Room-Temperature Single-Nucleotide Polymorphism and Multiallele DNA Detection Using Fluorescent Nanocrystals and Microarrays

2003 ◽  
Vol 75 (18) ◽  
pp. 4766-4772 ◽  
Author(s):  
Daniele Gerion ◽  
Fanqing Chen ◽  
Balaji Kannan ◽  
Aihua Fu ◽  
Wolfgang J. Parak ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Room Temperature ◽  
Dna Detection ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

193 BOVINE EMBRYO GENOTYPING USING A 50K SINGLE NUCLEOTIDE POLYMORPHISM CHIP

2011 ◽  
Vol 23 (1) ◽  
pp. 197 ◽  
Author(s):  
A. D. Le Bourhis ◽  
E. Mullaart ◽  
P. Humblot ◽  
W. Coppieters ◽  
C. Ponsart
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Room Temperature ◽  
Drop Out ◽  
Bovine Embryo ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Good Efficiency ◽  
Student’S T

Genomic tools are now available for most livestock species and are used routinely for marker-assisted selection (MAS) and genomic selection (GS) in cattle. Recently, multiple-marker detection has been achieved from biopsies of preimplantation stage embryos, thus allowing embryos to be selected before transfer (Le Bourhis et al. 2009 Reprod. Fertil. Dev. 21, 192 abst). This strategy provides the opportunity to estimate some traits of particular interest, the presence of genetic abnormalities, or both. The present work aimed to assess the efficiency of MAS/GS evaluation from biopsied bovine embryos by using the bovine 50K single nucleotide polymorphism (SNP) Illumina chip. A biopsy of 5 to 10 cells was obtained under laboratory conditions, using a microblade under a stereomicroscope, from 29 in vitro-cultured morulae and blastocysts. Biopsies were transferred individually as dry samples in tubes and sent frozen (n = 13) or at room temperature (n = 16) to the genotyping laboratory. The genomic DNA of each biopsy was amplified using a whole-genome amplification (WGA) kit according to the manufacturer’s instructions (Qiagen REPLI-g® Mini Kit, Qiagen, Valencia, CA). Following WGA, DNA concentration was determined by using PicoGreen. For subsequent genotyping, a custom CRV 50K Illumina chip was used. Call rates were calculated from 50 905 SNP. Percentage of allele drop-out (%ADO), which was estimated from the number of heterozygous markers [%ADO = (calculated hetero – observed hetero)/calculated hetero]. Parentage error was estimated from 12 embryos by using the genotypes of the parents of the embryos. Both groups of transport conditions were compared using Student’s t-test. Results are presented as mean ± SEM. A greater quantity of DNA was obtained after amplification of biopsies that were sent frozen to the laboratory when compared with those at room temperature (P < 0.05). However, the SNP call rate, %ADO, and parentage error did not differ between groups. These results indicate that genotyping from embryo biopsies following WGA can be achieved with good efficiency when using high-density marker chips. To validate the use of MAS/GS from early embryos in breeding schemes, a larger number of in vivo embryos are currently genotyped under field conditions. This will allow the reliability of this method to be assessed and the correlation between embryo and calf genetic evaluation to be quantified with the current WGA efficiency. Table 1.Amount of DNA after WGA and genotyping results

Detection of single nucleotide polymorphism by measuring extension kinetics with T7 exonuclease mediated isothermal amplification

The Analyst ◽  
2018 ◽  
Vol 143 (1) ◽  
pp. 116-122 ◽  
Author(s):  
Miao Cui ◽  
Xianjin Xiao ◽  
Meiping Zhao ◽  
Bo Zheng
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Sensitivity And Specificity ◽  
Room Temperature ◽  
High Sensitivity ◽  
Isothermal Amplification ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
T7 Exonuclease

Kinetics based detection of single nucleotide polymorphism at room temperature with high sensitivity and specificity.

UTILIZATION OF DNA MARKERS FOR EVALUATING AMYLOSE CONTENT OF GRAIN IN RICE

2013 ◽  
Vol 83 (5) ◽  
Author(s):  
Dương Thanh Thủy ◽  
Taiichiro Ookawa
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amylose Content ◽  
Waxy Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branching Enzymes ◽  
Wx Gene ◽  
High Amylose ◽  
Suitable Marker ◽  
Granule Bound Starch Synthase

The sensory and functional properties of rice are predominantly associated with its amylose content. Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose, while starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Some studies have demonstrated that Wx gene is the major controller of amylose content but there are one or more modifying genes affecting the amylose content. Three markers,  microsatellite, Single – nucleotide – polymorphism (G/T SNP) in Wx gene and Single – nucleotide – polymorphism (T/C SNP) in Sbe1 gene, were tested for their association with amylose content using sixty-nine  rice accessions from twenty countries. Of the three markers, two markers in Wx gene are significantly associated with amylose content. The combination of two markers in Wx gene (haplotypes) explained 83.8% of the variation in amylose content and discriminated the three market classes of glutinous, low, intermediate and high amylose content of rice from each other. And T/C SNP in Sbe1 locus was not a suitable marker for amylose content. Keywords: marker, amylose content, Waxy gene.

Sign in / Sign up

Export Citation Format

Share Document