scholarly journals Gene diversity analysis of mitochondrial DNA, microsatellites and allozymes in landlocked Atlantic salmon

1995 ◽  
Vol 47 (sa) ◽  
pp. 156-163 ◽  
Author(s):  
N. Tessier ◽  
L. Bernatchez ◽  
P. Presa ◽  
B. Angers
Keyword(s):  
Mitochondrial Dna ◽  
Atlantic Salmon ◽  
Gene Diversity ◽  
Diversity Analysis ◽  
Dna Microsatellites

Microsatellite gene diversity analysis in anadromous arctic char, Salvelinus alpinus, from Labrador, Canada

1998 ◽  
Vol 55 (5) ◽  
pp. 1264-1272 ◽  
Author(s):  
Louis Bernatchez ◽  
J Brian Dempson ◽  
Sylvain Martin
Keyword(s):  
Mitochondrial Dna ◽  
Salvelinus Alpinus ◽  
Gene Diversity ◽  
Arctic Char ◽  
Diversity Analysis ◽  
Fine Scale ◽  
Geographic Scale ◽  
Scale Population ◽  
Population Structuring ◽  
Heterozygous Deficiency

We analysed six loci among 257 Arctic char (Salvelinus alpinus) representing seven locations in Labrador and Newfoundland to provide a first assessment of microsatellites gene diversity in anadromous char and to determine the geographic scale of population structuring within the species. The number of alleles per locus varied between 9 and 48, and gene diversity ranged from 0.190 to 0.968. Significant FST and differences in allele frequencies were observed among most samples, as well as heterozygous deficiency, which was indicative of a Wahlund's effect. These results implied the existence of genetically distinct populations on a microgeographic scale (less than 10 km) and that our samples represented an admixture of char from those populations that interchange among rivers for owerwintering, in congruence with tagging investigations. These results indicate that microsatellites potentially offer more sensitivity than allozymes and mitochondrial DNA to infer fine-scale population structure in anadromous arctic char.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

Variation in the mitochondrial DNA of the potential biological control agent Chondrostereum purpureum

2000 ◽  
Vol 77 (10) ◽  
pp. 1490-1498 ◽  
Author(s):  
Tod D Ramsfield ◽  
Simon F Shamoun ◽  
Zamir K Punja ◽  
William E Hintz
Keyword(s):  
Biological Control ◽  
British Columbia ◽  
Mitochondrial Dna ◽  
New Zealand ◽  
Cytochrome B ◽  
Biological Control Agent ◽  
Gene Diversity ◽  
Restriction Enzymes ◽  
Sample Population ◽  
Chondrostereum Purpureum

The mitochondrial DNA (mtDNA) of Chondrostereum purpureum (Pers.:Fr.) Pouzar was extracted and purified, and the size ranged from 51.8 to 66.4 kb. One isolate each from British Columbia, Alberta, Finland, the Netherlands, and New Zealand were found to have identical BamHI mtDNA restriction patterns, resulting in a mitochondrial genome of 63.8 kb. An additional isolate from British Columbia and one from Switzerland had different banding patterns, however, resulting in mitochondrial genomes of 66.4 kb and 51.8 kb, respectively. A sequence-characterized amplified region (SCAR) assay, based on a polymerase chain reaction, was developed to rapidly screen a larger population of 84 isolates from North America, Europe, and New Zealand. Two SCARs, one encoding the NADH 4 gene (3 kb) and the second encoding the ATPase VI and cytochrome b genes (5.1 kb), were digested with 24 restriction enzymes. There were no polymorphisms in the NADH 4 containing SCAR, while a single polymorphism was detected by NsiI in the ATPase VI - cytochrome b containing SCAR. Two mitochondrial haplotypes that were distributed throughout the sample population were thus identified. The coancestry coefficient (<$Q7A0D00000010446D80BFFEFF88A524F5343905055B98C420120907B4DDA9ECB1F0>) for all subpopulations of the sample population was calculated to be 0.0353. The level of gene diversity in the mtDNA ofC. purpureum suggested that the chance introduction of novel mitochondrial genes following biological control applications of the fungus is relatively low.

Mitochondrial DNA variation in Pleistocene and modern Atlantic salmon from the Iberian glacial refugium

2002 ◽  
Vol 11 (10) ◽  
pp. 2037-2048 ◽  
Author(s):  
S. Consuegra ◽  
C. Garcia De Leaniz ◽  
A. Serdio ◽  
M. Gonzalez Morales ◽  
L. G. Straus ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Atlantic Salmon ◽  
Glacial Refugium ◽  
Dna Variation

scholarly journals Rare and fleeting: an example of interspecific recombination in animal mitochondrial DNA

2007 ◽  
Vol 3 (5) ◽  
pp. 554-557 ◽  
Author(s):  
Kate L Ciborowski ◽  
Sofía Consuegra ◽  
Carlos García de Leániz ◽  
Mark A Beaumont ◽  
Jinliang Wang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Atlantic Salmon ◽  
Salmo Trutta ◽  
Sequence Divergence ◽  
F1 Hybrid ◽  
Phylogenetic Studies ◽  
Recombinant Haplotype ◽  
The Individual ◽  
Historical Variation ◽  
Interspecific Recombination

Recombination is thought to occur only rarely in animal mitochondrial DNA (mtDNA). However, detection of mtDNA recombination requires that cells become heteroplasmic through mutation, intramolecular recombination or ‘leakage’ of paternal mtDNA. Interspecific hybridization increases the probability of detecting mtDNA recombinants due to higher levels of sequence divergence and potentially higher levels of paternal leakage. During a study of historical variation in Atlantic salmon ( Salmo salar ) mtDNA, an individual with a recombinant haplotype containing sequence from both Atlantic salmon and brown trout ( Salmo trutta ) was detected. The individual was not an F1 hybrid but it did have an unusual nuclear genotype which suggested that it was a later-generation backcross. No other similar recombinant haplotype was found from the same population or three neighbouring Atlantic salmon populations in 717 individuals collected during 1948–2002. Interspecific recombination may increase mtDNA variability within species and can have implications for phylogenetic studies.

The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar

Gene ◽  
1999 ◽  
Vol 239 (2) ◽  
pp. 237-242 ◽  
Author(s):  
Carolyn D. Hurst ◽  
Sylvia E. Bartlett ◽  
William S. Davidson ◽  
Ian J. Bruce
Keyword(s):  
Mitochondrial Dna ◽  
Atlantic Salmon ◽  
Dna Sequence ◽  
Salmo Salar ◽  
Atlantic Salmon Salmo Salar ◽  
Mitochondrial Dna Sequence

scholarly journals An RNA Sequencing Transcriptome Analysis and Development of EST-SSR Markers in Chinese Hawthorn through Illumina Sequencing

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 82 ◽  
Author(s):  
Suliya Ma ◽  
Wenxuan Dong ◽  
Tong Lyu ◽  
Yingmin Lyu
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Low Cost ◽  
Polymorphism Analysis ◽  
Diversity Analysis ◽  
Large Set ◽  
Mean Values ◽  
Genetic Diversity Analysis ◽  
Geographical Regions

Chinese hawthorn (Crataegus pinnatifida) is an important ornamental and economic horticultural plant. However, the lack of molecular markers has limited the development and utilization of hawthorn germplasm resources. Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) allow precise and effective cultivar characterization and are routinely used for genetic diversity analysis. Thus, we first reported the development of polymorphic EST-SSR markers in C. pinnatifida with perfect repeats using Illumina RNA-Seq technique. In total, we investigated 14,364 unigenes, from which 5091 EST-SSR loci were mined. Di-nucleotides (2012, 39.52%) were the most abundant SSRs, followed by mono- (1989, 39.07%), and tri-nucleotides (1024, 20.11%). On the basis of these EST-SSRs, a total of 300 primer pairs were designed and used for polymorphism analysis in 70 accessions collected from different geographical regions of China. Of 239 (79.67%) pairs of primer-generated amplification products, 163 (54.33%) pairs of primers showed polymorphism. Finally, 33 primers with high polymorphism were selected for genetic diversity analysis and tested on 70 individuals with low-cost fluorescence-labeled M13 primers using capillary electrophoresis genotyping platform. A total of 108 alleles were amplified by 33 SSR markers, with the number of alleles (Na) ranging from 2 to 14 per locus (mean: 4.939), and the effective number of alleles (Ne) ranging from 1.258 to 3.214 (mean: 2.221). The mean values of gene diversity (He), observed heterozygosity (Ho), and polymorphism information content (PIC) were 0.524 (range 0.205–0.689), 0.709 (range 0.132–1.000), and 0.450 (range 0.184–0.642), respectively. Furthermore, the dendrogram constructed based on the EST-SSR separated the cultivars into two main clusters. In sum, our study was the first comprehensive study on the development and analysis of a large set of SSR markers in hawthorn. The results suggested that the use of NGS techniques for SSR development represented a powerful tool for genetic studies. Additionally, fluorescence-labeled M13 markers proved to be a valuable method for genotyping. All of these EST-SSR markers have agronomic potential and constitute a scientific basis for future studies on the identification, classification, and innovation of hawthorn germplasms.

Microsatellite Gene Diversity Analysis in Landlocked Arctic Char from Maine

2002 ◽  
Vol 131 (6) ◽  
pp. 1106-1118 ◽  
Author(s):  
Louis Bernatchez ◽  
James G. Rhydderch ◽  
Frederick W. Kircheis
Keyword(s):  
Gene Diversity ◽  
Arctic Char ◽  
Diversity Analysis
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