scholarly journals The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Chang Seok Oh ◽  
Soong Deok Lee ◽  
Yi-Suk Kim ◽  
Dong Hoon Shin
Keyword(s):  
Sequence Analysis ◽  
Control Region ◽  
Dna Typing ◽  
Snp Markers ◽  
Snp Analysis ◽  
Coding Region ◽  
Single Nucleotide ◽  
Mtdna Haplogroups ◽  
Coding Regions ◽  
And Control

Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods.

scholarly journals Mutations in the Promoter and Coding Regions of Avr3a Cause Gain of Virulence of Phytophthora sojae to Rps3a in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanhong Hu ◽  
Zhihua He ◽  
Yebin Kang ◽  
Linkai Cui
Keyword(s):  
Sequence Analysis ◽  
Promoter Region ◽  
Transcript Level ◽  
Snp Markers ◽  
Phytophthora Sojae ◽  
Sequence Polymorphism ◽  
Coding Region ◽  
Coding Regions ◽  
Dna Mutations ◽  
Soybean Resistance

Phytophthora sojae threatens soybean production worldwide, and the cultivation of soybean cultivars carrying Rps genes is the most effective way to control this pathogen. However, DNA mutations in the Avr genes of P. sojae can escape recognization of the corresponding Rps genes, leading to the loss of soybean resistance. In this study, we investigated sequence polymorphism and transcript level of the Avr3a gene in Chinese isolates of P. sojae. Twenty-four mutations resulting in five unique Avr3a alleles were discovered in the Avr3a coding region from 32 P. sojae isolates. The Avr3a transcripts were detectable in the isolates containing Avr3a(I), Avr3a(II), Avr3a(III), and Avr3a(IV) but not in the isolates containing Avr3a(V). Promoter and 5'-UTR sequence analysis revealed eight unique mutations in the promoter region of Avr3a(V), suggesting that the mutations could result in the loss of Avr3a(V) transcription. Virulence tests indicated the isolates containing Avr3a(II) and Avr3a(IV) were virulent, suggesting that the mutations in the coding regions of Avr3a(II) and Avr3a(IV) caused the gain of virulence to Rps3a. Based on DNA mutations of Avr3a in virulent alleles, two SNP markers and one PCR-based marker were developed successfully for detecting the virulence of P. sojae isolates to Rps3a. These findings provide new insights into escape mechanisms of Avr3a and effective support for accurate pathotype identification of P. sojae using molecular methods.

scholarly journals DNA Fingerprinting of Closely Related Cultivars of Sweet Cherry

2018 ◽  
Vol 143 (4) ◽  
pp. 282-288 ◽  
Author(s):  
Paul A. Wiersma ◽  
Deniz Erogul ◽  
Shawkat Ali
Keyword(s):  
Ssr Markers ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Snp Markers ◽  
Dna Fingerprint ◽  
Snp Analysis ◽  
Single Nucleotide ◽  
Discriminating Power ◽  
Related Group ◽  
Development Center

Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were evaluated in an effort to reliably DNA fingerprint sweet cherry (Prunus avium L.) cultivars and advanced selections from the breeding program at the Summerland Research and Development Center (Summerland, BC, Canada). SSR markers were found that differentiated the 35 cultivars and selections tested. However, groups of cultivars closely related to the parental cultivars, Lapins and Sweetheart, were differentiated by only a few SSR markers each. These last few markers were discovered by specifically screening within these small groups of cultivars and the resulting markers had lower discriminating power (Dj) statistics within the full set of 35 cultivars and selections. To further characterize the differences in one of these closely related groups, SNP markers were identified in the cultivar Sweetheart and an analysis was made of how these markers segregated into three of its open-pollinated progeny. Large blocks of the ‘Sweetheart’ genome (34%) did not contain informative SNP markers, which was consistent with its ancestry where the cultivar Van is both a parent and grandparent. The three progeny cultivars differed from ‘Sweetheart’ at 14%, 31%, and 29% of the 3011 SNP positions tested. These were located in blocks of linked haplotypes covering from 2.5 to 20 million bps each and were distinct for the three cultivars. The cultivar Staccato®, which required the most effort for SSR marker discrimination, also had the lowest number of SNP position differences from ‘Sweetheart’ (14%). These informative SNP markers were located in only five small regions of the sweet cherry genome, which also contained the discriminating SSR markers and provides an explanation for the difficulty of locating SSR markers for this cultivar. In addition to clearly differentiating these cultivars, this SNP analysis shows the level of variation expected within this closely related group.

