scholarly journals Mutational Analysis of EXT1in a Chinese Family Affected by Hereditary Multiple Osteochondroma

2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Guangzhi Yuan ◽  
Qiang Su ◽  
Wenjun Liao ◽  
Wei Hou ◽  
Linke Huang ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Pathogenic Mutation ◽  
Chinese Family ◽  
Nucleotide Polymorphisms ◽  
Specific Pcr ◽  
Intron Boundary ◽  
Allele Specific ◽  
Exon 9 ◽  
First Time ◽  
Allele Specific Pcr

Objectives. To discuss the mutational features and their relationships with disease in a family with hereditary multiple osteochondroma (HMO) from Guangxi Province (GXBB-1 family), China. Methods. Genomic DNA and total mRNA were extracted from peripheral blood cells of GXBB-1 family members. Whole elements of the EXT1gene and its transcript, including exons, introns, exon-intron boundaries, and coding sequence (CDS) clones, were amplified and sequenced. Allele-specific PCR was used to confirm the position and type of mutation. Results. All patients from the GXBB-1 family harbored the cosegregating heterozygous c.1056+1G>A mutation located in EXT1at an exon-intron boundary. Another three single-nucleotide polymorphisms (SNPs) were also detected in the patients, including IVS2+1G>A in intron 2, c.1844 T>C [p.Pro (CCT) 614Pro (CCC)] in exon 3, and c.2534G>A [p.Glu (GAG) 844Glu (GAA)] in exon 9. The latter two SNPs were synonymous variations. Conclusions. The heterozygous c.1056+1G>A mutation cosegregated with the phenotype, indicating that it is a pathogenic mutation in the GXBB-1 family. This mutation is reported for the first time in Chinese HMO patients. IVS2+1G>A and c.2534G>A have no relationship with the occurrence of disease. However, c.1844 T>C and c.1056+1G>A are linked, and their interaction needs to be further studied. c.1844T>C is a new SNP that has not been reported internationally.

scholarly journals Preventing Favism by Selecting Faba Bean Mutants Using Molecular Markers

2017 ◽  
Vol 3 (1) ◽  
pp. 2-6 ◽  
Author(s):  
Melody Song
Keyword(s):  
Faba Bean ◽  
Expressed Sequence Tag ◽  
Nucleotide Polymorphisms ◽  
Seed Selection ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Faba Beans ◽  
Allele Specific ◽  
Haemolytic Anemia ◽  
Allele Specific Pcr

Faba bean (Vicia faba) is an ancient legume species known for its high protein content. The usage and consumption of the faba bean is limited by a glycoside, vicine-convicine (VC). Consumption of VC causes haemolytic anemia in individuals with the genetic condition called favism. Faba beans with low VC concentration are opening the possibility of reduction of favism disease, but there are many challenges in analyzing VC concentration. The objective of this study was to develop expressed sequence tag (EST) markers that can differentiate between low VC content (LVC) and high VC content (HVC) faba bean genotypes. Three single nucleotide polymorphisms (SNPs) were discovered that distinguished between LVC and HVC genotypes. The SNPs were validated using Kompetitive Allele Specific PCR (KASP) and mass spectrometry phenotyping. Molecular marker SNP 316 (Intron of Medtr2g009270 at 1,851,012 bp) was the most successful marker in differentiating between LVC, HVC, and heterozygous faba bean genotypes. This marker has applications in seed selection and acceleration of breeding programs, which is the first step towards allowing all consumers concerned with the effects of favism to enjoy the nutritional value of faba bean.

scholarly journals Presence of the HPPD Inhibitor Sensitive 1 Gene and ALSS653N Mutation in Weedy Oryza sativa Sensitive to Benzobicyclon

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1576
Author(s):  
Chad Brabham ◽  
Jason K. Norsworthy ◽  
Fidel González-Torralva
Keyword(s):  
Weedy Rice ◽  
Japonica Rice ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Herbicide Resistant ◽  
Rice Plants ◽  
Specific Pcr ◽  
Kasp Assay ◽  
Allele Specific ◽  
Allele Specific Pcr

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha−1, SC formulation) at 30 days after treatment (DAT). Thirty-four percent of plants were homozygous for the HIS1 allele and 98% of these plants exhibited field tolerance. However, the his1 genotype did not always correlate with field data. Only 52% of his1 plants were considered sensitive, indicating that the single nucleotide polymorphisms (SNPs) chosen in the KASP assay are not a reliable tool in predicting his1 homozygous plants. In an additional experiment, 86% of the 344 plants with at least one copy of the ALSS653N trait harbored a HIS1 allele, suggesting fields infested with IMI herbicide-resistant weedy rice are unlikely to be controlled with benzobicyclon.

