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  • Genetic diversity  (3)
  • Germplasm  (2)
  • DNA typing  (1)
  • Fluorescence-based genotyping  (1)
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  • 1
    Electronic Resource
    Electronic Resource
    Assessment of Genetic Diversity in Three Subsets Constituted from the ICRISAT Sorghum Collection Using Random vs Non-Random Sampling Procedures B. Using molecular markers (2000)
    Springer
    Theoretical and applied genetics 101 (2000), S. 197-202 
    Details
    ISSN: 1432-2242
    Keywords: Key words Core collection ; Sorghum ; SSRs ; Genetic diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The large size of the sorghum [Sorghum bi-color (L.) Moench] landrace collection maintained by ICRISAT lead to the establishment of a core collection. Thus, three subsets of around 200 accessions were established from: (1) a random sampling after stratification of the entire landrace collection (L), (2) a selective sampling based on quantitative characters (PCS), and (3) a selection based on the geographical origin of landraces and the traits under farmers’ selection (T). An assessment was done of the genetic diversity retained by each sampling strategy using the polymorphisms at 15 microsatellite loci. The landraces of each subset were genotyped with three multiplex polymerase chain reactions (PCRs) of five fluorescent primer-pairs each with semi-automated allele sizing. The average allelic richness for each subset was equivalent (16.1, 16.3 and 15.4 alleles per locus for the subsets PCS, L, and T, respectively). The average genetic diversity was also comparable for the three subsets (0.81, 0.77 and 0.80 for the subsets PCS, L, and T, respectively). Allelic frequency distribution for each subset was compared with a chi-square test but few significant differences were observed. A high percentage of rare alleles (71 to 76% of 206 total rare alleles) was maintained in the three subsets. The global molecular diversity retained in each subset was not affected by a sampling procedure based upon phenotypic characters.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051469
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  • 2
    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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  • 3
    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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  • 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: 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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  • 5
    Electronic Resource
    Electronic Resource
    Characterization of genetic identities and relationships of Brassica oleracea L. via a random amplified polymorphic DNA assay (1992)
    Springer
    Theoretical and applied genetics 85 (1992), S. 190-196 
    Details
    ISSN: 1432-2242
    Keywords: DNA typing ; Genetic similarity ; Genetic structure ; Genetic resource conservation ; Vegetable and forage cole crops
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Effective conservation and the use of plant genetic resources are essential for future agricultural progress. Critical to this conservation effort is the development of genetic markers which not only distinguish individuals and accessions but also reflect the inherent variation and genetic relationships among collection holdings. We have examined the applicability of the random amplified polymorphic DNA (RAPD) assay for quick, cost-effective, and reliable use in addressing these needs in relation to collection organization and management. Twenty-five decamer oligonucleotide primers were screened individually with a test array composed of individuals representing a range of genetic relationships in Brassica oleracea L. (vegetable and forage cole crops). Over 140 reproducible, polymorphic fragments were generated for study. Each individual of the test array exhibited a unique molecular genotype and composites specific for accessions and botanical varieties could be established. An analysis of similarity based on amplified DNA fragments reflected the known genetic relationships among the selected entries. These results demonstrated that RAPD markers can be of great value in gene bank management for purposes of identification, measurement of variation, and establishment of genetic similarity at the intraspecific level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222859
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  • 6
    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: 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/BF00417944
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  • 7
    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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