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Horticulturae
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Edible Mushrooms: Genetics, Genomics, and Breeding
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Edible Mushrooms: Genetics, Genomics, and Breeding

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Medicinals, Herbs, and Specialty Crops".

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 9328

Special Issue Editors

Dr. Junjie Yan

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Guest Editor
Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
Interests: edible mushroom; gene function; fruiting bodies development; genetics and breeding
Dr. Jie Chen

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Guest Editor
Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
Interests: fungal diseases; molecular biology of fungi
Prof. Dr. Mingwen Zhao

E-Mail Website
Guest Editor
College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
Interests: cultivation physiology and genetic breeding in edible fungi
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Edible mushrooms exhibit remarkable morphological and genetic variability across both domesticated species with established cultivation practices and wild-harvested varieties. They play pivotal roles in numerous facets of our lives, significantly contributing to ecological balance, enhancing human health, and fostering socio-economic development. To unravel the mysteries surrounding their growth, development, and the genetic determinants of beneficial traits, molecular biology has emerged as a pivotal discipline. It can offer profound insights into the intricate genetic mechanisms regulating processes in these mushrooms, unlocking a vast treasure trove of potential innovation. Advances in genetics, genomics—particularly pan-genomics—and gene-editing technologies are presenting unprecedented opportunities to enhance agronomic traits, improve cultivation efficiency, and optimize nutritional profiles in edible mushrooms.

Our objective for this Special Issue is to publish contributions in the form of research articles, reviews, and short communications focused on the application of genetics and genomics across diverse domains related to edible mushrooms, including genetic resources, growth and development, nutrient synthesis, breeding strategies, and other pertinent areas.

Dr. Junjie Yan
Dr. Jie Chen
Prof. Dr. Mingwen Zhao
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Horticulturae is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • edible mushrooms
  • genetics and breeding
  • functional genomics
  • comparative genomics
  • structural genomics
  • epigenomics
  • pan-genomics

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Published Papers (5 papers)

