Genetic Resources and Crop Evolution

, Volume 61, Issue 1, pp 247–266 | Cite as

Nuclear intron-targeting markers in genetic diversity analysis of black nightshade (Solanum sect. Solanum, Solanaceae) accessions

  • Péter Poczai
  • István Cernák
  • Ildikó Varga
  • Jaakko Hyvönen
Research Article


Different molecular markers are routinely used in studies of potato (Solanum tuberosum) and the genus Solanum in general. Genome sequence databases provide potential to design new markers for various applications. Here we present the application of a recently developed core set of nuclear intron-targeting (indel) markers. These markers are based on the fact that in the plant genome introns are more variable than exons; therefore primers flanking exons can reveal polymorphisms related to introns. We detected such variation among accessions of the eight different species of black nightshades (Solanum sect. Solanum). Members of this group are important sources of food, mostly in Africa, while others are poisonous weeds with near global distribution. The tested 29 primers were designed previously for potato based on Solanaceae EST and other genomic databases and targeted 16 different genes. Our results showed that Solanum intron-targeting markers are not very polymorphic but identified considerable structure among accessions indicating fairly high interspecies differentiation. Further analyses showed that inbreeding is unlikely to be the major driving force in determining the genetic structure of the analyzed species. All phylogenetic analyses resolved the species included in our study as distinct clades with high support values, but provided weak information about their internal relationships. In summary, indel markers would be useful for the assignment of new Solanum germplasm to taxonomic groups or to identify certain taxa. They could also be used to address important question about genetic diversity and should yield results comparable to other markers covering the whole genome.


Cross-species amplification Expressed sequence tags Gene-targeted markers Genetic data mining Indels Marker transferability 



PP gratefully acknowledges support from a Marie Curie Fellowship Grant (PIEF-GA-2011-300186) under the seventh framework program of the European Union. This study was partially supported by a Hungarian Eötvös Research Grant and a Campus Hungary Grant provided to IV. IC is supported by the János Bolyai Research Fellowship of the Hungarian Academy of Sciences.

Supplementary material

10722_2013_31_MOESM1_ESM.png (63 kb)
Supplementary material Convergence of the sampler and posterior densities for θ B. Estimates are based on the f = 0 model. Plots show the posterior density (upper plot) and the sample history (lower plot) of θ B. (PNG 63 kb)
10722_2013_31_MOESM2_ESM.png (193 kb)
Supplementary material The plots show the partial graphical exploration of the output from the four different runs of the intron-targeting dataset analyzed in MrBayes v.3.2. The first graphs in the upper and lower row are trace plots of the log likelihood (lnL) and the sampled values. Burn in is not shown on the plots and all runs reach stationarity. Blue and red traces indicate run1 and run2 in the upper left, while in the lower left run3 and run4, respectively. The second graph is a bivariate plot of the split frequencies for run1 and run2 (upper right) and run3 and run4 (lower left) created with AWTY. The high correlation shows convergence of the runs. (PNG 193 kb)
10722_2013_31_MOESM3_ESM.png (84 kb)
Supplementary material Character reconstructions mapped on the strict parsimony consensus tree. Black dots represent synapomorphic changes while white dots designate homoplasies. (PNG 84 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Péter Poczai
    • 1
  • István Cernák
    • 2
  • Ildikó Varga
    • 1
  • Jaakko Hyvönen
    • 1
  1. 1.Plant Biology, Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
  2. 2.Potato Research Centre, Centre of Agricultural SciencesUniversity of PannoniaKeszthelyHungary

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