scholarly journals Comparative analysis of single nucleotide polymorphisms in the nuclear, chloroplast, and mitochondrial genomes in identification of phylogenetic association among seven melon (Cucumis melo L.) cultivars

2016 ◽  
Vol 66 (5) ◽  
pp. 711-719 ◽  
Author(s):  
Qianglong Zhu ◽  
Peng Gao ◽  
Shi Liu ◽  
Sikandar Amanullah ◽  
Feishi Luan
Keyword(s):  
Comparative Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Cucumis Melo ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)

2020 ◽  
Vol 12 (4) ◽  
pp. 611-620
Author(s):  
Chen Ling ◽  
Wu Lixia ◽  
Hou Rong ◽  
Shen Fujun ◽  
Zhang Wenping ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Snp Markers ◽  
Rhinopithecus Roxellana ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Parentage Testing ◽  
International Human

Abstract Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite loci were high informative (mean PIC = 0.599). Meanwhile, 24 of 37 SNP markers were polymorphic and most were low informative (mean PIC = 0.244). For microsatellites, the combined exclusion probability with one-parent-unknown/known (CE-1P/CE-2P) nearly reached 1, while for the SNP markers, CE-2P only reached 0.9582. Under the condition of one parent known/unknown, the CE-2P and CE-1P could meet the international human parental standard (0.9973) by using five or nine microsatellite loci respectively. For SNP markers, we doubled the loci (n = 48) and simulated parentage testing, and the data showed that the CE-2P was 0.998 while the CE-1P was still low. This result indicated that the SNP loci which we used here had low polymorphism and that more loci need to be developed in the future. In addition, we corrected one case of failed identification by excluding siblings and reducing the range of candidate paternities.

Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.)

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 352-360 ◽  
Author(s):  
M Morales ◽  
E Roig ◽  
A J Monforte ◽  
P Arús ◽  
J Garcia-Mas
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Cucumis Melo ◽  
Expressed Sequence Tag ◽  
Primer Extension ◽  
Nucleotide Polymorphisms ◽  
Snp Detection ◽  
Single Nucleotide ◽  
Cucumis Melo L ◽  
Single Primer ◽  
Expressed Sequence

A search was performed for single-nucleotide polymorphisms (SNP) and short insertions–deletions (indels) in 34 melon (Cucumis melo L.) expressed sequence tag (EST) fragments between two distantly related melon genotypes, a group Inodorus 'Piel de sapo' market class breeding line T111 and the Korean accession PI 161375. In total, we studied 15 kb of melon sequence. The average frequency of SNPs between the two genotypes was one every 441 bp. One indel was also found every 1666 bp. Seventy-five percent of the polymorphisms were located in introns and the 3′ untranslated regions. On average, there were 1.26 SNPs plus indels per amplicon. We explored three different SNP detection systems to position five of the SNPs in a melon genetic map. Three of the SNPs were mapped using cleaved amplified polymorphic sequence (CAPS) markers, one SNP was mapped using the single primer extension reaction with fluorescent-labelled dideoxynucleotides, and one indel was mapped using polyacrilamide gel electrophoresis separation. The discovery of SNPs based on ESTs and a suitable system for SNP detection has broad potential utility in melon genome mapping.Key words: SNP, CAPS marker, single primer extension.

Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains

2006 ◽  
Vol 291 (6) ◽  
pp. C1183-C1192 ◽  
Author(s):  
Nancy E. Schlick ◽  
Michael I. Jensen-Seaman ◽  
Kimberly Orlebeke ◽  
Anne E. Kwitek ◽  
Howard J. Jacob ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Model System ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Rat Strains ◽  
Single Nucleotide ◽  
Inbred Rat Strains ◽  
Wild Rat ◽  
Inbred Rat

