title: MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform.
abstract: Restriction-enzyme (RE)-based next-generation sequencing methods have revolutionized marker-assisted genetic studies; however, the use of REs has limited their widespread adoption, especially in field samples with low-quality DNA and/or small quantities of DNA. Here, we developed a PCR-based procedure to construct reduced representation libraries without RE digestion steps, representing de novo single-nucleotide polymorphism discovery, and its genotyping using next-generation sequencing. Using multiplexed inter-simple sequence repeat (ISSR) primers, thousands of genome-wide regions were amplified effectively from a wide variety of genomes, without prior genetic information. We demonstrated: 1) Mendelian gametic segregation of the discovered variants; 2) reproducibility of genotyping by checking its applicability for individual identification; and 3) applicability in a wide variety of species by checking standard population genetic analysis. This approach, called multiplexed ISSR genotyping by sequencing, should be applicable to many marker-assisted genetic studies with a wide range of DNA qualities and quantities.
authors.affiliation: Tohoku University, Kawatabi Field Science Center, Graduate School of Agricultural Science, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan.
authors.forename: Yoshihisa
authors.initials: Y
authors.lastname: Suyama
authors.affiliation: Tohoku University, Kawatabi Field Science Center, Graduate School of Agricultural Science, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Matsuki
mesh_terms: D000363:Agaricales / Q000145:classification / Q000235:genetics; D000818:Animals; D033342:Copepoda / Q000145:classification / Q000235:genetics; D017931:DNA Primers / Q000138:chemical synthesis / Q000737:chemistry; D049851:Gastropoda / Q000145:classification / Q000235:genetics; D005819:Genetic Markers; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D007076:Iguanas / Q000145:classification / Q000235:genetics; D018895:Microsatellite Repeats; D029595:Orchidaceae / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D047528:Stichopus / Q000145:classification / Q000235:genetics
chemical_list: D017931:DNA Primers; D005819:Genetic Markers