Functional markers for selection of potyvirus resistance alleles at the pvr2-eIF4E locus in pepper using tetra-primer ARMS–PCR

Genome ◽  
2008 ◽  
Vol 51 (9) ◽  
pp. 767-771 ◽  
Author(s):  
Manuel Rubio ◽  
Carole Caranta ◽  
Alain Palloix
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Phenotypic Variation ◽  
Marker Assisted Selection ◽  
Functional Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Arms Pcr ◽  
Codominant Markers ◽  
The World ◽  
Selection Of

Functional markers targeted on single nucleotide polymorphisms (SNPs) responsible for phenotypic variation constitute optimal tools for marker-assisted selection (MAS) of resistance alleles with different specificities. Here, we used the tetra-primer ARMS–PCR procedure to assay SNP signatures of four distinct alleles at the pvr2-eIF4E locus, which controls pepper resistance to several potyviruses. These simple, economical, and codominant markers open the way for MAS of pepper genotypes resistant to the potyviral strains and species that are prevalent in distinct cultivation areas across the world.

scholarly journals A Novel Multiplex Tetra-Primer ARMS-PCR for the Simultaneous Genotyping of Six Single Nucleotide Polymorphisms Associated with Female Cancers

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e62126 ◽  
Author(s):  
Chen Zhang ◽  
Ying Liu ◽  
Brian Z. Ring ◽  
Kai Nie ◽  
Mengjie Yang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Arms Pcr

scholarly journals Identification of Allelic Variation in Drought Responsive Dehydrin Gene Based on Sequence Similarity in Chickpea (Cicer arietinum L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Tapan Kumar ◽  
Neha Tiwari ◽  
Chellapilla Bharadwaj ◽  
Ashutosh Sarker ◽  
Sneha Priya Reddy Pappula ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Drought Tolerance ◽  
Cicer Arietinum ◽  
Allelic Variation ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Residual Moisture ◽  
Single Nucleotide ◽  
The World ◽  
Dehydrin Gene

Chickpea (Cicer arietinum L.) is an economically important food legume grown in arid and semi-arid regions of the world. Chickpea is cultivated mainly in the rainfed, residual moisture, and restricted irrigation condition. The crop is always prone to drought stress which is resulting in flower drop, unfilled pods, and is a major yield reducer in many parts of the world. The present study elucidates the association between candidate gene and morpho-physiological traits for the screening of drought tolerance in chickpea. Abiotic stress-responsive gene Dehydrin (DHN) was identified in some of the chickpea genotypes based on the sequence similarity approach to play a major role in drought tolerance. Analysis of variance revealed a significant effect of drought on relative water content, membrane stability index, plant height, and yield traits. The genotypes Pusa1103, Pusa362, and ICC4958 were found most promising genotypes for drought tolerance as they maintained the higher value of osmotic regulations and yield characters. The results were further supported by a sequence similarity approach for the dehydrin gene when analyzed for the presence of single nucleotide polymorphisms (SNPs) and indels. Homozygous indels and single nucleotide polymorphisms were found after the sequencing in some of the selected genotypes.

scholarly journals Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

2007 ◽  
Vol 89 (4) ◽  
pp. 215-220 ◽  
Author(s):  
B. J. HAYES ◽  
A. J. CHAMBERLAIN ◽  
H. McPARTLAN ◽  
I. MACLEOD ◽  
L. SETHURAMAN ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Single Nucleotide Polymorphisms ◽  
Quantitative Trait ◽  
Marker Assisted Selection ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Angus Cattle ◽  
Genome Wide

SummaryA key question for the implementation of marker-assisted selection (MAS) using markers in linkage disequilibrium with quantitative trait loci (QTLs) is how many markers surrounding each QTL should be used to ensure the marker or marker haplotypes are in sufficient linkage disequilibrium (LD) with the QTL. In this paper we compare the accuracy of MAS using either single markers or marker haplotypes in an Angus cattle data set consisting of 9323 genome-wide single nucleotide polymorphisms (SNPs) genotyped in 379 Angus cattle. The extent of LD in the data set was such that the average marker–marker r2 was 0·2 at 200 kb. The accuracy of MAS increased as the number of markers in the haplotype surrounding the QTL increased, although only when the number of markers in the haplotype was 4 or greater did the accuracy exceed that achieved when the SNP in the highest LD with the QTL was used. A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes.

scholarly journals Selection of single-nucleotide polymorphisms in disease association data

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S93 ◽  
Author(s):  
Jungnam Joo ◽  
Xin Tian ◽  
Gang Zheng ◽  
Jing-Ping Lin ◽  
Nancy L Geller
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Disease Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Association Data ◽  
Selection Of

Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS–PCR

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 414-420 ◽  
Author(s):  
E Chiapparino ◽  
D Lee ◽  
P Donini
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dna Sequences ◽  
Population Studies ◽  
Great Increase ◽  
Nucleotide Polymorphisms ◽  
Database Mining ◽  
Single Nucleotide ◽  
Detection Systems ◽  
Arms Pcr ◽  
Agronomically Important Traits

Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS–PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.Key words: single nucleotide polymorphisms (SNPs), genotyping, barley, tetra-primers ARMS–PCR.

scholarly journals Chromosome 9p21.3 is Associated with Early-Onset Coronary Heart Disease in the Irish Population

2008 ◽  
Vol 25 (2) ◽  
pp. 81-85 ◽  
Author(s):  
Weihua Meng ◽  
Anne E. Hughes ◽  
Chris C. Patterson ◽  
Christine Belton ◽  
Frank Kee ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Single Nucleotide Polymorphisms ◽  
Cause Of Death ◽  
Early Onset ◽  
Nucleotide Polymorphisms ◽  
Irish Population ◽  
Single Nucleotide ◽  
The World ◽  
Family Based

Coronary heart disease (CHD) remains a leading cause of death across the world. A region on chromosome 9p21.3 has been recently reported to be associated with CHD. We evaluated 3 SNPs and 3 common haplotypes in the 9p21.3 region in 1494 individuals from 580 Irish families, where at least 1 member had early-onset (males ≤55yr, females ≤60yr) CHD. Genotypes were determined by multiplex SNaPshot technology. Using the combined TDT/S-TDT test, the 3 single nucleotide polymorphisms (SNP), rs10757274, rs2383206 and rs1333049, were strongly associated with early-onset CHD (p= 2.7 × 10-6, 2.7 × 10-6, 3.8 × 10-7, respectively). Analysis of haplotypes by the TRANSMIT program also showed that the GGC haplotype was associated with early-onset CHD (p= 7.9 × 10-7). In conclusion, using a family-based approach in the Irish population, we have confirmed previous reports of association between a region on chromosome 9p21.3 and early-onset CHD.

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