Theoretical and Applied Genetics

, Volume 111, Issue 8, pp 1532–1544

Identification and mapping of SNPs from ESTs in sunflower

  • Z. Lai
  • K. Livingstone
  • Y. Zou
  • S. A. Church
  • S. J. Knapp
  • J. Andrews
  • L. H. Rieseberg
Original Paper

DOI: 10.1007/s00122-005-0082-4

Cite this article as:
Lai, Z., Livingstone, K., Zou, Y. et al. Theor Appl Genet (2005) 111: 1532. doi:10.1007/s00122-005-0082-4

Abstract

More than 67,000 expressed sequence tags (ESTs) have recently been generated for sunflower (Helianthus), including 44,000 from cultivated confectionery (RHA280) and oilseed (RHA801) lines of Helianthus annuus and 23,000 from drought- and salt-tolerant wild sunflowers, H. argophyllus and H. paradoxus, respectively. To create a transcript map for sunflower, we identified 605 ESTs that displayed small insertion–deletion polymorphism (SNP) variation in silico, had apparent tissue-specific expression patterns, and/or were ESTs with candidate functions in traits such as development, cell transport, metabolism, plant defense, and tolerance to abiotic stress. Primer pairs for 535 of the loci were designed from the ESTs and screened for polymorphism in recombinant inbred lines derived from a cross between the same cultivars (RHA280 × RHA801) employed for sequencing. In total, 273 of the loci amplified polymorphic products, of which 243 mapped to the 17 linkage groups previously identified for sunflower. Comparisons with previously mapped QTL revealed some cases where ESTs with putatively related functions mapped near QTLs identified in other crosses for salt tolerance and for domestication traits such as stem diameter, shattering, flowering time, and achene size.

Supplementary material

122_2005_82_MOESM1_ESM.pdf (83 kb)
Supplementary material

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Z. Lai
    • 1
  • K. Livingstone
    • 2
  • Y. Zou
    • 1
  • S. A. Church
    • 3
  • S. J. Knapp
    • 4
  • J. Andrews
    • 1
  • L. H. Rieseberg
    • 1
  1. 1.Department of Biology and Center for Genomics and BioinformaticsIndiana UniversityBloomingtonUSA
  2. 2.Department of BiologyTrinity UniversitySan AntonioUSA
  3. 3.Department of Biological SciencesGeorge Washington UniversityWashingtonUSA
  4. 4.Center for Applied Genetic Technologies, Department of Crop and Soil ScienceUniversity of GeorgiaAthensUSA