Mycobiology

The Korean Society of Mycology (한국균학회)
권호 표지
DOI QR코드

DOI QR Code

Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars

  • Received : 2019.07.25
  • Accepted : 2019.09.03
  • Published : 2019.12.01
Download PDF
⟨ Previous Next ⟩

Abstract

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.

Keywords

References

  1. Terashima K, Matsumoto T. Strain typing of shiitake (Lentinula edodes) cultivars by AFLP analysis, focusing on a heat-dried fruiting body. Mycoscience. 2004;45(1):79-82. https://doi.org/10.1007/S10267-003-0152-X
  2. Babasaki K, Neda H, Murata H. megB1, a novel macroevolutionary genomic marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem. 2007;71(8):1927-1939. https://doi.org/10.1271/bbb.70144
  3. Song XX, Zhao Y, Song CY, et al. Intergenic spacer 1 (IGS1) polymorphism map: a marker for the initial classification of cultivated Lentinula edodes strains in China. J Integr Agr. 2018;17(11):2458-2466. https://doi.org/10.1016/s2095-3119(18)61967-7
  4. Zhang R, Huang C, Zheng S, et al. Strain-typing of Lentinula edodes in China with inter simple sequence repeat markers. Appl Microbiol Biotechnol. 2007;74(1):140-145. https://doi.org/10.1007/s00253-006-0628-7
  5. Zhang Y, Molina FI. Strain typing of Lentinula edodes by random amplified polymorphic DNA assay. FEMS Microbiol Lett. 1995;131(1):17-20. https://doi.org/10.1016/0378-1097(95)00228-W
  6. Wu X, Li H, Zhao W, et al. SCAR makers and multiplex PCR-based rapid molecular typing of Lentinula edodes strains. Curr Microbiol. 2010;61(5):381-389. https://doi.org/10.1007/s00284-010-9623-4
  7. Lee HY, Moon S, Shim D, et al. Development of 44 novel polymorphic SSR markers for determination of shiitake mushroom (Lentinula edodes) cultivars. Genes. 2017;8(4):109. https://doi.org/10.3390/genes8040109
  8. Moon S, Lee HY, Shim D, et al. Development and molecular characterization of novel polymorphic genomic DNA SSR markers in Lentinula edodes. Mycobiology. 2017;45(2):105-109. https://doi.org/10.5941/MYCO.2017.45.2.105
  9. Guichoux E, Lagache L, Wagner S, et al. Current trends in microsatellite genotyping. Mol Ecol Resour. 2011;11(4):591-611. https://doi.org/10.1111/j.1755-0998.2011.03014.x
  10. Arima T, Morinaga T. Electrophoretic karyotype of Lentinus edodes. Trans Mycol Soc Japan. 1993;34:481-485.
  11. Miyazaki K, Huang F, Zhang B, et al. Genetic map of a basidiomycete fungus, Lentinula edodes (shiitake mushroom), constructed by tetrad analysis. Breed Sci. 2008;58(1):23-30. https://doi.org/10.1270/jsbbs.58.23
  12. Cipriani G, Marrazzo MT, Di Gaspero G, et al. A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping. BMC Plant Biol. 2008;8(1):127. https://doi.org/10.1186/1471-2229-8-127
  13. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 2004;5(6):435-445. https://doi.org/10.1038/nrg1348
  14. Butler JM. Genetics and genomics of core short tandem repeat loci used in human identity testing. J Forensic Sci. 2006;51(2):253-265. https://doi.org/10.1111/j.1556-4029.2006.00046.x
  15. Munyard KA, Ledger JM, Lee CY, et al. Characterization and multiplex genotyping of Alpaca tetranucleotide microsatellite markers. Small Ruminant Res. 2009;85(2-3):153-156. https://doi.org/10.1016/j.smallrumres.2009.07.012
  16. De la Rosa R, Belaj A, Mu-noz-Merida A, et al. Development of EST-derived SSR markers with long-core repeat in olive and their use for paternity testing. J Am Soc Hortic Sci. 2013;138(4):290-296. https://doi.org/10.21273/jashs.138.4.290
  17. Faria DA, Mamani EMC, Pappas GJ Jr., et al. Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests. Tree Genet Genomes. 2011;7(1):63-77. https://doi.org/10.1007/s11295-010-0315-9
  18. Kishine M, Tsutsumi K, Kitta K. A set of tetranucleotide core motif SSR markers for efficient identification of potato (Solanum tuberosum) cultivars. Breed Sci. 2017;67(5):544-547. https://doi.org/10.1270/jsbbs.17066
  19. Shim D, Park SG, Kim K, et al. Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes. J Biotechnol. 2016;223:24-25. https://doi.org/10.1016/j.jbiotec.2016.02.032
  20. Faircloth BC. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locusspecific primer design. Mol Ecol Resour. 2008;8(1):92-94. https://doi.org/10.1111/j.1471-8286.2007.01884.x
  21. Temnykh S, DeClerck G, Lukashova A, et al. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001;11(8):1441-1452. https://doi.org/10.1101/gr.184001
  22. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95-98.
  23. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5(1):113. https://doi.org/10.1186/1471-2105-5-113
  24. Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725-2729. https://doi.org/10.1093/molbev/mst197
  25. Blacket MJ, Robin C, Good RT, et al. Universal primers for fluorescent labelling of PCR fragments - an efficient and cost-effective approach to genotyping by fluorescence. Mol Ecol Resour. 2012;12(3):456-463. https://doi.org/10.1111/j.1755-0998.2011.03104.x
  26. Brownstein MJ, Carpten JD, Smith JR. Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. Biotechniques. 1996;20(6):1004-1010. https://doi.org/10.2144/96206st01
  27. Kalinowski ST, Taper ML, Marshall TC. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol. 2007;16(5):1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
  28. Chen L, Gong Y, Cai Y, et al. Genome sequence of the edible cultivated mushroom Lentinula edodes (Shiitake) reveals insights into lignocellulose degradation. PLoS One. 2016;11(8):e0160336. https://doi.org/10.1371/journal.pone.0160336
  29. Sakamoto Y, Nakade K, Sato S, et al. Lentinula edodes genome survey and postharvest transcriptome analysis. Appl Environ Microbiol. 2017;83:e02990-16.

Cited by

  1. Identification techniques and detection methods of edible fungi species vol.374, 2019, https://doi.org/10.1016/j.foodchem.2021.131803