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  • 1
    Electronic Resource
    Electronic Resource
    Discovery and Characterization of Polymorphic Simple Sequence Repeats (SSRs) in Peanut (1999)
    Springer
    Crop science 39 (1999), S. 1243-1247 
    Details
    ISSN: 1435-0653
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Arachis hypogaea L.), an important agronomic crop, exhibits a considerable amount of variability for morphological traits and for resistance to diseases and pests. In contrast, molecular marker assays have detected little variation at the nucleic acid level. Identification of molecular markers would be of great help to peanut breeders, geneticists, and taxonomists. The objectives of this work were to identify simple sequence repeat (SSR) markers in cultivated peanut and to test these markers for their ability to discriminate among accessions. Peanut total genomic DNA libraries were constructed and screened with 32P-labeled dinucleotide repeats, (GT)10 and (CT)10. DNA sequences were obtained from the SSR-containing clones and, when possible, primer pairs were designed on the basis of DNA sequences flanking the repeat motif. Primer pairs were tested in polymerase chain reaction (PCR) assays using a collection of 22 peanut DNAs, representing both cultivated peanut and wild species. In all, six SSR markers, five from the library screening procedure and one additional marker obtained from a search of publicly available DNA sequences, detected polymorphisms among the peanut DNAs. Discrimination power was high among the cultivated peanuts, with 17 unique genotypes represented among the 19 accessions tested. From two to 14 DNA fragments were amplified per SSR marker, and as a group, the six markers may amplify up to 10 putive SSR loci. The SSR markers identified in this study were more effective in detecting molecular variation in cultivated peanut than all other DNA-based marker evaluated to date.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/
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  • 2
    Electronic Resource
    Electronic Resource
    Genetic Redundancy and Diversity among 'Orange' Accessions in the U.S. National Sorghum Collection as Assessed with Simple Sequence Repeat (SSR) Markers (1999)
    Springer
    Crop science 39 (1999), S. 1215-1221 
    Details
    ISSN: 1435-0653
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Sorghum bicolor (L.) Moench] accessions identified as 'Orange' presently maintained by the U.S. National Plant Germplasm system (NPGS) were assayed with 15 simple sequence repeat (SSR) markers. Genotyping was performed with fluorescent primers with five primer sets in each of three multiplex polymerase chain reactions (PCRs) and automated allele sizing. A total of 96 individuals were analyzed, five plants from each of 19 Orange accessions and one individual from an elite inbred line, 'RTx430'. The SSR markers provided substantial genetic resolution among the Orange entries. Average heterozygosity estimates were low, and phenetic analyses (neighbor-joining dendograms) were generally consistent with known historical relationships among accessions. Most accessions were genetically distinct, but two redundant groups (involving a total of five entries) were found among the 19 Orange accessions evaluated. The molecular variance analysis (AMOVA) showed that 90% of the total genetic variation was partitioned among accessions, while one-tenth of the variation resulted from genetic differences between individual plants within accessions. The variance analysis also indicated that it should be possible to reduce the number of Orange accessions held by NPGS by almost half without seriously jeopardizing the overall amount of genetic variation contained in these holdings. This study demonstrated that a limited number of SSR markers can be used in a cost-efficient manner to rapidly assess variation in accessions of Orange sorghum.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular characterization can quantify and partition variation among genebank holdings: a case study with phenotypically similar accessions of Brassica oleracea var. capitata L. (cabbage) `Golden Acre' (1997)
    Springer
    Theoretical and applied genetics 94 (1997), S. 227-234 
    Details
    ISSN: 1432-2242
    Keywords: Key words AMOVA ; Conservation ; Curation ; Genetic markers ; Molecular genetic screening ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To better characterize and conserve crop genetic resources, the assessment of genetic identity, relatedness, and structure among entries and collections becomes a priority. In the present study, a random amplified polymorphic DNA (RAPD) assay was applied as a quick, cost-effective, and preliminary screen to quantify and partition the molecular variation among accessions. Fourteen phenotypically uniform accessions of Brassica oleracea var. capitata L. (cabbage) similarly designated as `Golden Acre' were tested with nine decamer oligonucleotide primers. These amplifications generated 110 fragments, of which 80 were polymorphic ranging in size from 370 to 1720 bp. The 80 polymorphic fragments were sufficient to distinguish between all 14 accessions. Data based on the partitioning of variation among accessions indicated that `Golden Acre' entries could be reduced to as few as four groups, with the potential loss of variation being only 4.6% of the absolute current genetic variation in those holdings as estimated from RAPD analysis. This proposed grouping would concurrently save approximately 70% [$750–1000 (US) per accession] for each cycle of regeneration (approximately 20–25 years at most) which alternatively could then be used for other priorities in B. oleracea conservation and use. This case represents but one example where targeted use of a molecular-marker assay linked with rigorous statistical analysis will be useful for plant genebank management, particularly for questions at the intraspecific level. Molecular markers will provide genebank curators with additional sources of information to better plan and organize collection holdings and use finite financial support in a more effective manner.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050404
