Evaluation of the use of SCAR markers for screening genetic diversity of Lentinula edodes strains

Homologous Delta-12 Fatty Acid Desaturase (FAD2) Genes Affect Gene Expression and Linoleic Acid Levels in Lentinula edodes under Heat Stress

Delta-12 fatty acid desaturases (FAD2s) actively regulate stress responses and cell differentiation in living organisms. In this study, six homologous FAD2 genes were identified based on the genome sequence of Lentinula edodes. Then, the six FAD2 protein sequences were analyzed using bioinformatics tools, including ExPASy ProtParam, SignalP, TMHMM, and TargetP. These analyses were performed to predict the physical and chemical properties, signal peptides, and transmembrane and conserved domains of these proteins. The polypeptide sequences were aligned, and a maximum likelihood phylogenetic tree was constructed using MEGA 7.0 software to elucidate the phylogenetic relationships between homologous FAD2 sequences. The results demonstrated that the FAD2 proteins contained three conserved histidine-rich regions (HXXXH, HXXHH, and HXXHH), which included eight histidine residues. The linoleic acid content and FAD2 enzyme activity were further analyzed, and the levels in the mutagenic heat-tolerant strain 18N44 were lower than those in the wild-type strain 18. Interestingly, the expression levels of the FAD2-2 and FAD2-3 genes under heat stress in strain 18N44 were lower than those in strain 18. These findings indicated that FAD2-2 and FAD2-3 may play major roles in the synthesis of linoleic acid during heat stress.

GC⁻MS-Based Nontargeted and Targeted Metabolic Profiling Identifies Changes in the Lentinula edodes Mycelial Metabolome under High-Temperature Stress

To clarify the physiological mechanism of the Lentinula edodes (L. edodes) response to high-temperature stress, two strains of L. edodes with different tolerances were tested at different durations of high temperature, and the results showed that there were significant changes in their phenotypes and physiology. To further explore the response mechanism, we established a targeted GC–MS-based metabolomics workflow comprising a standardized experimental setup for growth, treatment and sampling of L. edodes mycelia, and subsequent GC–MS analysis followed by data processing and evaluation of quality control (QC) measures using tailored statistical and bioinformatic tools. This study identified changes in the L. edodes mycelial metabolome following different time treatments at high temperature based on nontargeted metabolites with GC-MS and further adopted targeted metabolomics to verify the results of the analysis. After multiple statistical analyses were carried out using SIMCA software, 74 and 108 differential metabolites were obtained, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the metabolic pathways with significant changes included those related to the following: amino acid metabolism, the glycolysis pathway, the tricarboxylic acid (TCA) cycle, and sugar metabolism. Most amino acids and carbohydrates enriched in these metabolic pathways were upregulated in strain 18, downregulated in strain 18N44, or the synthesis in strain 18 was higher than that in strain 18N44. This result was consistent with the physiological phenotypic characteristics of the two strains under high-temperature stress and revealed the reason why strain 18N44 was more heat-sensitive. At the same time, under high temperature, the decrease of intermediate products in glycolysis and the TCA cycle resulted in carbon starvation and insufficient energy metabolism, thus inhibiting the growth of L. edodes. In addition, the results also showed that the metabolites produced by different L. edodes strains under high-temperature stress were basically the same. However, different strains had species specificity, so the changes in the content of metabolites involved in the response to high-temperature stress were different. This provides a theoretical basis for further understanding the mechanism of the L. edodes response to high temperature and can be used to establish an evaluation system of high-temperature-resistant strains and lay the foundation for molecular breeding of new L. edodes strains resistant to high temperature.

Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2-11; the observed and expected heterozygosity were 0.00-1.00 and 0.10-0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.

Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom

Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (F_ST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom.

Analysis of Genetic Diversity and Development of SCAR Markers in a Mycogone perniciosa Population

The fungus Mycogone perniciosa is a major pathogen of the common button mushroom Agaricus bisporus. Analysis of genetic diversity in M. Perniciosa may assist in developing methods for prophylaxis and treatment of M. Perniciosa infections. For this, it is necessary to classify M. Perniciosa into relevant class groups quickly and efficiently. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and sequence-related amplified polymorphism (SRAP) markers were used to obtain genetic fingerprints and assess the genetic variation among 49 strains of M. perniciosa collected from different areas of Fujian Province in China. Analysis of DNA sequence polymorphism revealed two major distinct groups (Group I and Group II). Specific DNA fragments that were identified through RAPD, ISSR, and SRAP markers were sequenced and used for the designing of stable sequence-characterized amplified region (SCAR) markers. The resulting SCAR markers were then validated against the classified groups of M. perniciosa.