Submit to Agriculture Review for Agriculture Propose a Special Issue

Journal Menu

Journal Browser

Genetics and Breeding of Edible Mushroom

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 10801

Share This Special Issue

Special Issue Editor

Dr. Xiangli Wu

E-Mail Website
Guest Editor

Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: edible mushrooms; physiology; growth and development; stress response; molecular regulation mechanism; transcription factor

Special Issue Information

Dear Colleagues,

Edible mushrooms, well known for their high nutritional and medicinal value, have been widely cultivated across the globe. Studies involving germplasm resources, molecular markers, genetics, breeding systems, and cultivation techniques have been extensively performed over the last few decades and have greatly promoted the mushroom industry. However, both mushroom development and the formation of nutritional and medicinal characteristics are complicated systems involving gene regulatory networks and environmental stimulations. In recent years, with breakthroughs regarding high-throughput sequencing and omics, genetic transformation, gene editing technologies, etc., more and more researchers have focused on the molecular genetic mechanisms of mushroom yield and quality and have made some progress. An in-depth understanding of these mechanisms has further guided and facilitated breeding. Some studies have been carried out in the field of functional gene mapping and the marker-assisted breeding of edible mushrooms with agronomic traits.

This Special Issue focuses on the field of both basic research and technological applications in mushroom genetics and breeding. Authors are welcome to submit articles in the areas of omics analysis, gene identification, genetic engineering, marker-assisted breeding, environmental response, formation mechanisms of nutritional and medicinal value, and other related areas. Articles and reviews are both welcome.

Dr. Xiangli Wu
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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. Agriculture is an international peer-reviewed open access semimonthly 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 2600 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
omics
molecular mechanism
growth and development
breeding
environmental response
nutrition
medicinal value

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (9 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

14 pages, 8224 KiB

Open AccessArticle

Construction of an SNP Fingerprinting Database and Population Genetic Analysis of Auricularia heimuer

by Kaisheng Shao, Qiuyu Feng, Fangjie Yao, Lixin Lu, Ming Fang, Xiaoxu Ma and Xu Sun

Agriculture 2025, 15(8), 884; https://doi.org/10.3390/agriculture15080884 - 18 Apr 2025

Viewed by 176

Abstract

Auricularia heimuer is the second most widely cultivated edible fungus in China, with significant food and medicinal value, and is highly popular throughout Asia and globally. However, the differentiation of A. heimuer is simple, as its morphology is characterized by a small “black disc”, making it difficult to distinguish among germplasms with highly similar agronomic traits, thus posing challenges for germplasm identification. To address this issue, this study conducted whole-genome resequencing analysis on 150 A. heimuer germplasms. Through filtering 9,589,911 SNPs obtained from 280 G resequencing data, a total of 1,202,947 high-quality SNP sites were identified. Based on these high-quality SNPs, population structure analysis, principal component analysis (PCA), and phylogenetic tree analysis revealed that the 150 A. heimuer germplasms could be divided into five groups, with wild strains from the same geographical origin exhibiting significant geographical clustering patterns. This finding underscores the relationship between the genetic diversity of wild A. heimuer and its geographical distribution in China. A further selection of 71 SNP sites was made, and 61 KASP markers were successfully developed using kompetitive allele-specific PCR (KASP) technology, with 54 of them demonstrating good polymorphism. The average values for the polymorphism information content (PIC), minor allele frequency (MAF), gene diversity, and heterozygosity of these core KASP markers were 0.34, 0.35, 0.34, and 0.43, respectively. Based on the 54 core KASP markers, a DNA fingerprinting map of the 150 A. heimuer germplasms was constructed in this study. The findings provide important molecular marker resources and theoretical support for the identification of A. heimuer germplasm, molecular marker-assisted breeding, and the selection of superior varieties. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

19 pages, 3254 KiB

Open AccessArticle

Genomic Inference Unveils Population Bottlenecks and a North-to-South Migration Pattern of Wild Cordyceps militaris Across China

by Tianqiao Yong, Yuanchao Liu, Manjun Cai, Lijun Zhuo, Xiaoxian Wu, Huiyang Guo, Huiping Hu, Yichuang Gao, Shaodan Chen, Yizhen Xie and Wei Zhong

Agriculture 2025, 15(7), 686; https://doi.org/10.3390/agriculture15070686 - 24 Mar 2025

