Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 367-373 ◽  
Author(s):  
Kristina M Sefc ◽  
Ferdinand Regner ◽  
Eva Turetschek ◽  
Josef Glössl ◽  
Herta Steinkellner
Keyword(s):  
Simple Sequence Repeats ◽  
Genomic Library ◽  
Mendelian Inheritance ◽  
Null Alleles ◽  
Flanking Sequence ◽  
Vitis Species ◽  
Vitis Riparia ◽  
Expected Heterozygosity ◽  
And Performance ◽  
Simple Sequence

A Vitis riparia genomic library was screened for the presence of (GA)n simple sequence repeats (SSR) and 18 primer pairs yielding amplification products of the expected size were designed. Heterologous amplification with the primer pairs in related species (V. rupestris, V. berlandieri, V. labrusca, V. cinerea, V. aestivalis, V. vinifera, and interspecific hybrids) was successful in most primer-species combinations. Therefore, the new markers are applicable to the genotyping of a range of Vitis species. Variations in the SSR flanking sequence were detected between and within the species. The degree of polymorphism and performance of the markers were determined in up to 120 individuals of V. vinifera. Four of fifteen alleles per locus were detected and expected heterozygosity ranged between 0.37 and 0.88. Null alleles were shown to be present at two loci by a lack of heterozygous individuals and by transmission of the null alleles in a controlled cross. Regular Mendelian inheritance is indicated for all but one loci by a preliminary segregation analysis in 36 offspring. Thirteen of the markers were found suitable for the genotyping of grapevines (V. vinifera).Key words: microsatellites, simple sequence repeats, Vitis.

Exon-primed intron-crossing (EPIC) PCR markers ofHelicoverpa armigera(Lepidoptera: Noctuidae)

2008 ◽  
Vol 98 (5) ◽  
pp. 509-518 ◽  
Author(s):  
W.T. Tay ◽  
G.T. Behere ◽  
D.G. Heckel ◽  
S.F. Lee ◽  
P. Batterham
Keyword(s):  
Dna Markers ◽  
Nuclear Dna ◽  
Pcr Amplification ◽  
Mendelian Inheritance ◽  
Null Alleles ◽  
Flanking Sequence ◽  
Pcr Markers ◽  
Technical Problems ◽  
Size Homoplasy ◽  
Length Polymorphisms

AbstractApplying microsatellite DNA markers in population genetic studies of the pest mothHelicoverpa armigerais subject to numerous technical problems, such as the high frequency of null alleles, occurrence of size homoplasy, presence of multiple copies of flanking sequence in the genome and the lack of PCR amplification robustness between populations. To overcome these difficulties, we developed exon-primed intron-crossing (EPIC) nuclear DNA markers forH. armigerabased on ribosomal protein (Rp) and the Dopa Decarboxylase (DDC) genes and sequenced alleles showing length polymorphisms. Allele length polymorphisms were usually from random indels (insertions or deletions) within introns, although variation of short dinucleotide DNA repeat units was also detected. Mapping crosses demonstrated Mendelian inheritance patterns for these EPIC markers and the absence of both null alleles and allele ‘dropouts’. Three examples of allele size homoplasies due to indels were detected in EPIC markers RpL3, RpS6 and DDC, while sequencing of multiple individuals across 11 randomly selected alleles did not detect indel size homoplasies. The robustness of the EPIC-PCR markers was demonstrated by PCR amplification in the related species,H. zea,H. assultaandH. punctigera.

Development of microsatellite markers for the short-beaked echidna using three different approaches

2009 ◽  
Vol 57 (4) ◽  
pp. 219 ◽  
Author(s):  
C. Vanpé ◽  
E. Buschiazzo ◽  
J. Abdelkrim ◽  
G. Morrow ◽  
S. C. Nicol ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Population Genetic ◽  
High Probability ◽  
Genomic Library ◽  
Polymorphic Information Content ◽  
Null Alleles ◽  
Genomic Sequencing ◽  
Expected Heterozygosity ◽  
Study Population ◽  
Using Data

We used three different methods, size-selected genomic library, cross-species amplification of a mammal-wide set of conserved microsatellites and genomic sequencing, to develop a panel of 43 microsatellite loci for the short-beaked echidna (Tachyglossus aculeatus). These loci were screened against 13 individuals from three different regions (Tasmania, Kangaroo Island, Perth region), spanning the breadth of the range of the short-beaked echidna. Nine of the 43 tested loci amplified reliably, generated clear peaks on the electropherogram and were polymorphic, with the number of alleles per locus ranging from two to eight (mean = 3.78) in the individuals tested. Polymorphic information content ranged from 0.16 to 0.78, and expected heterozygosity ranged from 0.19 to 0.84. One of the nine microsatellites showed a heterozygote deficit, suggesting a high probability of null alleles. The genomic sequencing approach using data derived from the Roche FLX platform is likely to provide the most promising method to develop echidna microsatellites. The microsatellite markers developed here will be useful tools to study population genetic structure, gene flow, kinship and parentage in Tachyglossus sp. and potentially also in endangered Zaglossus species.

