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KMID : 0613820220320120947
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Journal of Life Science
2022 Volume.32 No. 12 p.947 ~ p.955
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Identification of Domesticated Silkworm Varieties Using a Whole Genome Single Nucleotide Polymorphisms-based Decision Tree
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Park Jong-Woo
Park Jeong-Sun
Jeong Chan-Young
Kwon Hyeok-Gyu
Kang Sang-Kuk
Kim Seong-Wan
Kim Nam-Suk
Kim Kee-Young
Kim Ik-Soo
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Abstract
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Silkworms, which have recently shown promise as functional health foods, show functional differences between varieties; therefore, the need for variety identification is emerging. In this study, we analyzed the whole silkworm genome to identify 10 unique silkworm varieties (Baekhwang, Baekok, Daebaek, Daebak, Daehwang, Goldensilk, Hansaeng, Joohwang, Kumkang, and Kumok) using single nucleotide polymorphisms (SNP) present in the genome as biomarkers. In addition, nine SNPs were selected to discriminate between varieties by selecting SNPs specific to each variety. We subsequently created a decision tree capable of cross-verifying each variety and classifying the varieties through sequential analysis. Restriction fragment length polymorphism (RFLP) was used for SNP867 and SNP9183 to differentiate between the varieties of Daehwang and Goldensilk and between Kumkang and Daebak, respectively. A tetra-primer amplification refractory (T-ARMS) mutation was used to analyze the re- maining SNPs. As a result, we could isolate the same group or select an individual variety using the nine unique SNPs from SNP780 to SNP9183. Furthermore, nucleotide sequence analysis for the
region confirmed that the alleles were identical. In conclusion, our results show that combining SNP analysis of the whole silkworm genome with the decision tree is of high value as a discriminative marker for classifying silkworm varieties.
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KEYWORD
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Markers, silkworm varieties, SNP, T-ARMS
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