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Discovery of markers for determining the maturity of silkworms by comparing gene expression patterns

  • Jong Woo Park (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Chan Young Jeong (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Hyeok Gyu Kwon (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Seul Ki Park (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Ji Hae Lee (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Sang Kuk Kang (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Seong-Wan Kim (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Hyun-Bok Kim (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Kee Young Kim (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA) ;
  • Chun Wan Park (Department of Agricultural Engineering, National Institute of Agricultural Sciences, RDA) ;
  • Seong-Ryul Kim (Department of Agricultural Biology, National Institute of Agricultural Sciences, RDA)
  • Received : 2023.08.17
  • Accepted : 2023.09.26
  • Published : 2023.09.30

Abstract

The advantages of silkworms as functional foods are well known and various products are being developed. In general, silkworms sold in the market include silkworm powder (3 days of fifth instars) and SukJam (7 days or more of fifth instars), In other words, product classification is made according to the maturity of the fifth instar silkworms. In this study, we analyzed the gene expression changes in the fifth instar silkworms and attempted to validate the use of deregulated genes in maturity analysis. After rearing BaekokJam, transcriptome analysis was performed on days 1, 3, 5, and 8 days of the fifth instar, and differentially expressed genes showing differences at each period were selected. Of the 31,841 contigs analyzed, 4012 contigs were identified with a log2 fold change of two or more between 5 and 8 days of the fifth instar. RT-PCR was performed for 18 contigs, which showed increased or decreased expression, but in c127159, c97909, c96974, c119920, c42251, and c80216 showed clear differences. To identify SukJam, a combination of the contigs c127159 (180 bp), c97909 (143 bp), and c80216 (120 bp) was amplified. Taken together, these results suggest that the harvest time of silkworms can be determined using gene expression pattern analysis.

Keywords

Acknowledgement

This study was supported by the 2023 RDA fellowship program of National Institute of Agricultural Science and was supported by a grant (No. RS-2022-RD010224) from the Rural Development Administration, Republic of Korea.

References

  1. Ahn, HY, Cha JY, Park KR, Kim YR, Cho YS (2013) Improvement effect of fermented silkworm (Bombyx mori L.) power against orotic acid-induced fatty liver in rats. J Life Sci 23, 789-795. https://doi.org/10.5352/JLS.2013.23.6.789
  2. Andrews S (2011) The FastQC Project. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  3. Ashburner M, Ball CA, Blake JA. Botstein D, Butler H, Cherry JM, et al. (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25, 25-29. https://doi.org 10.1038/75556
  4. Bo L, Colin ND (2011) RSEM: accurate transcript quantification from RNA-Seq data with orwithout a reference genome. BMC bioinformatics 12, 323. https://doi.org/10.1186/1471-2105-12-323
  5. Duan J, Xiz C, Zhao G, Jia J (2012) Optimizing de novo sommon wheat transcriptome assembly using short-read RNA-Seq data. BMC Genome 3, 392. https://doi.org/10.1186/1471-2164-13-392
  6. Forrest GL, Gonzalez B (2000) Carbonyl reductase. Chem Biol Interact 129, 1-40. https://doi.org/10.1016/s0009-2797(00)00196-4
  7. Freedman AH, Clamp M, Sackton TB (2019) Error, noise and bias in de nove transcriptome assemblies. Mol Ecol Resour 21, 18-29. https://doi.org/10.1111/1755-0998.13156
  8. Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150-3152. https://doi.org/10.1093/bioinformatics/bts565
  9. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology 9, 644. https://doi.org/10.1038/nbt.1883
  10. Hayashi Y (1961) Properties of xanthine dehydrogenase in the silkworm, Bombyx mori L. Nature 192, 56-757. https://doi.org/10.1016/0006-3002(62)91020-x
  11. Heng J, Liu H Xu J, Huang J, Sun X, Yang R, et al. (2022) KPI5 is involved in the regulation of the expression of antibacterial peptide genes and hemolymph melanization in the silkworm, Bombyx mori. Front Immunol 13, 907427. https://doi.org/10.3389/fimmu.2022.907427
  12. Hwang SY, Kim GS (2020) A study on quality characteristics of silkworm (Bombyx mori L.) by various pretreatment methods. Culi Sci & Hos Res 26, 6-12. https://doi.org/10.20878/cshr.2020.26.6.014
  13. International Silkworm Genome C (2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol. 38, 1036-1045. https://doi.org/10.1016/j.ibmb.2008.11.004
  14. Ji SD, Kim NS, Kweon HY, Choi BH, Kim KY, Koh YH (2016) Nutrition composition differences among steamed and freeze-dried mature silkworm larval powders made from 3 Bombyx mori varieties weaving different colored cocoons. Int J Indust ntomol 33, 6-14. https://doi.org/10.7852/ijie.2016.33.1.6
  15. Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25. https://doi.org/10.1186/gb-2009-10-3-r25
  16. Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie2. Nat Methods 9, 357-359. https://doi.org/10.1038/nmeth.1923
  17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
  18. Li Y, Wang G, Tian J, Liu H, Yang H, Yi Y, et al. (2012) Transcriptome analysis of the silkworm (Bombyx mori) by high-throughput RNA sequencing. PLoS One 7, e43713. https://doi.org/10.1371/journal.pone.0198077
  19. Livak KJ, Schmiigen TD (2011) Analysis of relative gene expression data using real-time quqntitative PCR and the 2-ΔΔCt method. Methods 5, 402-408. https://doi.org/10.1006/meth.2001.1262
  20. Meysick KC, Dimock K, Garber GE (1996). Molecular characterization and expression of a N-acetylneuraminate lyase gene from Trichomonas vaginalis. Mol Biochem Parasitol 76, 289-292. https://doi.org/10.1016/0166-6851(95)02544-8
  21. Papantonis A, Swevers L, Iatrou K. (2015) Chorion genes: a landscape of their evolution, structure, and regulation. Annu Rev Entomol 60, 177-194. https://doi.org/10.1146/annurev-ento-010814-020810
  22. Park JW, Park JS, Jeong CY, Kang SK, Kim SW, Kim NS, et al. (2022a) Identification of domesticated silkworm varieties using single nucleotide polymorphisms detected from mitochondrial genomes. Int J Indust Entomol 45, 29-34. http://dx.doi.org/10.7852/ijie.2022.45.1.29
  23. Park JW, Park JS, Jeong CY, Kang SK, Kim SW, Kim NS, et al. (2022b) Identification of domesticated silkworm varieties using a whole genome single nucleotide polymorphisms-based decision tree. J Life Sci 32, 947-955. https://doi.org/10.5352/JLS.2022.32.12.947
  24. Park JW, Lee CH, Jeong CY, Kwon HK, Park SK, Lee JH, et al. (2023) Gene expression changes in silkworm embryogenesis for prediction of hatching time. Int J Indust Entomol 46, 16-23. http://dx.doi.org/10.7852/ijie.2023.46.1.16
  25. Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, et al. (2015) WheatExp: An RNA-seq expression database for polyplioid wheat. BMC Plant Biol 15, 299. https://doi.org/10.1186/s12870-015-0692-1
  26. Ryu KS, Lee HS, Chung SH, Kang PD (1997) An activity of lowering blood-glucose levels according to preparative conditions of silkworm powder. Kor J Seric Sci 39, 79-85.
  27. Scott JG (1999) Cytochromes P450 and insecticide resistance. Insect Biochem Mol Biol 29, 757-777. https://doi.org/10.1016/S0965-1748(99)00038-7