Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars |
Saito, Teruaki
(Mushroom Research Laboratory, Hokuto Corporation)
Sakuta, Genki (Mushroom Research Laboratory, Hokuto Corporation) Kobayashi, Hitoshi (Mushroom Research Laboratory, Hokuto Corporation) Ouchi, Kenji (Mushroom Research Laboratory, Hokuto Corporation) Inatomi, Satoshi (Mushroom Research Laboratory, Hokuto Corporation) |
1 | 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. DOI |
2 | 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. |
3 | Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5(1):113. DOI |
4 | Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725-2729. DOI |
5 | 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. DOI |
6 | 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. DOI |
7 | 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. DOI |
8 | 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. DOI |
9 | Sakamoto Y, Nakade K, Sato S, et al. Lentinula edodes genome survey and postharvest transcriptome analysis. Appl Environ Microbiol. 2017;83:e02990-16. |
10 | 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. DOI |
11 | 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. DOI |
12 | 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. DOI |
13 | 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. DOI |
14 | 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. DOI |
15 | Zhang Y, Molina FI. Strain typing of Lentinula edodes by random amplified polymorphic DNA assay. FEMS Microbiol Lett. 1995;131(1):17-20. DOI |
16 | 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. DOI |
17 | 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. DOI |
18 | Guichoux E, Lagache L, Wagner S, et al. Current trends in microsatellite genotyping. Mol Ecol Resour. 2011;11(4):591-611. DOI |
19 | Arima T, Morinaga T. Electrophoretic karyotype of Lentinus edodes. Trans Mycol Soc Japan. 1993;34:481-485. |
20 | 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. DOI |
21 | 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. DOI |
22 | Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 2004;5(6):435-445. DOI |
23 | Butler JM. Genetics and genomics of core short tandem repeat loci used in human identity testing. J Forensic Sci. 2006;51(2):253-265. DOI |
24 | 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. DOI |
25 | 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. DOI |
26 | 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. DOI |
27 | 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. DOI |
28 | Faircloth BC. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locusspecific primer design. Mol Ecol Resour. 2008;8(1):92-94. DOI |
29 | 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. DOI |