Strain typing of Lentinula edodes by random amplified polymorphic DNA assay

Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.

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.

Identification of Single Nucleotide Polymorphism Markers in the Laccase Gene of Shiitake Mushrooms (Lentinula edodes)

We identified single nucleotide polymorphism (SNP) markers in the laccase gene to establish a line-diagnostic system for shiitake mushrooms. A total of 89 fungal isolates representing four lines, including Korean registered, Korean wild type, Chinese, and Japanese lines, were analyzed. The results suggest that SNP markers in the laccase gene can be useful for line typing in shiitake mushrooms.

Improving yield performance of Pleurotus pulmonarius through hyphal anastomosis fusion of dikaryons

High production and good quality are always the principal goals for agriculturally important crops, without the exception of mushrooms. P. pulmonarius is one of the commercially important edible mushrooms throughout the world. The yield performance improvement was carried out by cross bred P. pulmonarius with P. sapidus and P. ostreatus. The highest rate of 0.587 mm/days for spawn ramification and 53.33 % for percentage spawn productivity were obtained in hybrids LN LL910. The least day (11 and 12th) of the primodia mushroom sporophore were recorded in LL910 and LN 97 respectively, while longest day of 19th was recorded in wild type (NE 07). The highest biological efficiency (109.30 %) and production rate (3.77 %) obtained by LL910, while the least of 33.0 and 0.79 % were obtained by NE 07 for biological efficiency and production rate respectively. The morphological and molecular characterization of the hybrid strains established their true variation from their wild type. LL 910 (JF68088) is located at seventh subclusters from the root with boostrap value of 32 %, while only one parent (LAU 09: JF736658) out of the two has the close boostrap value of 43 % at the first subcluster to the root, with the other parent LAU 10 (JF736659) shows distance relationship after Blast. LN 97 (JF680992) is located at outgroup, while the parent strains NE 07 (boostrap value: 11 %) and LAU 09 (boostrap value: 44 %) located at tenth and second subclusters respectively. The results obtained from this study have shown the improved performance of the hybrids strain over wild type strains.

AFLP based assessment of genetic relationships among shiitake (Lentinula ssp.) mushrooms

Despite the economical importance of shiitake (Lentinula ssp.) mushrooms, until the present date little information exists on cultivated and wild species in correlation with geographic origin applying molecular techniques. Use of a high resolution molecular tool like AFLP for assessing genetic similarity and geographical diversity would be an important step towards understanding of different Lentinula species. Thirteen wild and 17 cultivated accessions of 3 Lentinula species were analysed with 64 EcoRI-MseI primer combinations and finally 32 reproducible and polymorphic primer combinations were considered for the analysis. A total of 816 informative AFLP markers were generated and scored as binary data. These data were analysed using various method packages for cluster analysis, genetic diversity and genetic differentiation. Percentage polymorphism was high (62.99%) among the species studied. Different clustering analysis segregated the wild and the cultivated species into two major branches, with the wild samples being further grouped according to their geographic location. Overall polymorphisms among cultivated strains in the USA were higher than that of the cultivated strains in Japan (58.9%).

Applying target region amplification polymorphism markers for analyzing genetic diversity of Lentinula edodes in China

The target region amplification polymorphism (TRAP) technique was utilized for assessing the genetic diversity of 55 wild strains and one cultivated strain of Lentinula edodes in China. From these strains, 932 DNA fragments were amplified using 12 primer combinations, 929 fragments (99.68%) of which were polymorphic between two or more strains. The average coefficient of pairwise genetic similarity was 0.696, within a range from 0.503 to 0.947. Cluster analysis and principal coordinate analysis separated the tested strains of L. edodes into two major groups. Group A was further divided into seven subgroups. In most cases, the strains from the same or adjoining regions could be preferentially clustered into small groups. The results from the average genetic similarity and the weighted average value of Shannon's Information Index among the tested strains of L. edodes from the same region revealed a vast genetic diversity in the natural germplasm found in China. Compared with the L. edodes strains from other regions, those found on the Yunnan Plateau, in the Hengduanshan Mountains, in Taiwan, South China, and Northeast China showed greater genetic diversity. The results of the present study indicated that the wild strains of L. edodes in China possessed abundant genetic variation, and the genetic relationships among them were highly associated with the geographic distribution. This is the first report demonstrating that TRAP markers were powerful for analyzing the genetic diversity of L. edodes, and the study lays the foundation for a further application of this remarkable technique to other fungi.

