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.

Role of ancient lakes in genetic and phenotypic diversification of freshwater snails

“…To obtain genome‐wide SNP information of these species groups from total DNA, we conducted MIG‐seq method (Suyama & Matsuki, ). MIG‐seq is a type of reduced representation sequencing such as restriction site‐associated DNA sequencing, and especially effective for low‐quality DNA and small quantities of DNA (Tamaki, Yoichi, Matsuki, Suyama, & Mizuno, ), which was performed for viviparid snails in previous research (Hirano et al, ).…”

“…MIG‐seq is a type of reduced representation sequencing such as restriction site‐associated DNA sequencing, and especially effective for low‐quality DNA and small quantities of DNA (Tamaki, Yoichi, Matsuki, Suyama, & Mizuno, ), which was performed for viviparid snails in previous research (Hirano et al, ). Preparation of the MIG‐seq library was executed under a method modified from Suyama and Matsuki () using an Illumina MiSeq Sequencer (Illumina), and an MiSeq Reagent Kit version 3 (150 cycle; Illumina) (Hirano et al, ; Y. Tsunamoto et al, unpublished data).…”

Understanding and monitoring the consequences of human impacts on intraspecific variation

“…Some common NGS approaches include whole genome resequencing, reduced‐representation sequencing (RRS), and pooled DNA sequencing (Pool‐seq). RRS methods include genotyping‐by‐sequencing (GBS; Davey et al., 2011), restriction site‐associated DNA sequencing (RADseq; Baird, Etter, Atwood, & Currey, 2008; Peterson, Weber, Kay, Fisher, & Hoekstra, 2012), and multiplexed ISSR genotyping‐by‐sequencing (MIGseq) (Suyama & Matsuki, 2015). By restricting sequencing to a fraction of the genome (e.g., restriction enzyme sites ~1% of the genome), GBS and RADseq can typically generate tens of thousands of polymorphisms for monitoring variation.…”

Descriptions of two new species of Platygaster Latreille that attack gall midges (Diptera, Cecidomyiidae) with notes on their biology (Hymenoptera, Platygastridae)

“…Our rearing experiments indicated that P. urniphila is a gregarious parasitoid because males and females were reared from a single host larva (Table 1). To confirm polyembryonic reproduction by P. urniphila , we need histological survey or MIG-seq analysis (Suyama and Matsuki 2015) that discriminate individuals originated from clonal division and sexual reproduction.…”