scholarly journals Fine Mapping of a Grain Shape Gene from a Rice Landrace Longliheinuo-Dwarf (Oryza sativa L. ssp. japonica)

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 380 ◽  
Author(s):  
Fei Shang ◽  
Xu Chao ◽  
Kaiwen Meng ◽  
Xianghe Meng ◽  
Qin Li ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Grain Shape ◽  
Agronomic Traits ◽  
Stop Codon ◽  
Oryza Sativa L ◽  
Premature Stop Codon ◽  
Nucleotide Polymorphisms ◽  
Genetic Population ◽  
Single Nucleotide

Identification of grain shape genes can facilitate breeding of rice cultivars with optimal grain shape and appearance quality. In this study, we selected two rice germplasms, namely Longliheinuo-dwarf (LH) and N643, with different grain shape, to construct a genetic population for quantitative trait locus (QTL) analysis. A major QTL (qGS7), controlling the ratio of grain length to grain width, was mapped on the chromosome 7 in a BC1F4 line. By high-resolution linkage analysis, qGS7 was delimited to a 52.8 kb region including eight predicted genes. Through sequence alignment and real-time PCR expression analysis of these ORFs, ORF3 (LOC_Os07g42410) was selected as the candidate gene for further analysis. Single nucleotide polymorphisms (SNP) diversity analysis of ORF3 revealed that a single nucleotide deletion in the 7th exon resulted in a frameshift in parent LH and the parent in which a premature stop codon was identified. It was a rare mutation that caused grain shape difference. Real-time PCR analyses showed that the expression characteristics of ORF3 was in accordance with the development of spikelets. Of the 18 agronomic traits investigation in qGS7 near isogenic lines (NILs) showed that qGS7 not only changed grain shape but also affected plant height, panicle curvature, panicle length, the length of second leaf from the top, and chalkiness.

Loss of heterozygosity testing using real-time PCR analysis of single nucleotide polymorphisms

2005 ◽  
Vol 132 (3) ◽  
pp. 200-204 ◽  
Author(s):  
Tamara Čačev ◽  
Mladen Jokić ◽  
Radan Spaventi ◽  
Krešimir Pavelić ◽  
Sanja Kapitanović
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Loss Of Heterozygosity ◽  
Real Time Pcr ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Short PNA molecular beacons for real-time PCR allelic discrimination of single nucleotide polymorphisms

2004 ◽  
Vol 18 (2) ◽  
pp. 117-122 ◽  
Author(s):  
Kenneth Petersen ◽  
Ulla Vogel ◽  
Eszter Rockenbauer ◽  
Kirsten Vang Nielsen ◽  
Steen Kølvraa ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Real Time Pcr ◽  
Molecular Beacons ◽  
Nucleotide Polymorphisms ◽  
Allelic Discrimination ◽  
Single Nucleotide

scholarly journals Detection of the Brachyspina mutation in Uruguayan Holstein cows using real time PCR and melting curve analysis

2021 ◽  
Vol 51 (9) ◽  
Author(s):  
María Teresa Federici Rodriguez ◽  
Rody Artigas ◽  
Sofía Guerra ◽  
Andrea Branda Sica ◽  
Noelia Vázquez ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Stop Codon ◽  
Low Cost ◽  
Melting Curve ◽  
Premature Stop Codon ◽  
Curve Analysis ◽  
Assay Method ◽  
Melting Curve Analysis ◽  
Group I

ABSTRACT: Brachyspina syndrome (BS) is a rare monogenic autosomal recessive hereditary disorder of the Holstein Fresian breed caused by a deletion of 3.3Kb in the Fanconi anemia complementation group I (FANCI) gene on BTA-21, which leads to a frame-shift and premature stop codon. Some of the consequences of BS are the reduction of the fertility rate and milk production. This study developed a simple, sensitive, rapid cost- effective assay method based on real time PCR and melting curve analysis for the detection of BS carrier animals. Sixty-eight normal homozygous and four heterozygous carrier genotypes were detected and confirmed through traditional PCR- electrophoresis analysis. We concluded that the assay we have developed proved to be a reliable, highly precise and low-cost tool, which could be used to monitor the presence of the BS mutation in uruguayan Holstein breed.

scholarly journals Real-Time PCR Assays of Single-Nucleotide Polymorphisms Defining the Major Brucella Clades

2008 ◽  
Vol 46 (7) ◽  
pp. 2474-2474
Author(s):  
J. T. Foster ◽  
R. T. Okinaka ◽  
R. Svensson ◽  
K. Shaw ◽  
B. K. De ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Real Time Pcr ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pcr Assays

scholarly journals Quantification of donor and recipient hemopoietic cells by real-time PCR of single nucleotide polymorphisms

Leukemia ◽  
2003 ◽  
Vol 17 (3) ◽  
pp. 630-633 ◽  
Author(s):  
F Maas ◽  
N Schaap ◽  
S Kolen ◽  
A Zoetbrood ◽  
I Buño ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Real Time Pcr ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hemopoietic Cells

scholarly journals Closed-Tube Genotyping with Unlabeled Oligonucleotide Probes and a Saturating DNA Dye

2004 ◽  
Vol 50 (8) ◽  
pp. 1328-1335 ◽  
Author(s):  
Luming Zhou ◽  
Alexander N Myers ◽  
Joshua G Vandersteen ◽  
Lesi Wang ◽  
Carl T Wittwer
Keyword(s):  
High Resolution ◽  
Real Time ◽  
Real Time Pcr ◽  
Oligonucleotide Probes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Melting Curves ◽  
Unlabeled Probe ◽  
Closed Tube ◽  
Melting Analysis

Abstract Background: Homogeneous PCR methods for genotyping usually require fluorescently labeled oligonucleotide probes. Amplicon melting with the DNA dye LCGreen™ I was recently introduced as a closed-tube method of genotyping that does not require probes or real-time PCR. However, some single-nucleotide polymorphisms (SNPs) could not be completely genotyped without addition of a known genotype, and high-resolution melting techniques were necessary. Methods: A 3′-blocked, unlabeled oligonucleotide probe and the saturating dye, LCGreen I, were added to standard PCR reagents before amplification. After PCR, the samples were melted at 0.1–0.3 °C/s in high-resolution (HR-1™), high-throughput (LightTyper™), and rapid-cycle, real-time (LightCycler®) instruments, and fluorescence melting curves were recorded. Results: Derivative melting curves of the probe–target duplexes were characteristic of the genotype under the probe. With synthetic plasmid templates, all SNP base combinations could be genotyped. For human genomic DNA, the technique was demonstrated with mutations associated with cystic fibrosis, including SNPs (G542X, I506V, and F508C) and 3-bp deletions (F508del and I507del). Conclusions: Genotyping of SNPs and small deletions by melting analysis of an unlabeled probe in the presence of LCGreen I is simple and rapid. Only three unlabeled oligonucleotides (two primers and one probe), a saturating DNA dye, PCR, and a melting instrument are required. The method is closed-tube, does not require fluorescently labeled probes or real-time PCR, and can be completed in <10 min on any instrument capable of monitoring melting curves by fluorescence.

scholarly journals TaqMan Real-Time PCR Assays for Single-Nucleotide Polymorphisms Which Identify Francisella tularensis and Its Subspecies and Subpopulations

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e107964 ◽  
Author(s):  
Dawn N. Birdsell ◽  
Amy J. Vogler ◽  
Jordan Buchhagen ◽  
Ashley Clare ◽  
Emily Kaufman ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Francisella Tularensis ◽  
Real Time Pcr ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pcr Assays
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