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http://dx.doi.org/10.4489/KJM.20170014

Development of Cleaved Amplified Polymorphic Sequence Markers for the Identification of Lentinula edodes Cultivars Sanmaru 1ho and Chunjang 3ho  

Moon, Suyun (Department of Biology, Chungbuk National University)
Lee, Hwa-Yong (Department of Biology, Chungbuk National University)
Kim, Myungkil (Wood Chemistry and Microbiology Division, National Institute of Forest Science)
Ka, Kang-Hyeon (Wood Chemistry and Microbiology Division, National Institute of Forest Science)
Ko, Han Kyu (Forest Mushroom Research Center, National Forestry Cooperative Federation)
Chung, Jong-Wook (Department of Industrial Plant Science and Technology, Chungbuk National University)
Koo, Chang-Duck (Department of Forest Science, Chungbuk National University)
Ryu, Hojin (Department of Biology, Chungbuk National University)
Publication Information
The Korean Journal of Mycology / v.45, no.2, 2017 , pp. 114-120 More about this Journal
Abstract
Lentinula edodes is an edible mushroom that is mainly cultivated in Asian countries. Recently, new cultivars of this mushroom have been developed in Korea; variety protection is very important, so the development of efficient molecular markers that can distinguish each variety is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanmaru 1ho and Chunjang 3ho). These markers were developed from whole genomic sequencing data from L. edodes monokaryon strain B17 and resequencing data from 10 dikaryon strains. A single nucleotide polymorphism changed in scaffold 9 POS 1630048 in Sanmaru 1ho($G{\rightarrow}T$), and in scaffold 13 POS 920681 in Chunjang 3ho ($G{\rightarrow}A$). The restriction enzymes TspR I and Xho I distinguished Sanmaru 1ho and Chunjang 3ho, respectively, from other strains. Thus, we developed 2 CAPS markers for the identification of the L. edodes cultivars Sanmaru 1ho and Chunjang 3ho.
Keywords
CAPS marker; Genome-wide; Lentinula edodes; Single nucleotide polymorphism;
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  • Reference
1 Kulkarni RK. DNA Polymorphisms in Lentinula edodes, the Shiitake mushroom. Appl Environ Microbiol 1991;57:1735-9.
2 Zhang Y, Molina FI. Strain typing of Lentinula edodes by random amplified polymorphic DNA assay. FEMS Microbiol Lett 1995;131:17-20.   DOI
3 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.   DOI
4 Wu X, Li H, Zhao W, Fu L, Peng H, He L, Cheng J, Wei H, Wu Q. SCAR makers and multiplex PCR-based rapid molecular typing of Lentinula edodes strains. Curr Microbiol 2010;61:381-9.   DOI
5 Terashima K, Matsumoto T. Strain typing of shiitake (Lentinula edodes) cultivars by AFLP analysis, focusing on a heat-dried fruiting body. Mycoscience 2004;45:79-82.   DOI
6 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.   DOI
7 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.   DOI
8 Liu J, Wang ZR, Li C, Bian YB, Xiao Y. Evaluating genetic diversity and constructing core collections of Chinese Lentinula edodes cultivars using ISSR and SRAP markers. J Basic Microbiol 2015;55:749-60.   DOI
9 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.   DOI
10 Yoon KH, Kim YY. Test guideline for Shiitake. Daejeon: Korea Forest Service; 2008.
11 Li HB, Wu XQ, Peng HZ, Fu LZ, Wei HL, Wu QQ, Jin QY, Li N. New available SCAR markers: potentially useful in distinguishing a commercial strain of the superior type from other strains of Lentinula edodes in China. Appl Microbiol Biotechnol 2008; 81:303-9.   DOI
12 Liu JY, Ying ZH, Liu F, Liu XR, Xie BG. Evaluation of the use of SCAR markers for screening genetic diversity of Lentinula edodes strains. Curr Microbiol 2012;64:317-25.   DOI
13 Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 2008;27:617-31.   DOI
14 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.   DOI
15 Chen L, Gong Y, Cai Y, Liu W, Zhou Y, Xiao Y, Xu Z, Liu Y, Lei X, Wang G, et al. Genome sequence of the edible cultivated mushroom Lentinula edodes (Shiitake) reveals insights into lignocellulose degradation. PLoS One 2016;11:e0160336.   DOI
16 Kunihisa M, Fukino N, Matsumoto S. Development of cleavage amplified polymorphic sequence (CAPS) markers for identification of strawberry cultivars. Euphytica 2003;134:209-15.   DOI
17 Korea Rural Economic Institute. Forestry observation for Lentinula edodes, November. Naju: Korea Rural Economic Institute; 2016.
18 Bak WC, Park YA, Park JH. Present situation and future of oak mushroom industry: KFRI forest policy issue 11. Seoul: Korea Forest Research Institute; 2013.
19 Royse DJ. A global perspective on the high five: Agaricus, Pleurotus, Lentinula, Auricularia & Flammulina. In: Proceedings of the 8th International Conference on Mushroom Biology and Mushroom Products; 2014 Nov 19-22; New Delhi, India. Solan: ICARDirectorate of Mushroom Research; 2014. p. 1-6.
20 Korea Forest Service. Statistical yearbook of forestry. Daejeon: Korea Forest Service; 2016.
21 Healey A, Furtado A, Cooper T, Henry RJ. Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 2014;10:21.   DOI
22 Konieczny A, Ausubel FM. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 1993;4:403-10.   DOI
23 Kaundun S, Matsumoto S. Development of CAPS markers based on three key genes of the phenylpropanoid pathway in Tea, Camellia sinensis (L.) O. Kuntze, and differentiation between assamica and sinensis varieties. Theor Appl Genet 2003;106:375-83.   DOI
24 Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 2008;5:183-8.   DOI
25 Moriya Y, Yamamoto K, Okada K, Iwanami H, Bessho H, Nakanishi T, Takasaki T. Development of a CAPS marker system for genotyping European pear cultivars harboring 17 S alleles. Plant Cell Rep 2007;26:345-54.   DOI
26 Caranta C, Thabuis A, Palloix A. Development of a CAPS marker for the Pvr4 locus: a tool for pyramiding potyvirus resistance genes in pepper. Genome 1999;42:1111-6.   DOI
27 Su Z, Hao C, Wang L, Dong Y, Zhang X. Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 2011;122:211-23.   DOI
28 Minamiyama Y, Kinoshita S, Inaba K, Inoue M. Development of a cleaved amplified polymorphic sequence (CAPS) marker linked to pungency in pepper. Plant Breed 2005;124:288-91.   DOI
29 Foulongne-Oriol M, Spataro C, Cathalot V, Monllor S, Savoie JM. An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporus $\times$ A. bisporus var. burnettii hybrid based on AFLP, SSR and CAPS markers sheds light on the recombination behaviour of the species. Fungal Genet Biol 2010;47:226-36.   DOI