Development and characterization of simple sequence repeat (SSR) markers for the mushroom Flammulina velutipes

Ten polymorphic SSR markers of Flammulina velutipes were developed and characterized with FIASCO methods. The polymorphism information content (PIC) ranged from 0.13 to 0.69. This is the first report on development of SSR markers in F. velutipe.

Mutagenesis and genetic characterisation of amylolytic Aspergillus niger

Aspergillus niger FCBP-198 was genetically modified for its ability to reveal extra cellular alpha-amylase enzyme activity. From 76 efficient mutants isolated after ultraviolet (UV) irradiation, An-UV-5.6 was selected as the most efficient UV mutant, with 76.41 units mL(-1) of alpha-amylase activity compared to wild (34.45 units mL(-1)). In case of ethyl methane sulphonate (EMS), among 242 survivors, 74 were assayed quantitatively and An-Ch-4.7 was found to be the most competent, as it exhibited a three-fold increase in alpha-amylase activity (89.38 units mL(-1)) than the parental strain. Genetic relationships of the mutants of A. niger FCBP-198 were analysed with a randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Results obtained from the comparison between genotypes of A. niger FCBP-198 showed differences in the sizes and numbers of amplified fragments per primer for each isolate. The dendrogram showed that genotypes An-Ch-4.7 and An-Ch-4.2 were distinctly classified into one category, while the isolates An-UV-5.6, An-UV-5.1 and A. niger FCBP-198 have the nearest genetic relationship. The five isolates from A. niger FCBP-198 genotypes shared an average of 65% bands.

New available SCAR markers: potentially useful in distinguishing a commercial strain of the superior type from other strains of Lentinula edodes in China

At present, more than 100 strains of Lentinula edodes are cultivated on a commercial scale in China. A simple, reliable, and effective method to distinguish some commercial strains of the superior type from other commercial strains is very important for the Lentinula industry. In this study, 23 commercial strains of L. edodes cultivated widely in China at present were collected and analyzed with randomly amplified polymorphic DNA (RAPD) technique. Three informative dominant sequence characterized amplified region (SCAR) markers were developed by designing three pairs of specific SCAR primers from three sequenced differential RAPD bands, respectively. Based on the three SCAR markers, three different multiplex polymerase chain reaction (PCR) phenotypes were detected among the 23 studied commercial strains and in which a multilocus phenotype characterizing a commercial strain Cr02 of the superior type could potentially be used to distinguish this strain from the other 22 studied commercial strains. To our knowledge, this study is the first to describe the development of a multiplex PCR technique based on SCAR markers for detecting the molecular phenotypes among commercial strains of L. edodes in China.

MushBase: A Mushroom Information Database Application

A database application, namely MushBase, has been built based on Microsoft Access in order to store and manage different kinds of data about mushroom biological information of species, strains and their physiological characteristics such as geometries and growth condition(s). In addition, it is also designed to store another group of information that is experimental data about mushroom classification by Random Amplification of Polymorphic DNA (RAPD). These two groups of information are stored and managed in the way so that it is convenient to retrieve each group of data and to cross-refer between them as well.

Strain-typing of Lentinula edodes in China with inter simple sequence repeat markers

To validate strain typing by inter simple sequence repeat (ISSR) analysis in Lentinula edodes cultivars, 17 Chinese L. edodes strains including 15 cultivated strains cultivated on a large scale and two wild strains were analyzed with the ISSR technique. With the use of two ISSR primers, a total of 32 DNA products were detected, of which, 31 DNA products (96.9% of the detected products) were polymorphic between two or more strains. The profiles of those two primers could be employed to differentiate all of the tested strains. A cluster analysis based on ISSR data revealed that the 17 strains could be classified into two distinct groups. One group consisted of eight strains in which the cultivated strains were H (high-temperature)-type or B (broad-temperature)-type, and the other group comprised cultivated strains that were of the L (low-temperature)-type or M (medium-temperature)-type. In contrast to the two wild strains, the genetic diversity of 15 cultivated strains was very rich based on a similarity coefficient analysis.