scholarly journals Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained

2021 ◽  
Vol 12 ◽  
Author(s):  
Fabien Degalez ◽  
Frédéric Jehl ◽  
Kévin Muret ◽  
Maria Bernard ◽  
Frédéric Lecerf ◽  
...  
Keyword(s):  
Companion Paper ◽  
Potential Effect ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Coding Region ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Variant Annotation ◽  
Coding Regions ◽  
Reliable Genotypes

Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potential effect of grouped or haplotypic variations, often called “multi-nucleotide variants” (MNVs). Here, we used a large RNA-seq dataset to survey MNVs, comprising 382 chicken samples originating from 11 populations analyzed in the companion paper in which 9.5M SNPs— including 3.3M SNPs with reliable genotypes—were detected. We focused our study on in-codon MNVs and evaluate their potential mis-annotation. Using GATK HaplotypeCaller read-based phasing results, we identified 2,965 MNVs observed in at least five individuals located in 1,792 genes. We found 41.1% of them showing a novel impact when compared to the effect of their constituent SNPs analyzed separately. The biggest impact variation flux concerns the originally annotated stop-gained consequences, for which around 95% were rescued; this flux is followed by the missense consequences for which 37% were reannotated with a different amino acid. We then present in more depth the rescued stop-gained MNVs and give an illustration in the SLC27A4 gene. As previously shown in human datasets, our results in chicken demonstrate the value of haplotype-aware variant annotation, and the interest to consider MNVs in the coding region, particularly when searching for severe functional consequence such as stop-gained variants.

scholarly journals Common genetic variants in the TP53 pathway and their impact on cancer

2019 ◽  
Vol 11 (7) ◽  
pp. 578-585 ◽  
Author(s):  
Thibaut Barnoud ◽  
Joshua L D Parris ◽  
Maureen E Murphy
Keyword(s):  
Human Cancer ◽  
Tp53 Gene ◽  
Negative Regulator ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Common Genetic Variants ◽  
Pathway Function ◽  
Tp53 Pathway

Abstract The TP53 gene is well known to be the most frequently mutated gene in human cancer. In addition to mutations, there are > 20 different coding region single-nucleotide polymorphisms (SNPs) in the TP53 gene, as well as SNPs in MDM2, the negative regulator of p53. Several of these SNPs are known to alter p53 pathway function. This makes p53 rather unique among cancer-critical genes, e.g. the coding regions of other cancer-critical genes like Ha-Ras, RB, and PI3KCA do not have non-synonymous coding region SNPs that alter their function in cancer. The next frontier in p53 biology will consist of probing which of these coding region SNPs are moderately or strongly pathogenic and whether they influence cancer risk and the efficacy of cancer therapy. The challenge after that will consist of determining whether we can tailor chemotherapy to correct the defects for each of these variants. Here we review the SNPs in TP53 and MDM2 that show the most significant impact on cancer and other diseases. We also propose avenues for how this information can be used to better inform personalized medicine approaches to cancer and other diseases.

scholarly journals Single Nucleotide Polymorphisms: A Modern Tool to Screen Plants for Desirable Traits

2021 ◽  
Author(s):  
Lovina I. Udoh ◽  
Willie Peggy Obaseojei ◽  
Chiebuka Uzoebo
Keyword(s):  
Marker Assisted Selection ◽  
Target Genes ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Modern Tool