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Research

19 pages, 4385 KB  
Article
Genome-Wide Analysis of the Heat Shock Transcription Factor Gene Family in Flammulina filiformis and Its Response to CO2-Mediated Fruit Body Development
by Xinlian Duan, Xing Han, Ruixiang Zhao, Ying Gan, Jie Chen, Renyun Miao, Junbin Lin, Rencai Feng, Zongjun Tong, Bingcheng Gan and Junjie Yan
Horticulturae 2026, 12(2), 132; https://doi.org/10.3390/horticulturae12020132 - 24 Jan 2026
Cited by 1 | Viewed by 500
Abstract
Flammulina filiformis is the key industrial edible fungus that requires elevated CO2 to promote the growth of long stipe and small pileus fruiting bodies. Heat shock transcription factors (HSFs) play vital roles in stress response and development regulation; yet the HSF gene [...] Read more.
Flammulina filiformis is the key industrial edible fungus that requires elevated CO2 to promote the growth of long stipe and small pileus fruiting bodies. Heat shock transcription factors (HSFs) play vital roles in stress response and development regulation; yet the HSF gene family and its expression dynamics during fruiting body development in F. filiformis remain uncharacterized. This study aims to identify and characterize the HSF gene family in F. filiformis and to investigate their expression patterns during fruiting body development and in response to CO2 treatments. In this study, 7 FfHSFs were identified, and their structures, sequence features, and phylogenetics were further analyzed. Expression patterns under CO2 regulation were examined via qRT-PCR. The FfHSFs exhibited CDS lengths of 618–2298 bp, encoding 301–765 hydrophilic amino acids, with molecular weights ranging from 23.4 to 83.8 kDa and theoretical pI values between 4.75 and 9.15. All were predicted to be nuclear-localized. Cis-element analysis revealed motifs associated with growth regulation and stress responses such as low temperature, drought, and hypoxia. Phylogenetically, fungal HSFs were grouped into five clusters, with FfHSFs distributed across four. In this study, we examined the expression levels at four time points (0 h, 2 h, 12 h, and 36 h), under three different carbon dioxide concentrations (0.1%, 5%, and 20%) and in two types of tissues (pileus and stipe) for each six biological replicates. CO2 treatments showed that 5% CO2 significantly suppressed pileus expansion but not stipe elongation, while 20% CO2 inhibited both. Under 20% CO2 treatment, the pileus diameter decreased by approximately 40%, and simultaneously, the expression level of FfHSF1 decreased by about 70%. qRT-PCR indicated that FfHSF1 decreased with pileus expansion, whereas FfHSF4 increased. All FfHSFs were highly expressed in the stipe elongation zone. Elevated CO2 down-regulated FfHSF1 in pileus and FfHSF6 in stipes. Based on these findings, it could be proposed that FfHSF1 and FfHSF6 might be candidate regulators in CO2-mediated morphogenesis, providing insights into hormonal and environmental control of fruiting body development in F. filiformis. Full article
(This article belongs to the Special Issue Edible Mushrooms: Genetics, Genomics, and Breeding)
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14 pages, 2862 KB  
Article
Transcriptomic Insights and Quantification of Free Amino Acids in Auricularia heimuer Cultivated on Corncob Substrate
by Xu Sun, Fangjie Yao, Fanchao Lai, Ming Fang, Lixin Lu, Xiaoxu Ma, Wei Wang, Jingjing Meng and Kaisheng Shao
Horticulturae 2025, 11(6), 563; https://doi.org/10.3390/horticulturae11060563 - 22 May 2025
Cited by 2 | Viewed by 1154
Abstract
Substrate type exerts a critical influence on the growth, development, and nutritional quality of Auricularia heimuer. In this study, agricultural waste-derived corncob was used as the treatment group (T1), with sawdust serving as the control (CK), to systematically investigate the variation in [...] Read more.
Substrate type exerts a critical influence on the growth, development, and nutritional quality of Auricularia heimuer. In this study, agricultural waste-derived corncob was used as the treatment group (T1), with sawdust serving as the control (CK), to systematically investigate the variation in free amino acid (FAA) content and transcriptomic expression profiles in fruiting bodies of A. heimuer under the two substrate conditions. Principal component analysis (PCA) revealed a clear separation between CK and T1 samples in terms of FAA composition, indicating that substrate type significantly affects FAA profiles. The corncob substrate notably increased the total FAA content in A. heimuer (2624.57 mg/kg), representing an 11.4% elevation compared to the sawdust group (2355.86 mg/kg), and markedly enhanced the proportion of flavor-associated amino acids (49.2% vs. 42.6%). In particular, the umami amino acid content was 74% higher than in the CK group. Transcriptome analysis identified 20 differentially expressed genes associated with FAA biosynthesis and degradation, including key enzymes involved in umami amino acid metabolism, such as aspartate decarboxylase (ADC), glutamate decarboxylase (GAD), and glutamate N-acetyltransferase (GNA), which were downregulated in T1. This suggests that glutamate and aspartate may have accumulated due to suppressed catabolism. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis further indicated that the differentially expressed genes were significantly enriched in pathways related to branched-chain amino acid metabolism, carbon metabolism, and secondary metabolism. Collectively, these findings demonstrate that corncob substrate significantly alters the accumulation and metabolic profile of FAAs in A. heimuer by modulating the expression of key metabolic enzymes, providing a theoretical foundation for the efficient cultivation of A. heimuer using agricultural waste and for enhancing its flavor quality. Full article
(This article belongs to the Special Issue Edible Mushrooms: Genetics, Genomics, and Breeding)
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24 pages, 44836 KB  
Article
Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of Cyclocybe chaxingu
by Qiang Yang, Haiyan Song, Ge Su, Xuncheng Wang, Haijing Hu, Zhijun Zhai, Minghui Chen, Jianping Zhou, Hua Yin, Yang Gao and Dianming Hu
Horticulturae 2025, 11(4), 409; https://doi.org/10.3390/horticulturae11040409 - 11 Apr 2025
Cited by 1 | Viewed by 1843
Abstract
Cyclocybe chaxingu is an edible wood-decaying fungus widely cultivated in China, valued for its nutritional and economic significance. Despite its importance, molecular and genetic breeding studies on C. chaxingu have been limited by the lack of comprehensive genomic information. In this study, we performed [...] Read more.
