Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat.

@article{Holland2001PolymorphismOP,
  title={Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat.},
  author={James Brendan Holland and S. J. Helland and Natalya Sharopova and David C. Rhyne},
  journal={Genome},
  year={2001},
  volume={44 6},
  pages={
          1065-76
        }
}
Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for… Expand
Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants
TLDR
It is proposed that this method could be used in conjunction with RAPD markers for applications such as genetic analysis, bulked segregant analysis, and quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis. Expand
Comparative Analysis of SSR Markers Developed in Exon, Intron, and Intergenic Regions and Distributed in Regions Controlling Fruit Quality Traits in Prunus Species: Genetic Diversity and Association Studies
TLDR
Values prove the low level of polymorphism of the exonic (gene-coding regions) markers of the SSR markers, highlighting the importance of using molecular markers able to discriminate between the functional roles of the gene allelic variants. Expand
Development of intron length polymorphism markers in cowpea [Vigna unguiculata (L.) Walp.] and their transferability to other Vigna species
TLDR
Dendrograms based on CilP markers clearly distinguished the cowpea genotypes as well as other Vigna species, demonstrating the utility of CILP markers in genetic diversity and phylogenetic studies. Expand
Expansion of PCR‐based Marker Resources in Oat by Surveying Genome‐Derived SSR Markers from Barley and Wheat
TLDR
This study indicates that genomic SSR primer pairs from wheat and barley may be a good way to efficiently generate PCR-based DNA markers for oat genetics research. Expand
CAAT box- derived polymorphism (CBDP): a novel promoter -targeted molecular marker for plants
TLDR
Given the high success rate of CBDP primers in generating markers in the tested species and advantages like ease in marker development and assay with reproducible profiles, they could potentially be exploited in other species as well for assessing genetic diversity, cultivar identification, construction of linkage map and marker- assisted selection. Expand
BREEDING AND GENETICS Predicting Intron Sites by Aligning Cotton ESTs with Arabidopsis Genomic DNA
TLDR
Cotton introns were identified with a 92% success rate, based on the alignment of Cotton ESTs with Arabidopsis genomic DNA, which demonstrated that this approach is both feasible and practical for predicting the locations of introns in cotton ESTs. Expand
From genes to markers: exploiting gene sequence information to develop tools for plant breeding.
TLDR
This chapter discusses how gene sequences are obtained and aligned and how polymorphic sites can be identified or predicted and explains how markers can be evaluated (validated) for use in plant breeding. Expand
Microsatellite markers - a new practice of DNA based markers in molecular genetics.
TLDR
The present review has described the various characteristic features and properties of these highly polymorphic microsatellite markers, which found beneficial in several molecular genetic and breeding applications. Expand
A Set of New Simple Sequence Repeat and Avenin DNA Markers Suitable for Mapping and Fingerprinting Studies in Oat (Avena spp.)
TLDR
The markers were able to distinguish closely related lines for fingerprinting purposes and were also useful for determining whether variation within a line was the result of residual heterozygosity or contamination and whether crossing and backcrossing had been successful. Expand
EST‐derived microsatellites as a rich source of molecular markers for oats
TLDR
A remarkable enhancing of the number of mapped oat microsatellite loci could be achieved using a set of recently published expressed sequence tags for microsatellites with dinucleotide, trinucleotide and tetranucleotide repeat motifs. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 45 REFERENCES
Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer.
TLDR
It is concluded that microsatellites can be a valuable tool for maize mapping by verifying the existence of the original SSRs in the segregating PCR products and reamplifying these products. Expand
Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.)
TLDR
The highest overall degree of genetic diversity was seen in GA-containing microsatellites of genomic library origin, while the most conserved markers contained CCG- or CAG-trinucleotide motifs and were developed from GenBank sequences. Expand
Simple sequence repeats for germplasm analysis and mapping in maize.
TLDR
Simple sequence repeats are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes that are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. Expand
Maize simple repetitive DNA sequences: abundance and allele variation.
TLDR
A database survey of 576 maize sequences from the GenBank and EMBL databases was made to determine the abundance of maize microsatellites and the three most abundant classes were (AG/CT), (CCT/GGA)n, and (CCG/GGC)n repeats. Expand
A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymousExpand
Polymorphic Intron Sequences Detected within and between Populations of the Oriental Fruit Fly (Diptera: Tephritidae)
TLDR
This work used the polymerase chain reaction (PCR) and exon-primed intron-crossing (EPIC) primers to amplify the intron sequences of an actin gene from individuals representing 2 different laboratory and 3 different wild Bactrocera dorsalis Hendel populations to identify 3 alleles that exist in different frequencies in these populations. Expand
The potential for cross-taxa simple-sequence repeat (SSR) amplification between Arabidopsis thaliana L. and crop brassicas
TLDR
Brassica products amplified by A. thaliana SSR primer pairs may be useful as markers, but additional tests are necessary in order to determine whether the products contain SSRs and whether they are amplified by one or two primers. Expand
Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
TLDR
It is concluded that the rDNA sl variants and/or associated loci are under selection in CCII, which demonstrates that Rrn1 and Rrn2 are useful as new genetic markers. Expand
The development of oat microsatellite markers and their use in identifying relationships among Avena species and oat cultivars
TLDR
The objectives of the present study were to construct oat microsatellite-enriched libraries, to isolate micros satellite sequences and evaluate their level of polymorphism in Avena species and oat cultivars. Expand
Utility of SSRs for Determining Genetic Similarities an Relationships in Maize Using an Agarose Gel System
TLDR
The utility of polymerase chain reaction (PCR)-based markers such as SSRs for measuring genetic diversity, for assigning lines to heterotic groups and for genetic fingerprinting equals or exceeds that of RFLP markers, a property that may prove a valuable asset for a maize breeding program. Expand
...
1
2
3
4
5
...