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

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Abstract

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.

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References

  • Ames M, Spooner DM (2010) Phylogeny of Solanum series Piurana and related species in Solanum section Petota based on five conserved ortholog sequences. Taxon 59:1091–1101

    Google Scholar 

  • Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Boris KV, Ryzhova NN, Kochieva EZ (2011) Identification and characterization of intraspecific variability of the sucrose synthase gene Sus4 of potato (Solanum tuberosum). Russ J Genet 47:168–175

    Article  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    CAS  PubMed Central  PubMed  Google Scholar 

  • Britten RJ, Rowen L, Williams J, Cameron RA (2003) Majority of divergence between closely related DNA samples is due to indels. PNAS 100:661–4665

    Article  Google Scholar 

  • Cai D, Rodríguez F, Teng Y, Ané C, Bonierbale M, Mueller LA, Spooner DM (2012) Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evol Biol 12:70

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19

    Article  PubMed Central  PubMed  Google Scholar 

  • Colon LT, Eijlander R, Budding DJ, Pieters MMJ, Hoogendoorn J, Van-Ijzendoorn MT (1993) Resistance to potato late blight (Phytophthora infestans (Mont.) de Bary) in Solanum nigrum, S. villosum and their sexual hybrids with S. tuberosum and S. demissum. Euphytica 66:55–64

    Article  Google Scholar 

  • D’Agostino N, Golas T, van de Geest H, Bombarely A, Dawood T, Zethof J, Driedonks N, Wijnker E, Bargsten J, Nap JP, Mariani C, Rieu I (2013) Genomic analysis of the native European Solanum species S. dulcamara. BMC Genomics 14:356

    Article  PubMed Central  PubMed  Google Scholar 

  • De Keyser E, De Riek J, Van Bockstaele E (2009) Discovery of species-wide EST-derived markers in Rhododendron by intron-flanking primer design. Mol Breeding 23:171–178

    Article  CAS  Google Scholar 

  • Dehmer KJ (2001) Conclusions on the taxonomy of the Solanum nigrum complex by molecular analysis of IPK germplasm accessions. In: van den Berg RG, Barendse GWM, van der Weerden GM, Mariani C (eds) Solanaceae V: advances in taxonomy and utilization. Nijmegen University Press, The Netherlands, pp 85–96

    Google Scholar 

  • Dehmer KJ, Hammer K (2004) Taxonomic status and geographic provenance of germplasm accessions in the Solanum nigrum L complex: AFLP data. Genet Resour Crop Evol 51:551–558

    Article  CAS  Google Scholar 

  • Dehmer KJ, Stracke S (1999) Molecular analyses of genebank accessions of the Solanum nigrum complex. In: Andrews S, Leslie AC, Alexander C (eds) Third international symposium on the taxonomy of cultivated plants. Royal Botanic Gardens, Kew, pp 343–345

    Google Scholar 

  • Draffehn AM, Meller S, Li L, Gebhardt C (2010) Natural diversity of potato (Solanum tuberosum) invertases. BMC Plant Biol 10:271

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M, Upadhyaya HD, Ortiz R (2007) The molecularization of public sector crop breeding: progress, problems, and prospects. Adv Agron 95:163–318

    Article  CAS  Google Scholar 

  • Edmonds JM (1979) Biosystematics of Solanum L. section Solanum (Maurella). In: Hawkes JG, Lester RN, Skelding AD (eds) The biology and taxonomy of the Solanaceae. Academic Press, London, pp 529–548

    Google Scholar 

  • Edmonds JM, Chweya JA (1997) Black nightshades. Solanum nigrum L. and related species. Promoting the conservation and use of underutilized and neglected crops, vol 15. International Plant Genetic Resources Institute, Rome, Italy

  • Eijlander R, Stiekema WJ (1994) Biological containment of potato (Solanum tuberosum): outcrossing to the related wild species black nightshade (Solanum nigrum) and bittersweet (Solanum dulcamara). Sex Plant Reprod 7:29–40

