Molecular Breeding

, Volume 28, Issue 1, pp 73–89

Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)

  • Corina M. Fusari
  • Verónica V. Lia
  • Verónica Nishinakamasu
  • Jeremías E. Zubrzycki
  • Andrea F. Puebla
  • Alberto E. Maligne
  • H. Esteban Hopp
  • Ruth A. Heinz
  • Norma B. Paniego
Article

DOI: 10.1007/s11032-010-9462-9

Cite this article as:
Fusari, C.M., Lia, V.V., Nishinakamasu, V. et al. Mol Breeding (2011) 28: 73. doi:10.1007/s11032-010-9462-9

Abstract

Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) are increasingly used for cultivar identification, construction of genetic maps, genetic diversity assessment, association mapping and marker-assisted breeding. Although there are several highly sensitive methods for the detection of polymorphisms, most of them are often beyond the budget of medium-throughput academic laboratories or seed companies. Heteroduplex analysis by enzymatic cleavage (CEL1CH) or denaturing high-performance liquid chromatography (dHPLC) has been successfully used to examine genetic variation in several plant and animal species. In this work, we assess and compare the performance of both methods in sunflower by genotyping SNPs from a set of 24 selected polymorphic candidate genes. The CEL1CH method allowed us to accurately detect allele differences in 10 out of 24 regions using an in-house prepared CEL1 enzyme (celery single strand endonuclease 1, Apium graveolens L.). Similarly, a total of 11 regions were successfully optimized for dHPLC analysis. As a scaling-up approach, both strategies were tested to genotype either 42 SNPs/indels in 22 sunflower accessions from the local germplasm bank or 33 SNPs/indels in 90 recombinant inbred lines (RILs) for genetic mapping purposes. Summarizing, a total of 601 genotypes were efficiently analyzed either with CEL1CH (110) or dHPCL (491). In conclusion, CEL1CH and dHPLC proved to be robust, complementary methods, allowing medium-scale laboratories to scale up the number of both SNPs and individuals to be included in genetic studies and targeted germplasm diversity characterization (EcoTILLING).

Keywords

SunflowerSNPsHeteroduplex analysisCEL1dHPLCHigh-throughput genotyping

Supplementary material

11032_2010_9462_MOESM1_ESM.pdf (126 kb)
(PDF 126 kb)
11032_2010_9462_MOESM3_ESM.pdf (3.2 mb)
(PDF 3326 kb)
11032_2010_9462_MOESM4_ESM.pdf (1.3 mb)
(PDF 1299 kb)
11032_2010_9462_MOESM5_ESM.pdf (117 kb)
(PDF 116 kb)

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Corina M. Fusari
    • 1
  • Verónica V. Lia
    • 1
    • 2
  • Verónica Nishinakamasu
    • 1
  • Jeremías E. Zubrzycki
    • 1
  • Andrea F. Puebla
    • 1
  • Alberto E. Maligne
    • 1
  • H. Esteban Hopp
    • 1
    • 2
  • Ruth A. Heinz
    • 1
    • 2
  • Norma B. Paniego
    • 1
  1. 1.Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA)Buenos AiresArgentina
  2. 2.Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresCiudad UniversitariaArgentina