SREL Reprint #3883

Methodological test of genetic population structure using MIG-seq analysis from noninvasively obtained wild boar (Sus scrofa) feces DNA

Rie Saito1,2,3, Natsuko Ito Kondo4, Masanori Tamaoki3,4, JaeIck Jo5, Kenji Inami6, and James C. Beasley1,7

1Savannah River Ecology Laboratory, University of Georgia, P O Drawer E, Aiken, SC, USA
2Department of Animal Science and Fisheries Science, Faculty of Agriculture, Iwate University, 18-8 Ueda 3-chome, Morioka, Japan
3Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, 10-2 Fukasaku, Miharu-machi, Japan
4Biodiversity Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Japan
5Research Division, Fukushima Prefectural Centre for Environmental Creation, 10-2 Fukasaku, Miharu-machi, Japan
6Wildlife Symbiosis Centre, 67 Nagakubo, Tamai, Ootama, Japan
7Warnell School of Forestry and Natural Resources, University of Georgia, 180 East Green St, Athens, GA, USA

Abstract: Ecological studies using noninvasive genetics are useful tools for obtaining important information for the management and protection of wildlife. Multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) is accepted as a powerful tool for clarifying the genetic population structure of wildlife because low quality DNA and any species can be used. However, no study of MIG-seq analysis using fecal samples has been conducted. Thus, we tested a method for MIG-seq analysis using fecal DNA of wild boars Sus scrofa by obtaining and securing a sufficient amount of DNA for MIG-seq and then extracting only varied single-nucleotide polymorphisms (SNPs) by comparing with the host DNA as a reference. Our results showed that samples with threshold cycle (Ct) values ≤ 32 indicated sufficient amplification by first PCR of MIG-seq analysis. The average number of effective SNPs of rectal feces covered 59% of the SNPs detected in muscle. However, in the case of trap fecal samples, exposed in the field, the average number of effective SNPs covered only 4% of SNPs detected in muscle. We concluded that sufficient SNP data could not be obtained with fecal samples collected from the field, and further optimization of the MIG-seq protocol would be necessary.

Keywords: Japan, mammal feces, noninvasive sample, RT-qPCR, SNPs

SREL Reprint #3883

Saito, R., N. I. Kondo, M. Tamaoki, J. Jo, K. Inami, and J. C. Beasley. 2026. Methodological test of genetic population structure using MIG-seq analysis from noninvasively obtained wild boar (Sus scrofa) feces DNA. Mammal Study 51(3).

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).