    Article  Google Scholar 

  • Farris JS (1989) The retention index and homoplasy excess. Syst Zool 38:406–407

    Article  Google Scholar 

  • Farris JS, Albert V, Källersjö M, Lipscomb D, Kluge AG (1996) Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99–124

    Article  Google Scholar 

  • García-Lor A, Luro F, Navarro L, Ollitrault P (2012) Comparative use of indel and SSR marker sin deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Mol Genet Genomics 287:77–94

    Article  PubMed  Google Scholar 

  • Golas TM, Sikkema A, Gros J, Feron RM, van den Berg RG, van der Weerden GM, Mariani C, Allefs JJ (2010) Identification of a resistance gene Rpi-dlc1 to Phytophthora infestans in European accessions of Solanum dulcamara. Theor Appl Genet 120:797–808

    Article  PubMed Central  PubMed  Google Scholar 

  • Golas TM, van de Geest H, Gros J, Sikkema A, D’Agostino N, Nap JP, Mariani C, Allefs JJ, Rieu I (2013) Comparative next-generation mapping of the Phytophthora infestans gene Rpi-dlc2 in the European species Solanum dulcamara. Theor Appl Genet 126:59–68

    Article  CAS  PubMed  Google Scholar 

  • Goloboff PA (1994) NONA: a tree searching program. Program and documentation. www.cladistics.com/aboutNona.htm

  • Gorji AM, Matyas KK, Dublecz Z, Decsi K, Cernak I, Hoffmann B, Taller J, Polgar Z (2012) In vitro osmotic stress tolerance in potato and identification of major QTLs. Am J Pot Res 89:453–464

    Article  Google Scholar 

  • Hachiken T, Sato K, Hasegawa T, Ichitani K, Kawase M, Fukunaga K (2013) Geographical distribution of waxy gene SNPs and indels in foxtail millet, Setaria italic (L.) P. Beauv. Genet Resour Crop Evol 60:1559–1570

    Article  Google Scholar 

  • Haile JK, Hammer K, Badebo A, Nachit MM, Röder MS (2013) Genetic diversity assessment of Ethiopian tetraploid wheat landraces and improved durum wheat varieties using microsatellites and markers linked with stem rust resistance. Genet Resour Crop Evol 60:513–527

    Article  CAS  Google Scholar 

  • Holland JB, Helland SJ, Sharapova N, Rhyne DC (2001) Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat. Genome 44:1065–1076

    Article  CAS  PubMed  Google Scholar 

  • Holsinger KE (1999) Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130:245–255

    Article  Google Scholar 

  • Holsinger KE, Lewis PO (2003) HICKORY: a package for the analysis of population genetic data, version 1.0.4. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA. Distributed by the authors

  • Horsman K, Bergervoet JEM, Jacobsen E (1997) Somatic hybridization between Solanum tuberosum and species of the S. nigrum complex: selection of vigorously growing and flowering plants. Euphytica 96:345–352

    Article  Google Scholar 

  • Hu J, Seiler G, Kole C (2010) Genetics, genomics and breeding of sunflower. CRC Press, Routledge

    Book  Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755

    Article  CAS  PubMed  Google Scholar 

  • Jacoby A, Labuschagne MT, Viljoen CD (2003) Genetic relationships between Southern African Solanum retroflexum Dun and other related species measured by morphological and DNA markers. Euphytica 132:109–113

    Article  CAS  Google Scholar 

  • Kimura M (1983) Rare variant alleles in the light of the neutral theory. Mol Biol Evol 1:84–93

    CAS  PubMed  Google Scholar 

  • Kimura M, Crow J (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738

    CAS  PubMed  Google Scholar 

  • Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of Anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Lebecka R (2008) Host–pathogen interaction between Phytophthora infestans and Solanum nigrum, S. villosum, and S. scabrum. Eur J Plant Pathol 120:233–240

