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Strain identification and population genetic analysis of Phlebopus portentosus based on MNP markers
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Guoliang MENG1, Jiajia LI1, Yao CAO2, Fan LI2, Yukang ZENG2, Vyacheslav Alexandrovich VLASENKO4, Rongchun LI2, 3, *, Caihong DONG1, *
Mycosystema | 2026, 45(3) : 250231
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Mycosystema | 2026, 45(3): 250231
• Research paper •
Strain identification and population genetic analysis of Phlebopus portentosus based on MNP markers
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Guoliang MENG1, Jiajia LI1, Yao CAO2, Fan LI2, Yukang ZENG2, Vyacheslav Alexandrovich VLASENKO4, Rongchun LI2, 3, *, Caihong DONG1, *
Affiliations
  • 1 State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • 2 Yunnan Junshijie Biotechnology Co. Ltd., Yunnan (Rare Edible Fungi) Enterprise Technology Center, Kunming (Edible Fungi) Enterprise Technology Center, Kunming 650200, Yunnan, China
  • 3 Institute of Edible Fungi, Yunnan Agricultural University, Kunming 650201, Yunnan, China
  • 4 Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
Published: 2026-03-22 doi: 10.13346/j.mycosystema.250231
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Phlebopus portentosus, the first successfully domesticated and cultivated bolete species, has undergone rapid industrial expansion in recent years, highlighting the growing need for accurate strain identification and germplasm protection. In this study, whole-genome resequencing was performed on 66 strains of P. portentosus collected from various regions, resulting in the construction of a database of multiple nucleotide polymorphism (MNP) markers containing 306 loci. Population structure and kinship analyses based on both single nucleotide polymorphisms (SNPs) and MNPs consistently grouped the strains into two distinct genetic clusters. The MNP markers exhibited high resolution and stability across successive subculturing generations, enabling precise strain discrimination. Clonal identification criteria were established using replicate sequencing data of the same strains, with thresholds set at PI_HAT>0.95 and genetic distance (D)<0.01, while a genetic similarity (GS) value of 100% within the MNP dataset was validated as a robust indicator of strain identity. Additionally, machine learning approaches were employed to identify key MNP loci indicative of population divergence, offering valuable markers for varietal authentication and functional genomics. This work established MNP molecular marker database for P. portentosus and validated the potential applications in genetic resource conservation and molecular breeding, providing scientific support for variety protection and germplasm innovation.

Phlebopus portentosus  /  population structure  /  multiple nucleotide polymorphism  /  genetic similarity  /  strain identification
Guoliang MENG, Jiajia LI, Yao CAO, Fan LI, Yukang ZENG, Vyacheslav Alexandrovich VLASENKO, Rongchun LI, Caihong DONG. Strain identification and population genetic analysis of Phlebopus portentosus based on MNP markers[J]. Mycosystema, 2026 , 45 (3) : 250231 - . DOI: 10.13346/j.mycosystema.250231
Funding
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  • Special Fund of Yunnan Province (Rare Edible Fungi) Enterprise Technology Center(JSJ2023016KJ)
Appendix
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Year 2026 volume 45 Issue 3
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52
23
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Article Info
doi: 10.13346/j.mycosystema.250231
  • Receive Date：2025-07-25
  • Online Date：2026-04-30
  • Published：2026-03-22
Article Data
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History
  • Received：2025-07-25
  • Accepted：2025-08-19
Funding
Special Fund of Yunnan Province (Rare Edible Fungi) Enterprise Technology Center(JSJ2023016KJ)
Affiliations
    1 State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
    2 Yunnan Junshijie Biotechnology Co. Ltd., Yunnan (Rare Edible Fungi) Enterprise Technology Center, Kunming (Edible Fungi) Enterprise Technology Center, Kunming 650200, Yunnan, China
    3 Institute of Edible Fungi, Yunnan Agricultural University, Kunming 650201, Yunnan, China
    4 Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia

Corresponding:

*DONG Caihong, ;
LI Rongchun,
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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