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  • 4
    Electronic Resource
    Electronic Resource
    Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench] (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 190-198 
    Details
    ISSN: 1432-2242
    Keywords: Microsatellite ; Germplasm ; Genetic resources ; Genetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00225745
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  • 5
    Electronic Resource
    Electronic Resource
    Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 534-538 
    Details
    ISSN: 1432-2242
    Keywords: Key words DNA marker ; Genetic analysis ; Genetic diversity ; Genotyping ; Microsatellite
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The application of simple sequence repeat (SSR) genotyping for the characterization of genetic variation in crop plants has been hindered by ready access to useful primer pairs and potentially limited conservation of the repeat sequences among related species. In this phase of work, we report on the identification and characterization of SSRs that are conserved in Brassica napus L. (rapeseed) and its putative progenitors, B. oleracea L. (cabbage, and related vegetable types) and B. rapa (vegetable and oil types). Approximately 140 clones from a size-fractionated genomic library of B. napus were sequenced, and primer pairs were designed for 21 dinucleotide SSRs. Seventeen primer pairs amplified products in the three species and, among these, 13 detected variation between and within species. Unlike findings on SSR information content in human, no relationship could be established between the number of tandem repeats within the target sequence and heterozygosity. All primer pairs have been designed to work under identical amplification conditions; therefore, single-reaction, multiplex polymerase chain reaction (PCR) with these SSRs is possible. Once moderate numbers of primer pairs are accessible to the user community, SSR genotyping may provide a useful method for the characterization, conservation, and utilization of agricultural crop diversity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050311
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  • 6
    Electronic Resource
    Electronic Resource
    Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability (1998)
    Springer
    Theoretical and applied genetics 97 (1998), S. 493-501 
    Details
    ISSN: 1432-2242
    Keywords: Key words Cassava ; Microsatellites ; Fluorescence-based genotyping ; Heterozygosity ; Linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Fourteen microsatellites containing GA-repeats were isolated and characterized in cassava (Manihot esculenta Crantz, Euphorbiaceae). Microsatellite heterozygosity (h) was estimated in 48 accessions using (32P)-end-labeled primers and in more than 500 accessions using fluorescence-based genotyping. Heterozygosity values ranged from 0.00 to 0.88 and the number of alleles detected varied from 1 to 15. The reproducibility of allele sizing was also assessed using fluorescence-based genotyping. The average inter-gel size difference was 1.03 nucleotides. Chi-square tests (χ2) were performed to analyse segregation distortion and the linkage between alleles segregating from either or both parents in an F1 mapping population. Most microsatellite loci segregated in the expected 1 : 1, 1 : 2 : 1 or 1 : 1 : 1 : 1 ratio. Linkage was detected between loci segregating from either parent, and segregation distortion from the male parent was detected for locus GA-131. Approximately 80% of the microsatellites detected one or two alleles per accession, suggesting a low degree of microsatellite locus duplication, an unexpected finding for a putative allopolyploid, highly heterozygous species. The high h values of most microsatellites, their amplification in other Manihot taxa and their suitability for high-throughput, fluorescence-based genotyping, make microsatellites the marker of choice for germplasm characterization and saturation of the cassava map.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050922
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  • 7
    Electronic Resource
    Electronic Resource
    Characterization and analysis of simple sequence repeat (SSR) loci in seashore paspalum (Paspalum vaginatum Swartz) (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 47-52 
    Details
    ISSN: 1432-2242
    Keywords: Simple sequence repeats ; Microsatellite ; Molecular marker ; Seashore paspalum ; Germ plasm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A size-fractionated TaqI genomic library of seashore paspalum (Paspalum vaginatum Swartz) was screened for the presence of (GA) n and (CA) n simple sequence repeats (SSRs). A total of 54 clones with a positive signal were detected among 13,000 clones screened. Forty-seven clones having repeats of n⩾ 3 were identified, of which 85% were perfect, 13% were imperfect and 2% were compound repeat sequences. Five of ten primer pairs synthesized to amplify selected loci resulted in a product in the expected size range and were subsequently used to examine SSR polymorphisms among 46 ecotypes of P. vaginatum. The number of alleles resolved on agarose or polyacrylamide gels were similar and ranged from 6 to 16 with an average of 14 per locus. Phenetic analysis of SSR polymorphisms revealed genetic relationships among the P. vaginatum ecotypes that were in general agreement with relationships determined previously by RAPD analysis of the same plant materials. Further screening of the genomic library did not identify (AT) n , trimeric or tetrameric repeats. Hybridization of an (ATT)8 oligonucleotide probe to genomic DNA isolated from I. batatas, E. coli, Citrullis lanatus and P. vaginatum suggested that the P. vaginatum genome contained significantly fewer ATT repeats than either the I. batatas or C. lanatus genome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220857