    Article  Google Scholar 

  • Lehmann C, Biela C, Töpfl S, Jansen G, Vögel R (2007) Solanum scabrum—a potential source of a coloring plant extract. Euphytica 158:189–199

    Article  Google Scholar 

  • Levin RA, Blanton J, Miller JS (2009) Phylogenetic utility of nuclear nitrate reductase: a multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae). Mol Phylogenet Evol 50:608–617

    Article  CAS  PubMed  Google Scholar 

  • Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:391–398

    Google Scholar 

  • Liu BH (1998) Statistical genomics: linkage, mapping and QTL analysis. CRC Press, Boca Raton

    Google Scholar 

  • Manoko MLK, van den Berg RG, Feron RMC, van der Weerden GM, Mariani C (2007) AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu stricto (Solanaceae). Plant Syst Evol 267:1–11

    Article  Google Scholar 

  • Manoko MLK, van den Berg RG, Feron RMC, van der Weerden GM, Mariani C (2008) Genetic diversity of the African hexaploid species of Solanum scabrum Mill. and Solanum nigrum L. (Solanaceae). Genetic Res Crop Evol 55:409–418

    Article  Google Scholar 

  • Morales M, Roig E, Monforte AJ, Arús P, Garcia-Mas J (2004) Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.). Genome 47:352–360

    Article  CAS  PubMed  Google Scholar 

  • Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y et al (2005) The SOL genomics network: a comparative resource for solanaceae biology and beyond. Plant Physiol 138:1310–1317

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497

    Article  CAS  Google Scholar 

  • Nagy S, Poczai P, Cernák I, Gorji AM, Hegedűs G, Taller J (2012) PICcalc: an online program to calculate polymorphic information content for molecular genetic studies. Biochem Genet 50:9–10

    Article  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. PNAS USA 70:3321–3323

    Article  CAS  PubMed  Google Scholar 

  • Nixon KC (1999) The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407–414

    Article  Google Scholar 

  • Nixon KC (2002) Winclada. Version 1.00.08. http://www.cladistics.com/aboutWinc.htm. Ithaca, NY

  • Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581–583

    Article  CAS  PubMed  Google Scholar 

  • Olet EA, Huen M, Lye KA (2005) African crop or poisonous nightshade; the enigma of poisonous or edible black nightshades solved. Afr J Ecol 43:158–161

    Article  Google Scholar 

  • Park S, Yu HJ, Mun JH, Lee SC (2010) Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Genet Genomics 283:135–145

    Article  CAS  PubMed  Google Scholar 

  • Poczai P, Hyvönen J (2011) On the origin of Solanum nigrum: can networks help? Mol Biol Rep 38:1171–1185

    Article  CAS  PubMed  Google Scholar 

  • Poczai P, Cernák I, Gorji AM, Nagy S, Taller J, Polgár J (2010) Development of intron-targeting (IT) markers for potato and cross-species amplification in Solanum nigrum (Solanaceae). Amer J Bot 97:e142–e145

    Article  CAS  Google Scholar 

  • Poczai P, Varga I, Bell NE, Hyvönen J (2011) Genetic diversity assessment of bittersweet (Solanum dulcamara, Solanaceae) germplasm using conserved DNA-derived polymorphism and intron-targeting markers. Ann Appl Biol 159:141–153

    Article  CAS  Google Scholar 

  • Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen JPT, Hyvönen J (2013) Advances in plant gene-targeted and functional markers: a review. Plant Methods 9:6

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195

    Article  Google Scholar 

  • Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivar. Theor Appl Genet 98:107–112

    Article  CAS  Google Scholar 

  • Rambaut A, Drummond AJ (2007) Tracer v1.4. http://tree.bio.ed.ac.uk/software/tracer/. Accessed 13 Feb 2013

