Molecular identification of the strains of the domestic silkworm, Bombyx mori (Lepidoptera: Bombycidae), which are endemic to Korea, based on single nucleotide polymorphisms in mitochondrial genome sequences

• Published in: Journal of Asia-Pacific entomology 2022, 25(2), , pp.1-8
• Main Authors: Park, Jeong Sun, Kim, Min Jee, Kim, Seong-Wan, Kim, Kee-Young, Kim, Seong-Ryul, Kim, Iksoo
• Format: Article
• Language: English
• Subjects: Endemic strains; Mitochondrial genome; Molecular identification; Silkworm; Single nucleotide polymorphism; 농학
• ISSN: 1226-8615; 1876-7990
• DOI: 10.1016/j.aspen.2022.101922

[Display omitted] •We developed molecular identification methods for three endemic silkworm strains.•We found 15 SNP in mitogenomes of 5 endemic and 34 stock strains.•We applied the RFLP-PCR and the tetra-primer ARMS-PCR methods.•We distinguished three endemic strains using both methods in agarose gels.•These methods could be useful for distinguishing endemic strains preserved in Korea. The domestic silkworm, Bombyx mori (Lepidoptera: Bombycidae), has been diversified into various strains over a long period. However, methods to distinguish silkworm strains remain limited partially owing to the genetic similarity caused by the long history of domestication. In this study, we developed molecular identification methods to distinguish three domestic silkworm strains, which are endemic to Korea. By comparing publicly available complete mitochondrial genome (mitogenome) sequences of five endemic strains and 34 stock silkworm strains analyzed in a previous study, we detected 15 single nucleotide polymorphisms (SNPs; SNP1–SNP15), which distinguished the following three endemic strains: Sun7ho (SN7), Sandongsammyeon (SDS), and Sammyeonhonghoeback (SMH). We used two SNPs for each strain to identify the three endemic strains. To distinguish each SN7 and SDS from the remaining four endemic and 34 stock strains, the PCR-restriction fragment length polymorphism method was employed using Acu I and Hpa I restriction enzymes, which recognize SNP1 and SNP8, respectively. Additionally, the tetra-primer amplification refractory mutation system PCR method was used to determine the regions containing SNP3, SNP11, and both SNP14 and SNP15 to distinguish SN7, SDS, and SMH, respectively, from the remaining strains. A validation test with additional individuals showed that each target strain was clearly recognized, suggesting that mitogenome SNP-based methods can be used to identify three endemic silkworm strains during culture and breeding.