Molecular haplotyping of tandem single nucleotide polymorphisms by allele-specific PCR

2007 ◽  
Vol 364 (2) ◽  
pp. 153-158 ◽  
Author(s):  
Carmen Cañadas ◽  
Ana Sánchez-de-Abajo ◽  
Juan Manuel Fernández ◽  
Miguel Martín ◽  
Eduardo Diaz-Rubio ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

scholarly journals Multiple SNPs detection for antimalarial pyrimethamine resistance via allele-specific PCR coupled with gold nanoparticles-based lateral flow biosensor

2020 ◽  
Author(s):  
Tingting Jiang ◽  
Yan Huang ◽  
Weijia Cheng ◽  
Yifei Sun ◽  
Wei Wei ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Genetic Diseases ◽  
Lateral Flow ◽  
Nucleotide Polymorphisms ◽  
Multiple Allele ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

Molecular genotyping holds tremendous potential to detect antimalarial drug resistance (ADR) related to single nucleotide polymorphisms (SNPs). However, it suffers from complicated procedures and expensive instruments. Thus, rapid point-of-care testing (POCT) molecular tools are urgently needed for field survey and clinical use. Herein, a POCT platform consisted of multiple allele-specific PCR (AS-PCR) and gold nanoparticles (AuNPs) based lateral flow biosensor was designed and developed for SNPs detection of Plasmodium falciparum dihydrofolate reductase (pfdhfr) gene related to pyrimethamine resistance. The multiple AS-PCR utilized 3' terminal artificial antepenultimate mismatch and double phosphorothioate-modified allele-specific primers. The duplex PCR amplicons with 5' terminal labeled with biotin and digoxin, respectively, could be recognized by streptavidin (SA)-AuNPs on the conjugate pad and then captured by anti-digoxin antibody through immunoreactions on the test line to produce a golden red line for detection. The system was applied to analyze SNPs in Pfdhfr N51I, C59R, and S108N of 98 clinical isolates from uncomplicated P. falciparum malaria patients. Compared with the results of nested PCR followed Sanger DNA sequencing, the sensitivity is all 97.96% (96/98) for the N51I, C59R, and S108N. For specificity, there were 100% (98/98), 95.92% (94/98), and 100% (98/98) for N51I, C59R, and S108N, respectively. The limit of detection is approximately 200 fg/μl for plasmid DNA as the template and 100 parasites/μl for blood filter paper. The established platform not only offers a powerful tool for molecular surveillance of ADR but also is easily extended to interrelated SNP profiles for infectious diseases and genetic diseases.

Authentication of official Da-huang by sequencing and multiplex allele-specific PCR of a short maturase K gene

Genome ◽  
2013 ◽  
Vol 56 (2) ◽  
pp. 109-113 ◽  
Author(s):  
Guojie Xu ◽  
Xueyong Wang ◽  
Chunsheng Liu ◽  
Weidong Li ◽  
Shengli Wei ◽  
...  
Keyword(s):  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Medicinal Treatment ◽  
Matk Gene ◽  
Allele Specific ◽  
Chinese Markets ◽  
Matk Sequence ◽  
Materials Used ◽  
Allele Specific Pcr

Rhubarb (official Da-huang) is an important medicinal herb in Asia. Many adulterants of official Da-huang have been discovered in Chinese markets in recent years, which has resulted in adverse effects in medicinal treatment. Here, novel molecular markers based on a short maturase K (matK) gene were developed for authenticating official Da-huang. This study showed that all the species from official Da-huang were clustered together in one clade in the polygenetic trees based on short matK. Two highly conserved single nucleotide polymorphisms of short matK were mined in the species from official Da-huang. Based on these polymophisms, four improved specific primers of official Da-huang were successfully developed that generated reproducible specific bands. These results suggest that the short matK sequence can be considered as a favorable candidate for distinguishing official Da-huang from its adulterants. The established multiplex allele-specific PCR was determined to be simple and accurate and may serve as a preferable tool for authentication of official Da-huang. In addition, we suggest that short-sized specific bands be developed to authenticate materials used in traditional Chinese medicine.

scholarly journals Developing KASP Markers for Identification of Basmati Rice Varieties

2020 ◽  
Author(s):  
Katherine Steele ◽  
Mark Quinton Tulloch ◽  
Malcolm Burns ◽  
Werner Nader
Keyword(s):  
Microsatellite Markers ◽  
Rice Genome ◽  
Basmati Rice ◽  
Nucleotide Polymorphisms ◽  
Rice Varieties ◽  
Specific Pcr ◽  
Wide Range ◽  
Allele Specific ◽  
Allele Specific Pcr ◽  
Kasp Markers

Abstract Authentication of Basmati rice has relied on microsatellite markers since 2004, but microsatellites cannot distinguish between all of the forty-one Basmati varieties approved in 2017. This study investigated whether single nucleotide polymorphisms (SNP) and insertion/deletion (InDel) variations developed into KASP™ (Kompetitive Allele Specific PCR; LGC Biosearch Technologies) could be used to distinguish between commercial Basmati varieties. Suitable loci were identified by comparing whole genome sequences of 120 diverse rice accessions. Sequences flanking these loci were standardized across a wide range of rice genomes to produce optimal KASP designs. We selected 364 KASP designs to use for genotyping; they were either near to informative microsatellite markers, within the Badh2 and Waxy genes, or distributed throughout the rice genome. Genotypes for 327 KASP were obtained with 255 loci revealing polymorphism in up to 41 samples of approved Basmati varieties and 20 non-Basmati varieties. The varieties genotyped had not been used in the KASP design process. KASP were able to distinguish between commercial Basmati varieties that could not be distinguished with currently available microsatellites. Thirty-seven Basmati varieties could be distinguished from all others with between 3 and 8 KASP markers out of a pool of 98 informative markers. A reduced set of 24 KASP markers could determine whether a sample belongs to one of eight family groups. All of the KASP markers used in this study can be purchased from LGC Biosearch Technologies. These markers have potential to be used by industry for routine testing and regulation.

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