title: Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform.
abstract: In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2,024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships.
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Monden
authors.affiliation: Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
authors.forename: Ayaka
authors.initials: A
authors.lastname: Yamamoto
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
authors.forename: Akiko
authors.initials: A
authors.lastname: Shindo
authors.affiliation: Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan tahara@cc.okayama-u.ac.jp.
authors.forename: Makoto
authors.initials: M
authors.lastname: Tahara
mesh_terms: D016172:DNA Fingerprinting; D056726:Genetic Association Studies; D005819:Genetic Markers; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D027723:Ipomoea batatas / Q000235:genetics*; D011110:Polymorphism, Genetic; D018626:Retroelements; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D018626:Retroelements
keywords: DNA fingerprinting; high-throughput sequencing; molecular marker; retrotransposon; sweet potato