Theoretical and Applied Genetics

, Volume 117, Issue 6, pp 977–985

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

  • Federico L. Iniguez-Luy
  • Amy V. Voort
  • Thomas C. Osborn
Original Paper

DOI: 10.1007/s00122-008-0837-9

Cite this article as:
Iniguez-Luy, F.L., Voort, A.V. & Osborn, T.C. Theor Appl Genet (2008) 117: 977. doi:10.1007/s00122-008-0837-9

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.

Supplementary material

122_2008_837_MOESM1_ESM.doc (810 kb)
MOESM1 ESM 1 FITO SSR name, B.oleracea clone used to mined SSR motif (NCBI clone accession number), repeat type, motif repeat type and primary A. thaliana chromosome homology and other relevant information for 587 primers pairs developed using B. oleracea sequence information (DOC 810 kb)
122_2008_837_MOESM2_ESM.doc (108 kb)
MOESM2 ESM 2 List of the 144 SSR names published in the scientific literature and UKCROPNET database that were surveyed for useful polymorphism in this study (DOC 107 kb)
122_2008_837_MOESM3_ESM.doc (1 mb)
MOESM3 ESM 3 FITOSSR name, priming sequences, TM’s and expected product size for 587 primers pairs developed using B.oleracea sequence information (DOC 1070 kb)
122_2008_837_MOESM4_ESM.doc (28 kb)
MOESM4 ESM 4 Distribution of primary homologous regions among the 5 chromosomes of the Arabidopsis genome for 260 SSR developed from B. oleracea sequence information (DOC 28 kb)
122_2008_837_MOESM5_ESM.doc (26 kb)
MOESM5 ESM 5 Information on SSR primer pairs from public resources screened for polymorphism in our parental lines of B. rapa and B. oleracea (DOC 26 kb)

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Federico L. Iniguez-Luy
    • 1
    • 3
  • Amy V. Voort
    • 1
  • Thomas C. Osborn
    • 2
  1. 1.Department of AgronomyUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Seminis Vegetables SeedsWoodlandUSA
  3. 3.Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUSA

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