Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype View Full Text


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Article Info

DATE

2008-10

AUTHORS

Federico L. Iniguez-Luy, Amy V. Voort, Thomas C. Osborn

ABSTRACT

The traditional development of simple sequence repeat (SSR) or microsatellite markers by probe hybridization can be time-consuming and requires the use of specialized laboratory equipment. In this study, probe hybridization was circumvented by using sequence information on 3,500 genomic clones mainly from Brassica oleracea to identify di, tri, tetra and penta-nucleotide repeats. A total of 587 primer pairs flanking SSR were developed using this approach. From these, 420 SSR markers amplified DNA in two parental lines of B. rapa (26% were polymorphic) and 523 in two parental lines of B. oleracea (32% were polymorphic). A diverse array of motif types was identified, characterized and compared with traditional SSR detection methods. The most abundant motifs found were di- (38%) and trinucleotides (33%) followed by penta- (16%) and tetranucleotide (13%) motifs. The type of motif class, motif length and repeat were not indicative of polymorphisms. The frequency of B. oleracea SSRs in genomic shotgun sequence was estimated to be 1 every 4 Kb. In general, the average motif length and repeat numbers were shorter than those obtained previously by probe hybridization, and they contained a more balanced representation of SSR motif types in the genome by identifying those that do not hybridize well to DNA probes. Brassica genomic DNA sequence information is a promising resource for developing a large number of SSR molecular markers in Brassica species. More... »

PAGES

977-985

References to SciGraph publications

  • 1996-09. Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species in THEORETICAL AND APPLIED GENETICS
  • 2003-01. Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars in THEORETICAL AND APPLIED GENETICS
  • 2004-04. Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species in THEORETICAL AND APPLIED GENETICS
  • 2005-11. Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population in MOLECULAR GENETICS AND GENOMICS
  • 2000-07. Use of 5´-anchored primers for the enhanced recovery of specific microsatellite markers in Brassica napus L. in THEORETICAL AND APPLIED GENETICS
  • 2002-03. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat in PLANT MOLECULAR BIOLOGY
  • 2004-07. EST derived SSR markers for comparative mapping in wheat and rice in MOLECULAR GENETICS AND GENOMICS
  • 1994-04. Survey of plant short tandem DNA repeats in THEORETICAL AND APPLIED GENETICS
  • 2005-04. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers in FUNCTIONAL & INTEGRATIVE GENOMICS
  • 1995-07. Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed) in THEORETICAL AND APPLIED GENETICS
  • 2005-11. Molecular characterization of marker-free transgenic lines of indica rice that accumulate carotenoids in seed endosperm in MOLECULAR GENETICS AND GENOMICS
  • 2002-02. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes in NATURE GENETICS
  • 2004-05. Genetic relationships of Brassica vegetables determined using database derived simple sequence repeats in EUPHYTICA
  • 2001-04. Microsatellite markers for genome analysis in Brassica. I. development in Brassica napus and abundance in Brassicaceae species in THEORETICAL AND APPLIED GENETICS
  • 2002-05. Isolation and characterization of microsatellites in Brassica rapa L. in THEORETICAL AND APPLIED GENETICS
  • 2002-11. Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench in THEORETICAL AND APPLIED GENETICS
  • 1992. Simple plant DNA isolation procedures in PLANT GENOMES: METHODS FOR GENETIC AND PHYSICAL MAPPING
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00122-008-0837-9

    DOI

    http://dx.doi.org/10.1007/s00122-008-0837-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1043917577

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/18651126


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