  • Rodríguez F, Spooner DM (2009) Nitrate reductase phylogeny of potato (Solanum sect. Petota) genomes with emphasis on the origins of the polyploid species. Syst Bot 34:207–219

    Article  Google Scholar 

  • Rodríguez F, Wu F, Ané C, Tanksley S, Spooner DM (2009) Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evol Biol 9:191

    Article  PubMed Central  PubMed  Google Scholar 

  • Schippers RR (2000) African indigenous vegetables. An overview of the cultivated species. Natural Resources Institute/ACPEU Technical Centre of Agriculture and Rural Cooperation, Catham, pp 147–176

    Google Scholar 

  • Silvestro D, Michalak I (2012) raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 12:335–337

    Article  Google Scholar 

  • Spooner DM, Rodríguez F, Polgár Z, Ballerd HE, Jansky SH (2008) Genomic origins of potato polyploids: GBSSI gene sequencing data. Crop Sci 48:S27–S36

    Google Scholar 

  • Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics 22:2688–2690

    Article  CAS  PubMed  Google Scholar 

  • Stöver BC, Müller KF (2010) TreeGraph2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7

    Article  PubMed Central  PubMed  Google Scholar 

  • Sun J, Loboda T, Sung SS, Black CC (1992) Sucrose synthase in wild tomato, Lycopersicon chmielewskii, and tomato fruit skin strength. Plant Physiol 98:1163–1169

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tepe EJ, Bohs L (2010) A molecular phylogeny of Solanum sect. Pteroidea (Solanaceae) and the utility of COSII markers in resolving relationships among closely related species. Taxon 59:733–743

    Google Scholar 

  • Vasemägi A, Gross R, Plam D, Paaver T, Primmer CR (2010) Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics 11:156

    Article  PubMed Central  PubMed  Google Scholar 

  • Walbot V, Warren C (1988) Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system. Mol Gen Genet 211:27–34

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Smith A, Brenner ML (1994) Temporal and spatial expression pattern of sucrose synthase during tomato fruit development. Plant Physiol 104:535–540

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wang Y, Chen J, Francis DM, Shen H, Wu T, Yang W (2010) Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information. Theor Appl Genet 121:1199–1207

    Article  CAS  PubMed  Google Scholar 

  • Weese TL, Bohs L (2007) A three-gene phylogeny of the genus Solanum (Solanaceae). Syst Bot 32:445–463

    Article  Google Scholar 

  • Wu F, Mueller LA, Crouzillat D, Pétiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174:1407–1420

    Article  CAS  PubMed  Google Scholar 

  • Xiong Z, Zhang S, Wang Y, Ford-Lloyd BV, Tu M, Jin X, Wu Y, Yan H, Yang X, Liu P et al (2010) Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers. Genet Resour Crop Evol 57:891–902

    Article  CAS  Google Scholar 

  • Xu G, Ma H, Nei M, Kong H (2009) Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. PNAS 106:835–840

    Article  CAS  PubMed  Google Scholar 

  • Yeh FC, Yang R-C, Boyle TJB, Ye Z-H, Mao JX (1997) POPGENE, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, MN

    Google Scholar 

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Acknowledgments

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.

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Authors and Affiliations

  1. Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, Finland

    Péter Poczai, Ildikó Varga & Jaakko Hyvönen

  2. Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, Festetics 7, 8360, Keszthely, Hungary

    István Cernák

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  1. Péter Poczai
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  2. István Cernák
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  3. Ildikó Varga
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Correspondence to Péter Poczai.

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Péter Poczai and István Cernák have contributed equally to this work.

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10722_2013_31_MOESM1_ESM.png

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

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

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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Poczai, P., Cernák, I., Varga, I. et al. Nuclear intron-targeting markers in genetic diversity analysis of black nightshade (Solanum sect. Solanum, Solanaceae) accessions. Genet Resour Crop Evol 61, 247–266 (2014). https://doi.org/10.1007/s10722-013-0031-z

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