Mycobiology

The Korean Society of Mycology (한국균학회)
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Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes

  • Moon, Suyun (Department of Biology, Chungbuk National University) ;
  • Lee, Hwa-Yong (Department of Biology, Chungbuk National University) ;
  • Shim, Donghwan (Division of Forest Genetic Resources, National Institute of Forest Science) ;
  • Kim, Myungkil (Division of Wood Chemistry & Microbiology, National Institute of Forest Science) ;
  • Ka, Kang-Hyeon (Division of Wood Chemistry & Microbiology, National Institute of Forest Science) ;
  • Ryoo, Rhim (Division of Wood Chemistry & Microbiology, National Institute of Forest Science) ;
  • Ko, Han-Gyu (Forest Mushroom Research Center, National Forestry Cooperative Federation) ;
  • Koo, Chang-Duck (Department of Forest Science, Chungbuk National University) ;
  • Chung, Jong-Wook (Department of Industrial Plant Science and Technology, Chungbuk National University) ;
  • Ryu, Hojin (Department of Biology, Chungbuk National University)
  • Received : 2017.05.01
  • Accepted : 2017.06.12
  • Published : 2017.06.30
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Abstract

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

Keywords

References

  1. Wasser SP. Shiitake (Lentinus edodes). In: Coates PM, Blackman MR, Cragg GM, Levine M, Moss J, White JD, editors. Encyclopedia of dietary supplements. New York: Marcel Dekker; 2005. p. 653-64.
  2. Finimundy TC, Dillon AJ, Henriques JA, Ely MR. A review on general nutritional compounds and pharmacological properties of the Lentinula edodes mushroom. Food Nutr Sci 2014;5:1095-105. https://doi.org/10.4236/fns.2014.512119
  3. Ng ML, Yap AT. Inhibition of human colon carcinoma development by lentinan from shiitake mushrooms (Lentinus edodes). J Altern Complement Med 2002;8:581-9. https://doi.org/10.1089/107555302320825093
  4. Rop O, Mlcek J, Jurikova T. Beta-glucans in higher fungi and their health effects. Nutr Rev 2009;67:624-31. https://doi.org/10.1111/j.1753-4887.2009.00230.x
  5. Qin LH, Tan Q, Chen MJ, Pan YJ. Use of intersimple sequence repeats markers to develop strain-specific SCAR markers for Lentinula edodes. FEMS Microbiol Lett 2006;257:112-6. https://doi.org/10.1111/j.1574-6968.2006.00145.x
  6. Zhang R, Huang C, Zheng S, Zhang J, Ng TB, Jiang R, Zuo X, Wang H. Strain-typing of Lentinula edodes in China with inter simple sequence repeat markers. Appl Microbiol Biotechnol 2007;74:140-5. https://doi.org/10.1007/s00253-006-0628-7
  7. Fu LZ, Zhang HY, Wu XQ, Li HB, Wei HL, Wu QQ, Wang LA. Evaluation of genetic diversity in Lentinula edodes strains using RAPD, ISSR and SRAP markers. World J Microbiol Biotechnol 2010;26:709-16. https://doi.org/10.1007/s11274-009-0227-8
  8. Xiao Y, Liu W, Dai Y, Fu C, Bian Y. Using SSR markers to evaluate the genetic diversity of Lentinula edodes' natural germplasm in China. World J Microbiol Biotechnol 2010; 26:527-36. https://doi.org/10.1007/s11274-009-0202-4
  9. Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, et al. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 2009;118:327-38. https://doi.org/10.1007/s00122-008-0902-4
  10. Saha MC, Cooper JD, Mian MR, Chekhovskiy K, May GD. Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet 2006;113: 1449-58. https://doi.org/10.1007/s00122-006-0391-2
  11. Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW, Howieson JG. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 2012;13:318. https://doi.org/10.1186/1471-2164-13-318
  12. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 2011;12:499-510. https://doi.org/10.1038/nrg3012
  13. Shim D, Park SG, Kim K, Bae W, Lee GW, Ha BS, Ro HS, Kim M, Ryoo R, Rhee SK, et al. Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes. J Biotechnol 2016;223:24-5. https://doi.org/10.1016/j.jbiotec.2016.02.032
  14. Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 2005;21:2128-9. https://doi.org/10.1093/bioinformatics/bti282
  15. Zhang RY, Hu DD, Gu JG, Hu QX, Zuo XM, Wang HX. Development of SSR markers for typing cultivars in the mushroom Auricularia auricula-judae. Mycol Prog 2012;11: 587-92. https://doi.org/10.1007/s11557-011-0798-2
  16. Zhang R, Hu D, Zhang J, Zuo X, Jiang R, Wang H, Ng TB. Development and characterization of simple sequence repeat (SSR) markers for the mushroom Flammulina velutipes. J Biosci Bioeng 2010;110:273-5. https://doi.org/10.1016/j.jbiosc.2010.04.001
  17. Dangi RS, Lagu MD, Choudhary LB, Ranjekar PK, Gupta VS. Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers. BMC Plant Biol 2004;4:13. https://doi.org/10.1186/1471-2229-4-13
  18. Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 2010;11:569. https://doi.org/10.1186/1471-2164-11-569
  19. Shi J, Huang, S, Zhan J, Yu J, Wang X, Hua W, Liu S, Liu G, Wang H. Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species. DNA Res 2014;21:53-68. https://doi.org/10.1093/dnares/dst040
  20. Wang Q, Fang L, Chen J, Hu Y, Si Z, Wang S, Chang L, Guo W, Zhang T. Genome-wide mining, characterization, and development of microsatellite markers in Gossypium species. Sci Rep 2015;5:10638. https://doi.org/10.1038/srep10638
  21. Zhou R, Wu Z, Jiang FL, Liang M. Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars (Solanum lycopersicum L.). Genet Mol Res 2015;14:13184-94. https://doi.org/10.4238/2015.October.26.14