Maize simple repetitive DNA sequences: abundance and allele variation

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 866-873 ◽  
Author(s):  
E. C. L. Chin ◽  
H. Shu ◽  
J. S. C. Smith ◽  
M. L. Senior
Keyword(s):  
Dna Sequences ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Inbred Lines ◽  
Agarose Gels ◽  
Maize Germplasm ◽  
Mammalian Genomes ◽  
Key Words Maize ◽  
Allele Variation ◽  
Simple Sequence

Microsatellites or simple sequence repeats, first demonstrated in human and other mammalian genomes, are being identified in many plant species. A database survey of 576 maize sequences from the GenBank and EMBL databases was made to determine the abundance of maize microsatellites. Two hundred potential microsatellites were identified. The relative abundance of the different repetitive motifs varied considerably and all possible dinucleotide and trinucleotide motif types were found. The three most abundant classes of microsatellites identified in this search were (AG/CT)n, (CCT/GGA)n, and (CCG/GGC)n repeats. Allelic variation was surveyed with 9 maize inbred lines representing diverse pedigrees. Amplification of DNA from these lines and analysis using high resolution agarose gels showed that 69 of the 200 potential microsatellites were polymorphic and yielded 2–4 alleles. A more complete screen of these loci against a wider array of maize germplasm using denaturing sequencing gels is now being conducted to more thoroughly evaluate these loci. Key words : maize, microsatellites, simple sequence repeat, molecular marker.

scholarly journals Analysis of allelic variation in wild potato (Solanum) species by simple sequence repeat (SSR) markers

3 Biotech ◽  
2019 ◽  
Vol 9 (7) ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Nilofer Ali ◽  
Sapna Devi ◽  
Rasna Zinta ◽  
Vinod Kumar ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Solanum Species ◽  
Wild Potato ◽  
Sequence Repeat ◽  
Simple Sequence

Abundance and variation of microsatellite DNA sequences in beans (Phaseolus andVigna)

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Kangfu Yu ◽  
Soon J Park ◽  
Vaino Poysa
Keyword(s):  
Common Bean ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Allelic Variation ◽  
Pcr Analysis ◽  
Or Groups ◽  
Recombinant Inbred Population ◽  
Nucleotide Repeats ◽  
Eukaryotic Genomes ◽  
Simple Sequence

Microsatellites or simple sequence repeats (SSRs) have been demonstrated to be abundant and hypervariable in some eukaryotic genomes. Although the presence of microsatellites is very well documented in many plant species, no information on microsatellites in beans (Phaseolus andVigna) is available. To assess the abundance and usefulness of bean microsatellites as genetic markers, 326 DNA sequences from the GenBank databases were searched. Sixty-one simple repetitive DNA sequences with 23 different types of repetitive DNA motifs were identified as potential microsatellites. Among these were 49 microsatellites from common bean (Phaseolus vulgaris) entries and 12 microsatellites from the genus Vigna. The most abundant type of microsatellite found in this search was that with di-nucleotide repeats of AT/TA. Microsatellites with tri- and tetra-nucleotide motifs were also identified. PCR analysis of 12 of the microsatellite-containing loci revealed that 11 of the 12 primer pairs could produce easily-scorable fragments, or groups of fragments. Allelic variation of the 11 loci was surveyed in 12 common bean inbred lines representing a diversity of germplasms. Seven of the 11 microsatellite loci were polymorphic and yielded 2-10 alleles. Analyses of the polymorphic loci in a common bean F6 recombinant inbred population showed that each segregated in a Mendelian fashion.Key words: microsatellite, simple sequence repeat, molecular marker, bean.

Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles: Applications to Maize Inbred Lines and Soybean Varieties

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 331-342
Author(s):  
Donald A Berry ◽  
Jon D Seltzer ◽  
Chongqing Xie ◽  
Deanne L Wright ◽  
Elizabeth S Jones ◽  
...  
Keyword(s):  
Prior Knowledge ◽  
Simple Sequence Repeat ◽  
Large Scale ◽  
Fundamental Problem ◽  
Inbred Lines ◽  
Laboratory Errors ◽  
The Face ◽  
Ssr Loci ◽  
Simple Sequence ◽  
Hypervariable Loci

Abstract Determining parentage is a fundamental problem in biology and in applications such as identifying pedigrees. Difficulties inferring parentage derive from extensive inbreeding within the population, whether natural or planned; using an insufficient number of hypervariable loci; and from allele mismatches caused by mutation or by laboratory errors that generate false exclusions. Many studies of parentage have been limited to comparisons of small numbers of specific parent-progeny triplets. There have been few large-scale surveys of candidates in which there is no prior knowledge of parentage. We present an algorithm that determines the probability of parentage in circumstances where there is no prior knowledge of pedigree and that is robust in the face of missing data and mistyped data. The focus is parentage of an inbred line having uncertain ancestry. The algorithm is a variation of a previously published hybrid-focused algorithm. We describe the algorithm and demonstrate its performance in determining parentage of 43 inbred varieties of soybean that have been profiled using 236 SSR loci and from seven inbred varieties of maize that were profiled using 70 SSR loci. We include simulations of additional levels of missing and mistyped data to show the algorithm's utility and flexibility.

scholarly journals Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4266 ◽  
Author(s):  
Ging Yang Siew ◽  
Wei Lun Ng ◽  
Sheau Wei Tan ◽  
Noorjahan Banu Alitheen ◽  
Soon Guan Tan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Resources ◽  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Dna Sequences ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Direct Result ◽  
Sequence Repeat ◽  
Simple Sequence

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, HE = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10−3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called “clones”, “varieties”, or “cultivars”. Such matters have a direct impact on the regulation and management of durian genetic resources in the region.

scholarly journals Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

2018 ◽  
Vol 2 (3) ◽  
pp. 144
Author(s):  
Ramlah Ramlah ◽  
Isna Rasdianah Aziz ◽  
Cut Muthiadin ◽  
Mashuri Masri ◽  
Muhammad Khalifah Mustami ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Agricultural Research ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Maize Germplasm ◽  
South Sulawesi ◽  
Simple Sequence

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

scholarly journals Simple Sequence Repeat Markers Reveal Hungarian Plum (Prunus domestica L.) Germplasm as a Valuable Gene Resource

HortScience ◽  
2017 ◽  
Vol 52 (12) ◽  
pp. 1655-1660 ◽  
Author(s):  
Noémi Makovics-Zsohár ◽  
Magdolna Tóth ◽  
Dezső Surányi ◽  
Szilvia Kovács ◽  
Attila Hegedűs ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Genetic Relationships ◽  
Principal Component ◽  
Bootstrap Support ◽  
Limited Information ◽  
Sequence Repeat ◽  
Prunus Domestica ◽  
Simple Sequence

The hexaploid European plum (Prunus domestica L.) is an economically important fruit species with limited information on its genetic structure. Our objective was to fingerprint 55 cultivars using seven simple sequence repeat (SSR) markers to estimate the polymorphism level and determine allelic variation and genetic relationships among local and international cultivars. The primer pairs amplified a total of 135 alleles ranging from six to 27 alleles per locus, displaying high polymorphism. All genotypes were clearly distinguished with the seven SSRs used in this study. In a neighbor-joining cluster analysis, cultivars belonging to the same species did not group together. Foreign modern cultivars clustered together, and Hungarian landraces positioned distantly from those. STRUCTURE analysis indicated three genetically distinct groups of the studied genotypes. Each cluster of Hungarian landrace cultivars received strong bootstrap support (89% to 100%). Most genotypes kept under identical name showed different DNA fingerprints. A principal component analysis (PCA) confirmed the information provided by the dendrogram and clarified the origin of ʻFehérszilva’. Our results confirmed the potential of the application of SSR markers in plum breeding.

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