Viewed by 279

Abstract

The Ascomycete genus Cordyceps affects plant crops significantly, filling an important ecological niche. Cordyceps militaris (L.) Fr. presents many health benefits for humans, but its population history has not been reported. The objective of this research was to report the collection, population structure, demographic history, diversity, and cytosine deaminases of 43 wild strains of C. militaris in China through resequencing using an Illumina HiseqTM platform. All strains were assigned to the warm, subtropical, and middle temperate zone populations, confirmed by ADMIXTURE-1.3.0, PCA, and phylogenic analysis. Their population sizes declined historically, suggesting that this species suffered from bottlenecks in the wild. LD decays (r²) revealed a north-to-south migration pattern of wild C. militaris, consistent with the MSMC2-v2.1.4 analysis. The regions of high Pi were aggregating at the chromosomes CP023325.1 (51) and CP023323.1 (9), playing a key role in adaptation, especially for the sites on cytosine deaminase. Within the species, genetic differentiation was relatively high among the three populations (F_st = 0.083, 0.092, and even 0.109). According to the artificial intelligence-assisted (RoseTTAFold) predicted structures of the cytosine deaminases, they were classified into eight clades with unique, distinct, and structurally conserved domains, offering a potential suite of single- and double-stranded deaminases of great promise as tunable base editors for therapeutic and agricultural breeding applications. These provided new insights for mining novel proteins from macrofungi, structurally and functionally. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

18 pages, 7807 KiB

Open AccessArticle

The Molecular Mechanism of Mycelial Incubation Time Effects on Primordium Formation of Pleurotus tuoliensis Through Transcriptome and Lipidomic Analyses

by Qi He, Chenyang Huang, Lijiao Zhang, Wei Gao and Mengran Zhao

Agriculture 2024, 14(12), 2277; https://doi.org/10.3390/agriculture14122277 - 11 Dec 2024

Cited by 1 | Viewed by 963

Abstract

Pleurotus tuoliensis is a precious edible mushroom with a long cultivation cycle. Despite being cultivated in China for nearly 30 years, research on the molecular mechanisms underlying its primordium formation remains limited. In this study, the molecular mechanisms by which incubation time affects the primordium formation of P. tuoliensis were investigated using RNA-seq technology and lipid content detection. Our research revealed that the transcription of genes involved in lipid metabolism and lipid levels changed significantly during different incubation periods. Distinct differences were observed in gene transcription associated with signaling pathways, sphingolipid metabolism, fatty acid metabolism, and steroid biosynthesis in mycelia cultured for varying days and then stimulated by low temperature and light. These findings indicate that lipid accumulation and alterations in mycelial cell membrane components during incubation may affect the mycelial response to environmental signals, subsequently regulating primordium formation. This study revealed the crucial role of lipid metabolism during incubation in the primordium formation of P. tuoliensis, providing a novel perspective for investigating the molecular mechanism underlying fruiting body development. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

24 pages, 4644 KiB

Open AccessArticle

Study of the Degradation and Utilization of Cellulose from Auricularia heimuer and the Gene Expression Level of Its Decomposition Enzyme

by Xianqi Shan, Fangjie Yao, Lixin Lu, Ming Fang, Jia Lu and Xu Sun

Agriculture 2024, 14(11), 2027; https://doi.org/10.3390/agriculture14112027 - 11 Nov 2024

Viewed by 847

Abstract

Auricularia heimuer is a wood-rotting edible mushroom, and with the continuous development of the industry, the research on its grass-rotting cultivation is becoming more and more important. In this study, A. heimuer was cultivated using herbaceous substrate (reed) completely replacing the traditional woody substrate (oak), and the correlation between the relative expression of cellulase gene, cellulase activity, cellulose degradation and yield of different strains of A. heimuer were studied by combining qRT-PCR technology at different growth stages. The results showed that the cellulose degradation were positively correlated with the yield of reed and sawdust substrate at two growth stages, and were positively correlated with three cellulase activities. The relative expression of four cellulase genes were positively correlated with enzyme activity. There were inter-strain differences in the expression of the enzyme genes, which were basically consistent with the trend of the enzyme activity of the strains; g5372 and g7270 were more actively expressed in the mycelium period, while g9664 and g10234 were more actively expressed in the fruiting period. The results of SEM showed that the mycelium of A15 and A125 were different in their ability to degrade and utilize lignocellulose in reed substrate. The parental hybridization test further verified that qRT-PCR could be used as a rapid method to evaluate the cellulose degradation ability of A. heimuer strains. Seven strains (A12, A15, A184, A224, Z6, Z12, and Z18) with high cellulose degradation ability were screened. This study provides a reference for further understanding the role of A. heimuer cellulase genes in the degradation and metabolism of cellulose and for breeding new varieties more suitable for herbaceous substrate cultivation. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

