title: Next generation sequencing based development of intron-targeting markers in tetraploid potato and their transferability to other Solanum species.
abstract: Intron-targeting (IT) markers were developed from next generation sequencing (NGS) derived transcript sequencing data from the potato cultivar White Lady. The applicability of the IT markers was analyzed in other potato genotypes, and their transferability was studied in other Solanum species: section Archaesolanum (5 species), sect. Solanum (6 species) and a Solanum nigrum population (11 genotypes). Out of 250 randomly chosen transcript sequences, 144 intron harboring loci could be identified for which primer pairs were designed on exons flanking the putative introns. The usefulness of the IT primers was experimentally analyzed on a subset of 40 randomly chosen loci. Statistical analysis of diversity parameters was performed using the ATETRA and POPGENE software packages. By localizing the detected 17 polymorphic loci 11 of the 12 potato chromosomes could be identified. Specificity of the designed IT primers was tested by sequence analysis of amplified IT fragments in a randomly chosen locus. The results revealed the efficiency of NGS derived IT marker development and indicated their utility in diverse molecular analyses including their applicability for cross-species studies.
authors.affiliation: Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, H-8360 Keszthely, Festetics u. 7, Hungary; Department of Plant Science and Biotechnology, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Festetics u. 7, Hungary; Seed and Plant Improvement Institute, Mahdasht Ave. 3185, Karaj, Iran. Electronic address: ahmadvandra@gmail.com.
authors.forename: Rahim
authors.initials: R
authors.lastname: Ahmadvand
authors.affiliation: Department of Biosciences, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland. Electronic address: peter.poczai@gmail.com.
authors.forename: Péter
authors.initials: P
authors.lastname: Poczai
authors.affiliation: Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, H-8360 Keszthely, Festetics u. 7, Hungary; Seed and Plant Improvement Institute, Mahdasht Ave. 3185, Karaj, Iran. Electronic address: hajianfarramin@yahoo.com.
authors.forename: Ramin
authors.initials: R
authors.lastname: Hajianfar
authors.affiliation: Department of Plant Science and Biotechnology, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Festetics u. 7, Hungary.
authors.forename: Balázs
authors.initials: B
authors.lastname: Kolics
authors.affiliation: Seed and Plant Improvement Institute, Mahdasht Ave. 3185, Karaj, Iran. Electronic address: mousapour_gorji@yahoo.com.
authors.forename: Ahmad Mousapour
authors.initials: AM
authors.lastname: Gorji
authors.affiliation: Potato Research Centre, Centre of Agricultural Sciences, University of Pannonia, H-8360 Keszthely, Festetics u. 7, Hungary. Electronic address: polg-zs@georgikon.hu.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Polgár
authors.affiliation: Department of Plant Science and Biotechnology, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Festetics u. 7, Hungary. Electronic address: taller@georgikon.hu.
authors.forename: János
authors.initials: J
authors.lastname: Taller
mesh_terms: D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D017343:Genes, Plant; D056426:Genetic Loci; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D011110:Polymorphism, Genetic; D017423:Sequence Analysis, RNA; D032322:Solanum / Q000235:genetics; D011198:Solanum tuberosum / Q000235:genetics*; D057891:Tetraploidy
chemical_list: D005819:Genetic Markers
keywords: Intron-targeting; Molecular marker; Next generation sequencing; Potato; Transcriptome analysis