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  • 8
    Electronic Resource
    Electronic Resource
    Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench] (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 190-198 
    Details
    ISSN: 1432-2242
    Keywords: Key words Microsatellite ; Germplasm ; Genetic resources ; Genetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050265
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  • 9
    Electronic Resource
    Electronic Resource
    Differentiation of bermudagrass (Cynodon spp.) genotypes by AFLP analyses (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 895-902 
    Details
    ISSN: 1432-2242
    Keywords: Key words AFLP (amplified fragment length polymorphism) ; Bermudagrass (Cynodon spp.) ; DNA fingerprinting ; Semi-automated fluorescence-based genotyping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Bermudagrasses (Cynodon spp.) are major turfgrasses for home lawns, public parks, golf courses and sport fields, and are widely adapted to tropical and warmer temperate climates. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subject to environmental influence. In this study, a DNA-typing technique, amplified fragment length polymorphism (AFLP), was used to differentiate bermudagrass genotypes and to explore their genetic relationships. Twenty seven bermudagrass cultivars and introductions, mostly from the Coastal Plain Experiment Station in Tifton, Ga., were assayed by the radioactive (32P) and the fluorescence-labeled AFLP methods. The AFLP technique produced enough polymorphism to differentiate all 27 bermudagrass genotypes, even the closely related ones. An average of 48–74 bands in the 30–600-bp size range was detected by the 32P-labeled AFLP method. The results indicated that most of the 14 primer combinations tested in this study could be used to distinguish bermudagrass genotypes, and that some single primer-pairs could differentiate all 27 of them. To test the reliability and reproducibility of the AFLP procedure, three DNA isolations (replications) of the 27 bermudagrass genotypes were assayed using five primer pairs. Only 0.6% of the bands were evaluated differently among the three replications. One replication of one genotype (which was most likely a planting contaminant) was grouped in an unexpected cluster using the Unweighted Pair Group Mean Average (UPGMA) method. A one- or two-band difference in scoring did not change the clustering of genotypes or the replications within genotypes. The 27 genotypes were grouped into three major clusters, many of which were in agreement with known pedigrees. Trees constructed with different primer combinations using 32P- and fluorescence-labelling formed similar major groupings. The semi-automated fluorescence-based AFLP technique offered significant improvements on fragment sizing and data handling. It was also more accurate for detection and more efficient than the radioactive labelling method. This study shows that the AFLP technique is a reliable tool for differentiating bermudagrass genotypes and for determining genetic relationships among them.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051148
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  • 10
    Electronic Resource
    Electronic Resource
    Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed) (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 206-211 
    Details
    ISSN: 1432-2242
    Keywords: Genetic analysis ; Fluorescence-based detection ; STR ; Microsatellite DNA ; Multiplex PCR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A size-fractionated library of Brassica napus L. (rapeseed), composed of 15000 clones, was screened for the presence of GA-, CA-, and GATA-simple-sequence repeats (SSRs). GA-SSRs were four- and five-fold more abundant than CA- and GATA-SSRs, respectively, and present at a frequency of approximately one SSR for every 100 kb of DNA. Following the sequencing of 124 positive clones, primer pairs were designed and evaluated for seven selected SSRs. Products were amplified in an array of individuals of B. napus, B. oleracea and B. rapa, demonstrating that the seven SSRs were conserved among species. Two SSRs were polymorphic. Among 11 accessions, the dinucleotide (GA)-repeat, B.n.9A, yielded 12 fragments, while the tetranucleotide-repeat (GATA), B.n.6A2, revealed two fragments. Automated, fluorescence-based detection of polyacrylamide gels has been employed to simultaneously increase throughput, reduce unit cost, improve analytical resolution, and expedite data acquisition of SSR analysis. Though initial financial investment and technical capabilities may prevent some from directly employing our documented approach, SSR analysis warrants further investigation as a tool in genetic studies for enhancing both the conservation and utilization of genetic resources.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220879
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