19 pages, 5413 KiB

Open AccessArticle

Genetic Diversity and Genome-Wide Association Study of Pleurotus pulmonarius Germplasm

by Qian Li, Xuebing Ying, Yashu Yang and Wei Gao

Agriculture 2024, 14(11), 2023; https://doi.org/10.3390/agriculture14112023 - 11 Nov 2024

Viewed by 1029

Abstract

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

20 pages, 5452 KiB

Open AccessArticle

Transcriptome Analysis of Ganoderma lingzhi Liquid Fermentation Process Using Corn Straw as Matrix

by Sheng Wang, Jintao Li, Qi Fan, Shufang Wang, Changwei Sun and Meixia Yan

Agriculture 2024, 14(8), 1271; https://doi.org/10.3390/agriculture14081271 - 2 Aug 2024

Viewed by 1240

Abstract

Ganoderma lingzhi, a species of white rot fungus, possesses the highest abundance of lignocellulose-degrading enzymes among these fungi, as well as a relatively high carbon conversion rate. Corn straw, as an important sustainable resource, is used as a substrate for the liquid culture of G. lingzhi. However, little is known about the genes encoding the lignocellulose degradation and polysaccharide and triterpenoid biosynthetic pathways involved in this process. This paper employs transcriptomics to uncover the key genes involved in lignocellulose degradation and the synthesis of polysaccharides and triterpenoids during the liquid fermentation of G. lingzhi using corn straw as the substrate, as well as their associations. Carbohydrate-Active enzymes analysis of differential genes in the sequencing results was used to analyze the genes related to lignocellulose degradation. Among these, 43 core genes encoding CAZymes were obtained after 0 to 5 days of fermentation, and 25 core genes encoding CAZymes were obtained after 5 to 12 days of fermentation. The differential expression levels of DN3690_c0_g1 (EGL), DN3627_c0_g2 (XYN), DN4778_c0_g1 (XYN), DN2037_c0_g1 (LACC), and DN277_c2_g1 (MnP) were used to identify the key genes. The polysaccharide synthesis metabolic pathway favored mannitol synthesis, and the expression of triterpene precursor-metabolizing enzyme genes revealed higher expression levels of key enzyme genes such as ACAT, HMGS, and MPK. A correlation clustering analysis of genes related to lignocellulose degradation, polysaccharide, and triterpene anabolism during liquid fermentation showed that lignocellulose degradation genes mainly influenced arabinose and mannitol anabolism, as well as the synthesis of triterpene precursors. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

13 pages, 4435 KiB

Open AccessArticle

Study on the Effects of Different Light Supply Modes on the Development and Extracellular Enzyme Activity of Ganoderma lucidum

by Yihan Liu, Yuan Luo, Wenzhong Guo, Xin Zhang, Wengang Zheng and Xiaoli Chen

Agriculture 2024, 14(6), 835; https://doi.org/10.3390/agriculture14060835 - 27 May 2024

Cited by 2 | Viewed by 1939

Abstract

Edible fungi have certain photo-sensitivity during the mushroom emergence stage, but there have been few relevant studies on the responses of Ganoderma lucidum to different light irradiation conditions. Ganoderma lucidum were planted in an environmentally controllable mushroom room with different light supply modes that were, respectively, continuous white light (CK), red light (R), green light (G), blue light (B), and intermittent red light (R-), green light (G-), and blue light (B-), with a total light intensity of 15 μmol·m⁻²·s⁻¹ and a light/dark (L/D) period of 12 h/12 h for each treatment. The interval in intermittent light treatments was 30 min. The optimal light supply mode suitable for the growth of Ganoderma lucidum was explored by analyzing the characteristics, nutritional quality, and extracellular enzyme activity in mushrooms exposed to different light treatments. The results showed that red light (whether in continuous or intermittent supply modes) inhibited the fruiting body differentiation of Ganoderma lucidum, showing delayed differentiation or complete undifferentiation. The highest stipe length and pileus diameter of fruiting bodies were detected under G- treatment, which were, respectively, increased by 71.3% and 3.2% relative to the control. The highest weight of fruiting bodies was detected under G treatment, which was significantly increased by 21.4% compared to the control (p < 0.05). Intermittent light mode seemed to be more conducive to the size development of the fruiting body, while continuous light mode was beneficial for increasing the weight. The highest contents of crude protein and total triterpenes in pileus were detected under G treatment (significantly 14.9% and 28.1% higher than the control, respectively), while that of the crude polysaccharide was detected under G- treatment (significantly 35.7% higher than the control) (p < 0.05). The highest activities of extracellular enzymes such as cellulase, hemicellulase, laccase, lignin peroxidase, and amylase were detected in fruiting bodies subjected to G treatment, which were significantly increased by 11.9%~30.7% in the pileus and 9.5%~44.5% in the stipe. Green light might increase the weight and nutrient accumulation in the pileus of Ganoderma lucidum via up-regulating the extracellular enzyme activities. This study provides an effective light supply strategy for regulating the light environment in the industrial production of Ganoderma lucidum. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