Single nucleotide polymorphism (SNP) represent a change in a single nucleotide within the genome. This can alter the phenotype of an individual within the same species if it occurs in a coding region of the gene. The change in nucleotide can produce desirable characteristic in plants and can become an object for selection. New SNPs have been discovered and subsequently converted to molecular markers using various non-gel based and next generation sequencing platforms. Considering that SNP markers are based on target genes, its abundance in the genome, high automation and multiplexability, has made it a marker of choice and an effective tool for screening plant germplasm for desirable traits. This chapter considers SNP as molecular marker, their discovery and different SNP genotyping methods was documented. A few case studies of SNP as allele specific markers and their association with traits of interest was considered. Thus, highlighting their efficacy as useful tool for marker assisted selection and plant germplasms screening.

scholarly journals Classification of European mtDNAs From an Analysis of Three European Populations

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1835-1850 ◽  
Author(s):  
Antonio Torroni ◽  
Kirsi Huoponen ◽  
Paolo Francalacci ◽  
Maurizio Petrozzi ◽  
Laura Morelli ◽  
...  
Keyword(s):  
Control Region ◽  
Restriction Site ◽  
Sequence Data ◽  
Restriction Analysis ◽  
Nucleotide Substitutions ◽  
Mtdna Haplogroups ◽  
Mtdna Mutations ◽  
Mtdna Sequence ◽  
And Control

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations

Molecular phylogenetics of Acacia subgenera Acacia and Aculeiferum (Fabaceae : Mimosoideae), based on the chloroplast matK coding sequence and flanking trnK intron spacer regions

2003 ◽  
Vol 16 (1) ◽  
pp. 27 ◽  
Author(s):  
Joseph T. Miller ◽  
Randall J. Bayer
Keyword(s):  
Sequence Analysis ◽  
Molecular Phylogenetics ◽  
New World ◽  
Coding Region ◽  
Coding Sequence ◽  
Coding Regions ◽  
Close Affinity ◽  
Molecular Studies ◽  
Cladistic Analyses ◽  
Trnk Intron

The genus Acacia is subdivided into the following three subgenera: subg. Acacia, subg. Aculeiferum and the predominantly Australian subg. Phyllodineae. Morphological and molecular studies have suggested that the tribe Acacieae and genus Acacia are artificial and have a close affinity to the tribe Ingeae. Sequence analysis of the chloroplast trnK intron, including the matK coding region and flanking non-coding regions, were undertaken to examine taxon relationships within Acacia subgenera Acacia and Aculeiferum. Subgenus Acacia is monophyletic while subgenus Aculeiferum is paraphyletic. Within the subgenera, major divisions are found based on biogeography, New World versus African–Asian taxa. These data suggest that characters such as inflorescence and prickle and/or stipule type are polymorphic and homoplasious in cladistic analyses within the subgenera.

scholarly journals Germline mutation analysis of Tpit in Poodle dogs with ACTH-dependent hyperadrenocorticism

2012 ◽  
Vol 64 (4) ◽  
pp. 853-859
Author(s):  
V. De Marco ◽  
L.R. Carvalho ◽  
A.E.C. Billerbeck ◽  
B.B. Mendonça
Keyword(s):  
Genomic Dna ◽  
Terminal Differentiation ◽  
Germline Mutations ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Control Groups ◽  
Single Nucleotide ◽  
Automatic Sequence ◽  
High Incidence ◽  
And Control

There is a high incidence of pituitary-dependent hyperadrenocorticism (PDH) in Poodle dogs, with family members being affected by the disease, suggesting a genetic involvement. Tpit is an obligate transcription factor for the expression of pro-opiomelanocortingene and for corticotroph terminal differentiation. The aim of the present study was to screen the Tpit gene for germline mutations in Poodles with PDH. Fifty Poodle dogs (33 female, 8.71±2.8 years) with PDH and 50 healthy Poodle dogs (32 females, 9.4241 2.8 years) were studied. Genomic DNA was isolated from peripheral blood, amplified by PCR and submitted to automatic sequence. No mutation in the coding region of Tpit was found, whereas the new single nucleotide polymorphism p.S343G, in heterozygous state, was found in the same frequency in both PDH and control groups. We concluded that Tpit gain-of-function mutations are not involved in the etiology of PDH in Poodle dogs.

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