Given the discriminatory power and the applicability of SSCP-PCR, this method can be proposed as a means of following the evolution of the frequencies of the different inhibitor-resistant β-lactamases.

Allelic diversity of DQA2 exon 2 gene in Egyptian goat populations

2017 ◽  
Author(s):  
Sahar S. Ahmed ◽  
Salah M. Abdel-Rahman ◽  
Paul J. Grobler ◽  
Antoinette Kotzé
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Single Strand Conformation Polymorphism ◽  
Immune Gene ◽  
Exon 2 ◽  
Goat Population ◽  
Allele Composition ◽  
The Difference ◽  
Conformation Polymorphism

The study aimed to assess the genetic diversity of 2-decyl-4-quinazolinyl amine exon2 (DQA2 exon2) gene among the Egyptian goat populations from different agro-climatic areas. Data of diseases distribution as well as blood samples were collected. The data collected for diseases distribution showed differences in the types of diseases between the agro-climatic areas. The Single Strand Conformation Polymorphism technique (SSCP) was used to assess the genetic diversity of DQA2 exon2 gene among the goat populations. The results showed that the DQA2 exon2 gene locus displayed 21 alleles with different frequencies in each of goat population. The gene diversity values among the populations ranged from 0.950± 0.022 to 0.887± 0.033. The difference between the most southern population (Aswan) and the remaining populations translate to significant (P less than 0.05) differentiation for only one population pair (Aswan – Baladi, with FST= 0.055; P= 0.001). Scrutiny of allele composition in these two goat populations showed unique alleles in each population (six in Aswan and four in Baladi). The results of the study suggested that the allelic numbers and allelic composition for the DQA2 exon2 gene among the Egyptian goat populations showed diversity in the immune gene due to the different pathogens exposure.

scholarly journals High Genetic Stability of the Begomovirus Tomato yellow leaf curl Sardinia virus in Southern Spain Over an 8-Year Period

2002 ◽  
Vol 92 (8) ◽  
pp. 842-849 ◽  
Author(s):  
S. Sánchez-Campos ◽  
J. A. Díaz ◽  
F. Monci ◽  
E. R. Bejarano ◽  
J. Reina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Strand Conformation Polymorphism ◽  
Tomato Yellow Leaf ◽  
Sscp Analysis ◽  
Southern Spain ◽  
Yellow Leaf ◽  
Low Genetic Diversity ◽  
Genomic Regions ◽  
Conformation Polymorphism ◽  
Leaf Curl

The evolution of the plant single-stranded DNA virus Tomato yellow leaf curl Sardinia virus (TYLCSV) (genus Begomovirus, family Geminiviridae) has been monitored for 8 years after its appearance in southern Spain. Variation within three genomic regions of 166 TYLCSV isolates collected from three locations was assessed by single-strand conformation polymorphism (SSCP) analysis. According to SSCP, the intergenic region (IR) was the most variable. Low genetic diversity was found within the population and geographical or temporal differences were not evident. Nucleotide sequences of specific genomic regions of haplotypes identified by SSCP indicated close relationships among them. Therefore, the Spanish TYLCSV population appears to represent a single, undifferentiated population. The analysis of IR sequences for a subsample of 76 randomly chosen isolates confirmed the limited genetic diversity revealed by the SSCP analysis. A tendency to a lineal increase in diversity over time was observed in Málaga and Almería subpopulations; however, no accumulation of mutations in single isolates was evident. Negative selection to variation seems to operate to conserve certain regions of the genome. Thus, the low genetic diversity found in the studied TYLCSV population might be the result of a founder effect with subsequent selection against less fit variants arising by mutation.

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