Simple sequence repeats for germplasm analysis and mapping in maize

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 277-287 ◽  
Author(s):  
Graziana Taramino ◽  
Scott Tingey
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Trinucleotide Repeats ◽  
High Rate ◽  
Rflp Markers ◽  
Sequence Motifs ◽  
Genomic Libraries ◽  
Expected Heterozygosity ◽  
Germplasm Analysis ◽  
Simple Sequence

Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)n repeats, 15 (AC)n repeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population. Key words : simple sequence repeats, microsatellites, maize, germplasm analysis, mapping.

scholarly journals UJI POLIMORPIK DAN HETEROZIGOSITAS PADA PROGENI F4 KEDELAI (Glycine max (L.) Merril) TAHAN SALIN DENGAN MENGGUNAKAN MARKA SSR (Simple Sequence Repeats)

2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Evi Julianita Harahap ◽  
Rosmayanti Rosmayanti ◽  
Diana Sofia Hanafiah
Keyword(s):  
Glycine Max ◽  
Simple Sequence Repeats ◽  
Ssr Marker ◽  
Specific Primers ◽  
Allele Number ◽  
Map Construction ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Glycine Max L ◽  
Simple Sequence

SSR marker has some merits such as quickness, simplicity, rich polymorphism and stability, thus being widely applied in genetic diversity analysis, molecular map construction and gene mapping. the purpose of this study was to determine polymorpic test and heterozygosity in F4 soybean (Glycine max (L.) Merril) progeni saline resistant characters using SSR (Simple Sequence Repeats) markers. This research was conducted in Biomolecular Laboratory, Socfindo Seed Production Laboratory (SSPL), Kebun Bangun Bandar Village Martebing District Dolok Masihul Regency Serdang Bedagai on December-May 2017. The number of samples were used 44. The five SSR primers (QS080465, QS1101, QS1112, QS100011, and Sat_091) used were specific primers, with a band pattern that was clearly visible around one or two bands. The percentage of polymorphic primers (PLP) of these three populations is high, all populations with a PLP of 100% of the saline resistant character. The effective allele number (Ne) of  7,160 for the progeny population is lower than the number of observed alleles (Na) of 10,000 which means that many progeny individuals are homozygous. The expected heterozygosity (He) value of 0.854 in the progeny population was higher than the observed heterozygosity (Ho) value of 0.027. The overall average observed heterozygosity (Ho) was 0.009 lower than the overall expected heterozygosity (He) of 0.61. This means that each character has a low heterozygosity.Keywords: Progeny F4, soybean, SSR, saline resistant, polymorphic, heterozygosity

Development of simple sequence repeat markers in rye (Secale cereale L.)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 964-972 ◽  
Author(s):  
B Saal ◽  
Günter Wricke
Keyword(s):  
Ssr Markers ◽  
Secale Cereale ◽  
Simple Sequence Repeats ◽  
Rflp Markers ◽  
Dinucleotide Repeats ◽  
Genomic Libraries ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
Secale Cereale L ◽  
Simple Sequence

Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.Key words: simple sequence repeats, microsatellites, mapping, rye, Secale cereale.

Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 433-441 ◽  
Author(s):  
R. L. Jarret ◽  
L. C. Merrick ◽  
T. Holms ◽  
J. Evans ◽  
M. K. Aradhya
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Genetic Relatedness ◽  
Genomic Library ◽  
Citrullus Lanatus ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.Key words: Citrullus, watermelon, simple sequence repeats, genetic diversity.

Microsatellite isolation and characterization in sunflower (Helianthus annuus L.)

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 34-43 ◽  
Author(s):  
Norma Paniego ◽  
Mercedes Echaide ◽  
Marianne Muñoz ◽  
Luis Fernández ◽  
Susana Torales ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Simple Sequence Repeats ◽  
Genomic Library ◽  
Genetic Relationships ◽  
Inbred Lines ◽  
Helianthus Annuus L ◽  
Isolation And Characterization ◽  
Polymorphic Microsatellites ◽  
Microsatellite Isolation ◽  
Simple Sequence

Development of microsatellite markers for sunflower (Helianthus annuus L.) was performed to estimate their frequency, nature (structure), levels of polymorphism, usefulness for genotype identification, and calculation of genetic relationships between inbred lines representing the species diversity. Isolation was performed from a small-insert genomic library followed by hybridization screening using oligonucleotide probes containing different nucleotide arrays. In this work, 503 unique microsatellite clones were sequenced and 271 PCR primer sequences bordering the microsatellite repeat were designed. For polymorphism assessment, 16 H. annuus germplasm accessions were checked and 170 of the primers tested were shown to be polymorphic for the selected lines. The polymorphic microsatellites produced an average of 3.5 alleles/locus and an average polymorphism information content (PIC) of 0.55. The most frequently found motifs within polymorphic simple-sequence repeats (SSRs) were: (GA)n, (GT)n, (AT)n, followed by trinucleotides (ATT)n, (TGG)n and (ATC)n, and the tetranucleotide (CATA)n. Most of the 170 SSRs obtained showed important differences in the 16 reference inbred lines used for their characterization. In this work, 20 of the most informative SSRs destined to sunflower genotyping and legal fingerprinting purposes are fully described.Key words: sunflower, molecular markers, microsatellites, simple-sequence repeats.

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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