Rat remains a major biomedical model system for common, complex diseases. The rat continues to gain importance as a model system with the completion of its full genomic sequence. Although the genomic sequence has generated much interest, only three complete sequences of the rat mitochondria exist. Therefore, to increase the knowledge of the rat genome, the entire mitochondrial genomes (16,307–16,315 bp) from 10 inbred rat strains (that are standard laboratory models around the world) and 2 wild rat strains were sequenced. We observed a total of 195 polymorphisms, 32 of which created an amino acid change (nonsynonymous substitutions) in 12 of the 13 protein coding genes within the mitochondrial genome. There were 11 single nucleotide polymorphisms within the tRNA genes, six in the 12S rRNA, and 12 in the 16S rRNA including 3 insertions/deletions. We found 14 single nucleotide polymorphisms and 2 insertion/deletion polymorphisms in the D-loop. The inbred rat strains cluster phylogenetically into three distinct groups. The wild rat from Tokyo grouped closely with five inbred strains in the phylogeny, whereas the wild rat from Milwaukee was not closely related to any inbred strain. These data will enable investigators to rapidly assess the potential impact of the mitochondria in these rats on the physiology and the pathophysiology of phenotypes studied in these strains. Moreover, these data provide information that may be useful as new animal models, which result in novel combinations of nuclear and mitochondrial genomes, are developed.

scholarly journals ASSOCIATION OF IL5, CCL26 AND CCL5 GENE POLYMORPHISMSWITH ATOPIC BRONCHIAL ASTHMA

2010 ◽  
Vol 7 (6) ◽  
pp. 20-24
Author(s):  
O E Voronko ◽  
E V Dmitrieva-Zdorova ◽  
E A Latysheva ◽  
M G Aksenova ◽  
G I Storozhakov ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Bronchial Asthma ◽  
Asthma Severity ◽  
Moscow Region ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Atopic Bronchial Asthma ◽  
Healthy Donors

The purpose of the work. In order to investigate whether single nucleotide polymorphisms С(-703)Т in IL5 gene, T(+2497)G in CCL26 and A(-403)G in CCL5 gene contribute to atopic bronchial asthma development we performed a comparative analysis of alleles and genotypes frequencies of these polymorphisms in Russian patients from Moscow region. Materials and methods. DNA samples from 283 patients with atopic bronchial asthma and 227 healthy donors were genotyped. Results. There were associations neither of С(-703)Т in IL5 gene, T(+2497)G in CCL26 and A(-403)G in CCL5 gene with asthma nor with asthma severity. Conclusion. Therefore, we may conclude that genes responsible for activation and chemotaxis of eosinophils play an insignificant role in susceptibility to development of atopic bronchial asthma, and probably may influence indirectly specific processes that occur in asthma.-

scholarly journals SINGLE NUCLEOTIDE POLYMORPHISMS IN THE D-LOOP REGION OF THE MITOCHONDRIAL GENOMES OF INDIVIDUALS FROM TWO ETHNIC GROUPS KINH AND MANG OF AUSTRO-ASIATIC LANGUAGE FAMILY

2018 ◽  
Vol 16 (2) ◽  
pp. 231-240
Author(s):  
Nguyen Thy Ngoc ◽  
Nguyen Bao Trang ◽  
Nguyen Quang Huy ◽  
Nguyen Dang Ton ◽  
Nguyen Thuy Duong
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Ethnic Group ◽  
Ethnic Groups ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Language Family ◽  
Single Nucleotide ◽  
Loop Region ◽  
Pcr Products ◽  
D Loop

The two hypervariable regions HV-I and HV-II in the D-loop region are the most diverse region in the mitochondrial human genome. These DNA regions have an important role in population genetics and human evolution research. In this study, we identified single nucleotide polymorphisms (SNPs) in the D-loop region of the human mitochondrial DNA genomes of individuals in two Vietnamese ethnic groups: Kinh and Mang. 81 blood samples from 50 Kinh and 31 Mang unrelated individuals were collected for genomic DNA extraction. Using PCR and specific primers, we successfully amplified the two HV-I and HV-II regions with respective sizes of 693 bp and 689 bp. The PCR products then were purified and sequenced. After alignment to the reference mitochondrial genome rCRS (NC_012920.1), 96 SNPs were detected in the Kinh ethnic group, of which many polymorphisms were firstly found in this ethnic and 36 SNPs in the Mang ethnic group. Of the identified 132 SNPs, 16 SNPs were significantly different between the two ethnic groups (p < 0.05). Eight out of the 16 SNPs (T146C, T199C, A16182C, T16217C, T16297C, T16140C, A16183C, T16189C) were frequently found in the Kinh ethnic group but not or only rarely in the Mang ethnic group. On the other hand, 4 SNPs (C151T, A16162G, A16269G, T16271C) were commonly found in the Mang population but rarely in the Kinh population. These findings suggest that although Kinh and Mang belong to one language family (Austro-Asiatic), there is a noticeable diversity in the mitochondrial genomes between these two Vietnamese ethnic groups.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide
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