Projects

STV: EST Derived Microsatellite Markers from Multiple Tissues of Gossypium hirsutum

• Contributors
  Jodi Scheffler
  USDA-ARS CG&PRU, 141 Experiment Station Road, Stoneville, MS 38776
  
  Earl Taliercio
  USDA-ARS S&NFRU, 3127 Ligon Street, Raleigh, NC 27607
  
  Brian Scheffler
  USDA-ARS CGRU, 141 Experiment Station Road, Stoneville, MS 38776
  
  
• Project Description
  All the plant material used to derive ESTs was from upland cotton (Gossypium hirsutum L). The tissues sampled included immature bolls, cotyledons, seedlings, stems and leaves. A total of 17,056 ESTs were assembled. Assembly of these sequences and Gossypium hirsutum EST from GenBank (Gossypium hirsutum [ORGN] on 2/2005) identified 6100 tentative consensus sequences (TCs) and 22,377 unique ESTs called singletons. There were 1,486 TCs assembled only from ESTs derived from this study and 8189 singletons ESTs derived from this study. Repeat Finder was used to select 192 primers. The cost of labeling 192 primers with fluorescent dye to monitor the amplicon was prohibitive so the “hanging tail” method developed for catfish BACs was adapted for cotton genomic DNA (Waldbieser et al. 2003). In this protocol the common “long sequence” was added to one primer of each set and a short sequence was added to the reverse primer to help balance the Tm. Each PCR mix contained a Hex-labeled version of the long sequence and the primer concentrations are kept low to necessitate the incorporation of the third Hex labeled primer. The 150 primer pairs were screened on the CMD panel.
    View / Download the standardized panel screened STV marker data (150).
    Download the STV markers (Excel format).
    Download the STV primers (Excel format).
    Download the STV microsatellite sequences (fasta format).
    Search your sequences against the STV microsatellites using the BLAST or FASTA server.
    References
  • Taliercio E, Allen RD, Essenberg M, Klueva N, Henry Nguyen, Patil MA, Payton P, Millena ACM, Phillips AL, Pierce ML, Scheffler B, Turley R, Wang J, Zhang D, Scheffler J. 2006. Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs. Genome. 49: 306-319.