Cyclocybe chaxingu is an edible wood-decaying fungus widely cultivated in China, valued for its nutritional and economic significance. Despite its importance, molecular and genetic breeding studies on C. chaxingu have been limited by the lack of comprehensive genomic information. In this study, we performed whole-genome sequencing of the type strain JAUCC1847 of C. chaxingu for the first time and conducted extensive genomic and transcriptomic analyses. We assembled a high-quality genome of the C. chaxingu strain C27, with a total length of 50.79 Mb and a GC content of 50.90%. Comparative genomic analysis revealed a close evolutionary relationship with species from the genera Agrocybe and Stropharia, suggesting a recent common ancestor. The high ANI values between C. chaxingu, Agrocybe chaxingu, and Agrocybe cylindracea indicate a close phylogenetic relationship, raising the possibility of synonymy among these strains. Genome annotation identified a rich array of 573 carbohydrate-active enzymes, highlighting the metabolic diversity of C. chaxingu, particularly in lignocellulose degradation. Comprehensive analysis of the A and B mating-type locus in C. chaxingu revealed the distribution and structural characteristics of mating-type genes, providing crucial genetic information for further studies on the reproductive biology of this species. Transcriptomic analysis revealed distinct gene expression patterns in mycelia, stipe, and cap, reflecting their functional specialization. GO and KEGG enrichment analyses demonstrated the stipe’s association with structural integrity and transport, while the cap is linked to metabolic activity, gene regulation, stress responses, and DNA repair. These insights clarify the taxonomic status of C. chaxingu, supporting its recognition within the genus Cyclocybe and providing a valuable resource for future research and breeding programs. Full article
(This article belongs to the Special Issue Edible Mushrooms: Genetics, Genomics, and Breeding)
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15 pages, 1378 KB  
Article
Distribution of Two Mating-Type Idiomorphs in Commercially Cultivated Morchella sextelata Unveiling Unique Life Cycle of Morels
by Jingting Wang, Dezheng Zhu, Xiaobo Li, Xia Gao, Yan Zhang, Meixiu Liu, Weidong Lu, Lili Xu, Hao Yu and Xiuqing Yang
Horticulturae 2025, 11(4), 385; https://doi.org/10.3390/horticulturae11040385 - 4 Apr 2025
Viewed by 1539
Abstract
The outdoor cultivation of true morels has been successfully commercialized in China in recent years. However, unstable yields make it a high-risk business. A lack of understanding of the morel life cycle has led to chaotic spawn production processes, further affecting cultivation. In [...] Read more.
The outdoor cultivation of true morels has been successfully commercialized in China in recent years. However, unstable yields make it a high-risk business. A lack of understanding of the morel life cycle has led to chaotic spawn production processes, further affecting cultivation. In this study, the life cycle of Morchella sextelata, the most widely cultivated species of true morels, was characterized. A disproportion in the two mating-type idiomorphs, MAT1-1 and MAT1-2, was observed in the mycelia during vegetative growth, successive subcultures, and different parts of the fruiting body. Homokaryotic hyphae were found to dominate the mycelia and fruiting body of M. sextelata through the separation and detection of protoplast-regenerated single strains. The findings suggest that two homokaryotic hyphae with different mating types fuse to form heterokaryotic hyphae just before ascospore production in the life cycle of M. sextelata. The observed disproportion of mating-type idiomorphs is a primary reason for strain degeneration during spawn production. This study offers new insights into the life cycle of M. sextelata, particularly the role of mating-type distribution, which may inform strategies for improving the artificial cultivation of true morels. Full article
(This article belongs to the Special Issue Edible Mushrooms: Genetics, Genomics, and Breeding)
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15 pages, 3777 KB  
Article
Quality Characteristics and Metabolomics Analysis of Two New Varieties of Tremella fuciformis
by Jianqiu Chen, Lingli Wei, Jiacheng Xie, Yuanyuan Zhang, Jiahui Jia, Liding Chen and Shujing Sun
Horticulturae 2025, 11(3), 273; https://doi.org/10.3390/horticulturae11030273 - 3 Mar 2025
Cited by 3 | Viewed by 3391
Abstract
Tremella fuciformis Berk., also known as white fungus and snow fungus, is one of the important edible and medicinal mushrooms in China. The quality characteristics and metabolites of different T. fuciformis varieties directly affect the stability of their processed products. In this study, [...] Read more.
Tremella fuciformis Berk., also known as white fungus and snow fungus, is one of the important edible and medicinal mushrooms in China. The quality characteristics and metabolites of different T. fuciformis varieties directly affect the stability of their processed products. In this study, two new varieties of Tremella fuciformis, namely ’TYH-SD1’ (yellow) and ’TWH-SD2’ (white), which were obtained by the team through single-spore crossbreeding and its control varieties Tr21 (yellow) and Tr01 (white), were used as test materials. The characteristics and nutritional quality of the four varieties of substrates were comparatively analyzed, while metabolomics was employed to investigate the differences in flavor substances. The results demonstrate that TYH-SD1 and TWH-SD2 had a higher rehydration rate and faster rehydration speed compared with the control strains Tr21 and Tr01, with a smaller stem and higher yield. Notably, TWH-SD2 had a 29.06% increase in its rehydration rate and it had higher contents of crude polysaccharide and vitamin D3. The surface of TYH-SD1 ear pieces exhibited a porous structure with a larger pore size and the surface of TWH-SD2 ear pieces displayed a surface characterized by connected gully-like protrusions and fewer indentations, which were significantly different from that of Tr21 and Tr01 ear pieces. The textural analysis shows that TYH-SD1 and TWH-SD2 ear pieces were softer and more elastic, with greater cohesion and recovery, indicating that they had high tensile and deformation recovery ability. Metabolomics analysis revealed that the relative content of aldehydes in the volatile flavor substances TYH-SD1 and TWH-SD2 was high in n-alpha-aldehyde, nonanaldehyde, and n-pentanal. The relative content of alkanes in TYH-SD1 was second only to that of aldehydes, with decane having the highest content, contributing to its more almond aroma, fruity aroma, and fat aroma. TWH-SD2 exhibited the highest concentration of alcohols, accounting for 43.57%, which may result in a clear, mushroom, and lipid odor. The above results will provide theoretical basis for the further production, processing, and application of the new varieties. Full article
(This article belongs to the Special Issue Edible Mushrooms: Genetics, Genomics, and Breeding)
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