13 pages, 11253 KiB

Open AccessArticle

ISSR-Assisted Breeding of Excellent New Strains of Ganoderma lingzhi through Single-Spore Selfing

by Jintao Li, Sheng Wang, Qi Fan, Linling Liu, Yanliang Gao, Changwei Sun and Meixia Yan

Agriculture 2024, 14(5), 745; https://doi.org/10.3390/agriculture14050745 - 10 May 2024

Viewed by 1424

Abstract

To improve our understanding of the selfing of G. lingzhi basidiospore monokaryons and increase the efficiency of breeding excellent strains, 52 basidiospore monokaryons were isolated from a commercial G. lingzhi strain (laboratory number P). A severe partial segregation was observed using the chi-square test, the growth rate of the monokaryotic strains was normally distributed, and colonies exhibited 5 forms. The genetic diversity of the monokaryotic strains was further demonstrated by intersimple sequence repeat (ISSR) analysis, and the similarity coefficient was in the range of 0.49–1, which was consistent with the genotype classification results. In total, 14 AxBx monokaryotic strains were randomly selected for selfing with the 1 AyBy strain when the similarity coefficient was 0.76, and a total of 14 offspring were obtained via selfing, all of which were incompatible with their parents. The traits of the selfing progenies were diverse. The mycelial growth rate, fruiting body yield, and polysaccharide, triterpene, and sterol contents were the main indices. According to the membership function value, 71.43% of the selfing progeny were super parent, and the A88 strain with the best comprehensive traits was selected. These findings prove that ISSR molecular marker-assisted breeding reduces blindness, greatly reduces workload, and improves work efficiency. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Figure 1

Review

Jump to: Research

23 pages, 4554 KiB

Open AccessReview

Exploring the Potential of Russula griseocarnosa: A Molecular Ecology Perspective

by Yuanchao Liu, Tianqiao Yong, Manjun Cai, Xiaoxian Wu, Huiyang Guo, Yizhen Xie, Huiping Hu and Qingping Wu

Agriculture 2024, 14(6), 879; https://doi.org/10.3390/agriculture14060879 - 31 May 2024

Cited by 1 | Viewed by 1354

Abstract

Russula griseocarnosa, an edible and medicinal mushroom abundant in nutrients and notable bioactivities, is predominantly grown in the broad-leaved forest with trees of the family Fagaceae in southern China. This species forms ectomycorrhizal associations with plant roots and cannot be artificially cultivated currently. Previous research indicates a strong correlation between the growth of R. griseocarnosa and factors such as the host plant, climate variables (specifically mean temperature and precipitation from June to October), and the rhizosphere microbiota of its habitat. However, comprehensive studies on the fundamental biology of this species are lacking. The interaction between R. griseocarnosa and its host plant, as well as the mechanisms underlying the microbial community dynamics within its habitat, remain ambiguous. The limited repertoire and diversity of carbohydrate-active enzymes (CAZymes) in R. griseocarnosa relative to saprophytic fungi may contribute to its recalcitrance to cultivation on synthetic media. The specific core enzyme and the substances provided by the host plant to facilitate growth are yet to be elucidated, posing a significant challenge in the artificial cultivation of R. griseocarnosa. The habitat of R. griseocarnosa harbours unique microbial communities, indicating the presence of potentially beneficial microorganisms that could be exploited for artificial propagation and conservation efforts. However, the lack of definitive functional verification experiments hinders the realization of this promising prospect. This review offers a comprehensive overview of the nutritional profile and health benefits of R. griseocarnosa, emphasizing recent developments in its isolation, molecular ecology, and artificial cultivation. Additionally, it explores prospective advancements in R. griseocarnosa research, aiming to enrich our foundational understanding for applied purposes and fostering progress in the realm of ectomycorrhizal edible mushrooms. Full article

(This article belongs to the Special Issue Genetics and Breeding of Edible Mushroom)

► Show Figures

Journal Menu

Journal Browser

Genetics and Breeding of Edible Mushroom

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (9 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI