Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Fei, Wang, Shi-Hui, Jia, Ding-Hong, Tan, Hao, Wang, Bo, Zhao, Rui-Lin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10056640/
https://www.ncbi.nlm.nih.gov/pubmed/36983498
http://dx.doi.org/10.3390/jof9030330
_version_ 1785016172271370240
author Liu, Fei
Wang, Shi-Hui
Jia, Ding-Hong
Tan, Hao
Wang, Bo
Zhao, Rui-Lin
author_facet Liu, Fei
Wang, Shi-Hui
Jia, Ding-Hong
Tan, Hao
Wang, Bo
Zhao, Rui-Lin
author_sort Liu, Fei
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10056640
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-100566402023-03-30 Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification Liu, Fei Wang, Shi-Hui Jia, Ding-Hong Tan, Hao Wang, Bo Zhao, Rui-Lin J Fungi (Basel) Article 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. MDPI 2023-03-07 /pmc/articles/PMC10056640/ /pubmed/36983498 http://dx.doi.org/10.3390/jof9030330 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Liu, Fei
Wang, Shi-Hui
Jia, Ding-Hong
Tan, Hao
Wang, Bo
Zhao, Rui-Lin
Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification
title Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification
title_full Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification
title_fullStr Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification
title_full_unstemmed Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification
title_short Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification
title_sort development of multiple nucleotide polymorphism molecular markers for enoki mushroom (flammulina filiformis) cultivars identification
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10056640/
https://www.ncbi.nlm.nih.gov/pubmed/36983498
http://dx.doi.org/10.3390/jof9030330
work_keys_str_mv AT liufei developmentofmultiplenucleotidepolymorphismmolecularmarkersforenokimushroomflammulinafiliformiscultivarsidentification
AT wangshihui developmentofmultiplenucleotidepolymorphismmolecularmarkersforenokimushroomflammulinafiliformiscultivarsidentification
AT jiadinghong developmentofmultiplenucleotidepolymorphismmolecularmarkersforenokimushroomflammulinafiliformiscultivarsidentification
AT tanhao developmentofmultiplenucleotidepolymorphismmolecularmarkersforenokimushroomflammulinafiliformiscultivarsidentification
AT wangbo developmentofmultiplenucleotidepolymorphismmolecularmarkersforenokimushroomflammulinafiliformiscultivarsidentification
AT zhaoruilin developmentofmultiplenucleotidepolymorphismmolecularmarkersforenokimushroomflammulinafiliformiscultivarsidentification