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Article

Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification

by
Fei Liu
1,
Shi-Hui Wang
1,2,
Ding-Hong Jia
3,
Hao Tan
3,
Bo Wang
3,* and
Rui-Lin Zhao
1,4,*
1
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
2
School of Plant Protection, Jilin Agricultural University, Changchun 130118, China
3
National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
4
College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
*
Authors to whom correspondence should be addressed.
J. Fungi 2023, 9(3), 330; https://doi.org/10.3390/jof9030330
Submission received: 11 January 2023 / Revised: 17 February 2023 / Accepted: 6 March 2023 / Published: 7 March 2023
(This article belongs to the Special Issue Edible and Medicinal Macrofungi)
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Abstract

The enoki mushroom (Flammulina filiformis) is one of the most important and popular edible mushrooms commercially in China. However, traditional mushroom cultivar identification is challenging due to poor accuracy, heavy workloads, and low reproducibility. To overcome this challenge, we developed a method for identifying F. filiformis strains using multiple nucleotide polymorphism sequencing (MNP-seq). This involved screening 179 universal MNP markers based on whole-genome sequencing data, constructing an MNP sequence library, and performing multiplex PCR amplification and high-sequencing. We further screened 69 core MNP markers and used them to build a neighbor-joining (NJ) phylogenetic tree of 232 cultivated and wild strains. Our analysis showed that all cultivars could be accurately separated by computing genetic similarity values and that the cultivars could be separated into 22 distinct evolutionary pedigrees. The specific value of genetic similarity can be used as the standard to distinguish F. filiformis cultivars, however, it needs to be comprehensively defined by the additional phenotype and biological characteristics of those strains in the future work.
Keywords: mushroom; MNP marker; sequencing; cultivar mushroom; MNP marker; sequencing; cultivar

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MDPI and ACS Style

Liu, F.; Wang, S.-H.; Jia, D.-H.; Tan, H.; Wang, B.; Zhao, R.-L. Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification. J. Fungi 2023, 9, 330. https://doi.org/10.3390/jof9030330

AMA Style

Liu F, Wang S-H, Jia D-H, Tan H, Wang B, Zhao R-L. Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification. Journal of Fungi. 2023; 9(3):330. https://doi.org/10.3390/jof9030330

Chicago/Turabian Style

Liu, Fei, Shi-Hui Wang, Ding-Hong Jia, Hao Tan, Bo Wang, and Rui-Lin Zhao. 2023. "Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification" Journal of Fungi 9, no. 3: 330. https://doi.org/10.3390/jof9030330

APA Style

Liu, F., Wang, S.-H., Jia, D.-H., Tan, H., Wang, B., & Zhao, R.-L. (2023). Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification. Journal of Fungi, 9(3), 330. https://doi.org/10.3390/jof9030330

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