Theoretical and Applied Genetics

, Volume 127, Issue 1, pp 193–209 | Cite as

Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs

  • Zahirul I. Talukder
  • Brent S. HulkeEmail author
  • Lili Qi
  • Brian E. Scheffler
  • Venkatramana Pegadaraju
  • Kevin McPhee
  • Thomas J. Gulya
Original Paper


Key message

Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana.


Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r 2 = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r 2 = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.


Linkage Disequilibrium Association Mapping Linkage Disequilibrium Decay Candidate Gene Locus Sunflower Line 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank the staff of the USDA-ARS North Central Regional Plant Introduction Station, Ames, Iowa, USA for providing us with germplasm and National Sunflower Association for providing SNP markers. We are very grateful to Drs. John Burke and John Bowers for providing map positions of the candidate genes and critically reviewing the manuscript. We also thank Dr. Z. Liu, M. Ramsett, N. Balbyshev, A. Hogness, A. Jani, and D. Weiskopf for technical assistance. This research was supported by the USDA-ARS National Sclerotinia Initiative, grant number 58-5442-8-230.

Conflict of interest

All experiments detailed herein were conducted in compliance with the applicable laws of the United States and the state of North Dakota. The authors declare that they have no conflict of interest.

Supplementary material

122_2013_2210_MOESM1_ESM.doc (32 kb)
Supplementary material 1 (DOC 31 kb)
122_2013_2210_MOESM2_ESM.docx (682 kb)
Patterns of linkage disequilibrium (LD) between all pairwise marker combinations for eight candidate gene sequences. Marks on the bars above each marker indicate the relative position of the marker in their respective gene sequences in bp. LD between pairs of markers is displayed in the squares as r 2, expressed as a percentage. Darker shading indicates stronger LD between the markers, and the black squares without a number indicate that marker pairs are in perfect LD (r 2 = 1.0) (DOCX 681 kb)
122_2013_2210_MOESM3_ESM.tiff (1.8 mb)
Linkage disequilibrium (LD) decay of individual candidate gene loci of sunflower stalk rot resistance. LD was measured by squared correlations of allele frequency (r 2) values against genetic distance (bp) between pairs of polymorphic sites within candidate gene sequences. Inner fitted trendlines are based on a nonlinear regression of r 2 against distance, using a mutation–recombination–drift model (Hill and Weir 1988). Trendline model R2 for the HaABI1-1, HaCOI1-1, HaCOI1-2, HaDET3-1, HaEIN2-1, and HaLACS2-1 genes were 0.27, 0.002, 0.004, 0.06, 0.16, and 0.002, respectively. LD decay of two candidate genes, HaABI1-2 and HaEIN1-2, were not plotted due to few polymorphic sites in the loci (TIFF 1859 kb)
122_2013_2210_MOESM4_ESM.tif (175 kb)
Phylogenetic tree of the COI1-like genes of 52 species including Helianthus annuus and Arabidopsis thaliana. Arabidopsis TIR1, a member of the same gene family as COI1, was included as an internal check. The tree was developed from a maximum parsimony model in the software TNT. Heuristic searches were performed from 20 Wagner trees with tree bisection reconnection branch swapping. Node support was determined by 100 jackknife replicates (TIFF 175 kb)


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© Springer-Verlag Berlin Heidelberg (outside the USA) 2013

Authors and Affiliations

  • Zahirul I. Talukder
    • 1
  • Brent S. Hulke
    • 2
    Email author
  • Lili Qi
    • 2
  • Brian E. Scheffler
    • 3
  • Venkatramana Pegadaraju
    • 4
  • Kevin McPhee
    • 1
  • Thomas J. Gulya
    • 2
  1. 1.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  2. 2.USDA-ARS, Northern Crop Science LaboratoryFargoUSA
  3. 3.USDA-ARS, Genomics and Bioinformatics Research UnitStonevilleUSA
  4. 4.BioDiagnostics Inc.River FallsUSA

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