Copia-SSR: A simple marker technique which can be used on total genomic DNA

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 363-366 ◽  
Author(s):  
J Provan ◽  
WTB Thomas ◽  
B P Forster ◽  
W Powell
Keyword(s):  
Genetic Markers ◽  
Efficient Method ◽  
Doubled Haploid ◽  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Mapping Population ◽  
Repetitive Elements ◽  
Eukaryotic Genomes ◽  
Simple Sequence ◽  
Copia Retrotransposons

We have developed a PCR-based assay which uses a combination of two classes of repetitive elements found in eukaryotic genomes, namely Ty1-Copia retrotransposons and simple sequence repeats, to amplify multiple polymorphic products from total genomic DNA. Using the technique, seven markers were mapped to four different chromosome arms using a barley doubled haploid mapping population. This technique offers a simple and efficient method of generating both dominant and codominant genetic markers in virtually any eukaryote for mapping and diversity studies.Key words: Copia-SSR, microsatellite, retrotransposon, barley, genotyping.

scholarly journals ISSR (Inter Simple Sequence Repeats) as genetic markers in Noctuids (Lepidoptera)

Hereditas ◽  
2002 ◽  
Vol 136 (3) ◽  
pp. 251-253 ◽  
Author(s):  
C. LUQUE ◽  
L. LEGAL ◽  
H. STAUDTER ◽  
C. GERS ◽  
M. WINK
Keyword(s):  
Genetic Markers ◽  
Simple Sequence Repeats ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

scholarly journals Instability of simple sequence DNA in Saccharomyces cerevisiae

1992 ◽  
Vol 12 (6) ◽  
pp. 2749-2757 ◽  
Author(s):  
S T Henderson ◽  
T D Petes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Simple Sequence Repeats ◽  
Repeat Unit ◽  
Yeast Saccharomyces Cerevisiae ◽  
Minimal Rate ◽  
Eukaryotic Genomes ◽  
Simple Sequence

All eukaryotic genomes thus far examined contain simple sequence repeats. A particularly common simple sequence in many organisms (including humans) consists of tracts of alternating GT residues on one strand. Allelic poly(GT) tracts are often of different lengths in different individuals, indicating that they are likely to be unstable. We examined the instability of poly(GT) and poly(G) tracts in the yeast Saccharomyces cerevisiae. We found that these tracts were dramatically unstable, altering length at a minimal rate of 10(-4) events per division. Most of the changes involved one or two repeat unit additions or deletions, although one alteration involved an interaction with the yeast telomeres.

scholarly journals Instability of simple sequence DNA in Saccharomyces cerevisiae.

1992 ◽  
Vol 12 (6) ◽  
pp. 2749-2757 ◽  
Author(s):  
S T Henderson ◽  
T D Petes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Simple Sequence Repeats ◽  
Repeat Unit ◽  
Yeast Saccharomyces Cerevisiae ◽  
Minimal Rate ◽  
Eukaryotic Genomes ◽  
Simple Sequence

All eukaryotic genomes thus far examined contain simple sequence repeats. A particularly common simple sequence in many organisms (including humans) consists of tracts of alternating GT residues on one strand. Allelic poly(GT) tracts are often of different lengths in different individuals, indicating that they are likely to be unstable. We examined the instability of poly(GT) and poly(G) tracts in the yeast Saccharomyces cerevisiae. We found that these tracts were dramatically unstable, altering length at a minimal rate of 10(-4) events per division. Most of the changes involved one or two repeat unit additions or deletions, although one alteration involved an interaction with the yeast telomeres.

scholarly journals Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 847-854
Author(s):  
Linda Cardle ◽  
Luke Ramsay ◽  
Dan Milbourne ◽  
Malcolm Macaulay ◽  
David Marshall ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Sequence Data ◽  
Average Frequency ◽  
Dna Sequence Data ◽  
Ssr Frequency ◽  
Copy Dna ◽  
Simple Sequence

Abstract The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.

scholarly journals Analisis Cluster dan Seleksi Primer SSR (Simple Sequence Repeats) untuk Sifat Toleran Aluminium pada Cabai

2020 ◽  
Vol 11 (1) ◽  
pp. 61-71
Author(s):  
Catur Herison ◽  
Rustikawati ◽  
Ria Meita ◽  
Hasanudin
Keyword(s):  
Capsicum Annuum ◽  
Simple Sequence Repeats ◽  
Mapping Population ◽  
Simple Sequence

Perakitan varietas unggul cabai merah toleran Al (Aluminium) merupakan solusi terbaik untuk mengatasi persoalan rendahnya produkvitas cabai di lahan kering masam. Identifikasi tetua toleran dan marka SSR (Simple Sequence Repeats) sangat bermanfaat dalam meningkatkan efektifitas program pemuliaan tanaman untuk merakit varietas toleran terhadap cekaman aluminium. Seleksi primer SSR adalah bagian awal yang penting dalam pengembangan marka molekuler tersebut. Penelitian bertujuan untuk menentukan kelompok genotipe toleran alumunium dan menentukan primer prospektif dalam pengembangan marka SSR untuk sifat toleran terhadap Al pada tanaman cabai. Evaluasi tingkat toleransi 27 genotipe cabai terhadap cekaman aluminium dilakukan menggunakan hidroponik sistem sumbu dengan larutan hara AB mix ditambah 500 ppm AlCl3.6H2O. Tahap selanjutnya adalah menguji 20 primer SSR dalam mengamplifikasi DNA genom cabai toleran dan peka yang mewakili. Hasil analisis cluster sifat toleransi terhadap 27 genotipe cabai menghasilkan 7 kelompok tingkat toleransi terhadap aluminium. Individu PBC396 dan PBC518 adalah genotipe yang sangat toleran terhadap cekaman aluminium yang unik sehingga keduanya sangat baik digunakan sebagai tetua dalam pengembangan cabai toleran aluminium. Primer SSR yang potensial menghasilkan marka polimorfik untuk sifat toleran terhadap cekaman aluminium pada cabai adalah TMS7 dan CAMS358. Primer tersebut selanjutnya harus diuji pada mapping population untuk menentukan pita yang dapat digunakan sebagai penanda toleransi terhadap aluminium. Kata kunci:  Capsicum annuum, NTSYS, sidik gerombol, tenggang masam

scholarly journals Molecular genetics and SSR markers as a new practice in farm animal genomic analysis for breeding and control of disease disorders

2013 ◽  
Vol 29 (3) ◽  
pp. 405-429 ◽  
Author(s):  
A. Teneva ◽  
K. Dimitrov ◽  
Caro Petrovic ◽  
M.P. Petrovic ◽  
I. Dimitrova ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Molecular Genetics ◽  
Genetic Markers ◽  
Simple Sequence Repeats ◽  
Animal Health ◽  
Molecular Genetic ◽  
Genomic Analysis ◽  
Animal Breeding ◽  
Farm Animal ◽  
Simple Sequence

Molecular genetics investigates the genetic makeup of individuals at the DNA level. That includes the identification and mapping of molecular genetic markers and genetic polymorphisms. Molecular genetic markers (DNA markers) are one of the most powerful means for the genomic analysis and allow the connection of hereditary traits with genomic variation. Molecular marker technology has developed rapidly over the last decade and two shapes of specific DNA based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) prevail applications in modern genetic analysis. Genomic simple sequence repeats (SSRs, microsatellites) have been used for a variety of purposes, including gene tagging, physical mapping, genome mapping, estimation of genetic diversity, phylogenetic and conservation genetic purposes in farm animal breeding. SSR analyses are applied successfully in parentage verification and pedigree analysis, as disease markers and to locate the mutation in genetic disorders in livestock animals. The ultimate use of SSRs markers is for mapping quantitative trait loci (QTL), marker assisted selection (MAS) in order to practice genomic selection and improve the farm animal health. Developments in ?omics? technologies, such as genomic selection, may help overcome several of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. The current paper provides a brief overview of the present - day application of microsatellites markers in animal breeding and make significant contribution to the overall farm animal health and resistance to disease.

scholarly journals Simple Sequence Repeats (SSRs) in Watermelon (Citrullus lanatus L.)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 840E-840
Author(s):  
R.L. Jarret ◽  
S. Kresovich ◽  
T. Holms ◽  
Janelle Evans ◽  
Z. Liu
Keyword(s):  
New Hampshire ◽  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Citrullus Lanatus ◽  
Germplasm Characterization ◽  
Dna Library ◽  
Automated Dna Sequencing ◽  
Ssr Loci ◽  
Genomic Dna Library ◽  
Simple Sequence

Simple sequence repeats (SSRs) were isolated from a size-fractionated genomic DNA library of watermelon (Citrullus lanatus L. cv. New Hampshire Midget). Screening of the library with five oligonucleotide probes, including (GT)11, (AT)11, (CT)11, (GC)11, and (TAA)8, detected the occurrence of 96 positive colonies among ≈8000 recombinants. Automated DNA sequencing revealed the presence of SSRs. PCR primer pairs homologous to the regions flanking the SSR loci were synthesized commercially and used to screen 56 watermelon genotypes for the occurrence of SSR polymorphisms. Amplification products were separated using nondenaturing PAGE. Eighty percent of the primer pairs produced amplification products of the expected size and detected polymorphisms among the genotypes examined. The use of SSRs for watermelon germplasm characterization is discussed.

scholarly journals Simple Sequence Repeats (SSRs) in Sweetpotato [Ipomoea batatas (L.) Lam.]

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 841E-841
Author(s):  
R.L. Jarret ◽  
N. Bowen ◽  
S. Kresovich ◽  
Z. Liu
Keyword(s):  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Ipomoea Batatas ◽  
Oligonucleotide Probes ◽  
Germplasm Characterization ◽  
Amplification Product ◽  
Dna Library ◽  
Automated Dna Sequencing ◽  
Genomic Dna Library ◽  
Simple Sequence

Simple sequence repeats (SSRs) were isolated from a size-fractionated genomic DNA library of sweetpotato [Ipomoea batatas (L.) Lam.]. Screening of the library with five oligonucleotide probes, including; (GT)11, (AT)11, (CT)11, (GC)11, and (TAA)8, detected the occurrence of 142 positive colonies among ≈12,000 recombinants. Automated DNA sequencing revealed the presence of simple, compound, perfect, and imperfect SSRs. Five homologous PCR primer pairs were synthesized commercially and used to screen 30 sweetpotato clones for the occurrence of SSR polymorphisms. All primer pairs produced an amplification product of the expected size and detected polymorphisms among the genotypes examined. The potential for the use of SSRs as genetic markers for sweetpotato germplasm characterization is discussed.

Polymorphism revealed by simple sequence repeats

1996 ◽  
Vol 1 (7) ◽  
pp. 215-222 ◽  
Author(s):  
W POWELL ◽  
G MACHRAY ◽  
J PROVAN
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence
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