Restriction fragment length polymorphisms in the mushrooms Agaricus brunnescens and Agaricus bitorquis

Induced mutation in Agaricus bisporus by gamma ray to improve genetic variability, degradation enzyme activity, and yield

PURPOSE

Genetic variability in white button mushroom cultivars is very low due to the life cycle. Induction mutations using gamma irradiation is a useful way to generate diversity in white button mushrooms to obtain genotype(s) with desirable traits.

METHODS

Gamma irradiation Cobalt-60 was used for inducting genetic diversity in white button mushroom to obtain genotype(s) with desirable traits. Gamma irradiation with doses of 0-500 Gy was conducted on spores on Potato Dextrose Agar medium.

RESULTS

The results showed significant differences in days to pin production and harvest, fruit body number, fresh and dry weight, yield, laccase, and manganese peroxidase enzyme activity. After isolating variants, 15 variants were selected on the base of their high yield and enzyme degradation activity. Their genetic variation was confirmed by Sequence Related Amplified Polymorphism (SRAP) markers, and then incubated on three types of substrates (50:50, 75:25, and 100:0 % compost: raw straw). The results showed that all variants, except GR18, colonized in 75:25, and GR3, GR4, GR9, GR61, GR72, and GR74 variants colonized in 50:50. In 100:0 substrate, GR55 and GR63 were the earliest variants, and GR9 produced the highest fruit body number. In 75:25 substrate, GR9, GR3, GR61, GR4, GR74, GR4, GR61, and GR72 showed higher yields. The highest laccase and manganese peroxidase activity were recorded in GR3, GR4, GR9, GR72, and GR61. The isolated 15 variants were clustered into two main groups by cluster analysis and genetic variation was confirmed by SRAP markers.

CONCLUSION

The results showed that the diversity in the white button mushroom could be improved using gamma rays, and the variation would be useful for the development of future breeding programs.

Characterization of Pleurotus djamor neohaplonts recovered by production of protoplasts and chemical dedikaryotization

Production of hybrid strains is accomplished by mating monosporic isolates or neohaplonts, obtained either by chemical dedikaryotization or by production of protoplast. However, differences in growth rate among recovered neohaplonts have been reported. The presence of phenotypic and genetic changes among the neohaplonts recovered either by chemical dedikaryotization or by production of protoplast, was evaluated by measuring growth and morphology, and by molecular characterization using six ISSR markers to identify polymorphisms. Neohaplonts recovered by both methods presented variation in growth rate depending on their compatibility type and recovery method. Using ISSR markers, 59.2% polymorphism was established. Neohaplonts recovered by both monokaryotization procedures presented differences in growth rate and polymorphism.

Differentiation of homokaryons and heterokaryons of Agaricus bisporus with inter-simple sequence repeat markers

Morphologically different fifteen slow growing single spore isolates (SSIs) were screened from germinated basidiospores of Agaricus bisporus; assumed to be homokaryons, and subjected to growth rate, spawn run, fruiting and inter-simple sequence repeat (ISSR) analysis for confirmation of true homokaryons. The present studies are the first report of fingerprinting on differentiating homo- and hetero-karyotic SSIs using ISSR markers. The patterns were highly polymorphic and very reproducible. Among 40 primers tested, 7 ISSR primers were selected for the analysis of genomic DNA and generated a total of 54 ISSR fragments, sufficient to differentiate the 15 isolates from each other. ISSR fingerprinting detected 46.30% polymorphic loci. All appressed homokaryons carried a subset of ISSR markers found in the heterokaryons, and these were not able to produce a fruiting body. A test of cross-fertility and the following fruiting trial proved that 3 of the 15 SSIs with different ISSR fingerprints were homokaryons. None of the discarded SSIs have any missing bands present in the parental heterokaryotic control; these are heterokaryons derived from non-sister nuclear pairs. It is revealed that homokaryons are probably restricted to the assumed morphological classes of SSIs. These results demonstrate that ISSR markers provide an efficient alternate for identification of homokaryons and suggest these markers be considered as new tools for the survey of Agaricus species.

Localization of the Mating Type Gene in Agaricus bisporus

The cultivated mushroom Agaricus bisporus is secondarily homothallic. Most basidia produce two basidiospores, each of which receives two of the four postmeiotic nuclei. Usually, the two packaged nuclei carry compatible mating types. Previous studies suggested that there may be only a single mating type locus in A. bisporus. In this study, we determined whether the mating type segregated as a single Mendelian determinant in a cross marked with 64 segregating molecular markers. To score mating types, each of the 52 homokaryotic offspring from this cross was paired with each of the two progenitor homokaryons. Compatible matings were identified by the formation of genetically stable heterokaryons which were verified by assay of restriction fragment length polymorphisms (RFLPs). Data for screening mycelial interactions on petri plates as well as fruit body formation were compared with the RFLP results. Mating types of 43 of the 52 homokaryotic offspring were determined on the basis of RFLP analysis. Our results indicate (i) there is a segregating mating type gene in A. bisporus, (ii) this mating type gene is on the largest linkage group (chromosome I), (iii) mycelial interactions on petri plates were associated with heterokaryon formation under selected conditions, (iv) fruit body formation was dependent upon the mating type gene, and (v) compatible mating types may not always be sufficient for fruiting.

Comparison of random amplified polymorphic DNA markers and morphological characters in identification of homokaryon isolates of white button mushroom (Agaricus bisporus)

The secondarily homothallic life cycle of the white button mushroom that results in scarcity of uninucleate basidiospores (homokaryons) in its progeny, is the most important impediment for genetic improvement of the commercial strains. Identification of homokaryons for breeding programs of Agaricus bisporus (button mushroom) is, therefore, crucial. Verifying homokaryons through fruiting trial is time consuming and unreliable. In this study, ability of RAPD markers, compared to morphological characters for identification of homokaryon isolates, was investigated. Based on morphological characters, 42 isolates were screened and exposed to RAPD markers. The results showed that RAPD markers could discriminate homokaryons from heterokaryons, based on number of bands generated. The numbers of band in homokaryons were significantly less than those of heterokaryons. Results also showed that cluster analysis, based on average of band number generated, could separate homokaryon from heterokaryon isolates. It is suggested that RAPDs could be used to identify hyomokaryons from heterokaryons for breeding program of A. bisporus.

Molecular cloning of a widely distributed microsatellite core sequence from the cultivated mushroom Agaricus bisporus

An Agaricus bisporus microsatellite with the tetranucleotide motif TATG tandemly repeated was isolated from an A. bisporus library enriched in repeated sequences. The use of the 16-mer oligonucleotide (TATG)4 indicates that many loci contain nearby copies of the microsatellite in opposite orientations. The wide distribution of the microsatellite in the A. bisporus genome was assessed (i) by polyacrylamide gel electrophoresis of the products generated by directed amplification of microsatellite-region DNA (DAMD) and (ii) by hybridization of these products with A. bisporus chromosomes separated by pulsed-field gel electrophoresis. This is, to our knowledge, the first microsatellite reported in the cultivated edible mushrooms. DAMD-PCR products were generated using DNA of three Pleurotus species (P. pulmonarius, P. sajor-caju, and P. florida), indicating that (TATG)4 repeats are also present in these cultivated species. The variability found within closely related strains indicates that such microsatellites are useful in fingerprinting and studying genetic variability in wild and commercial mushrooms.

Cloning and characterization of NADP-mannitol dehydrogenase cDNA from the button mushroom, Agaricus bisporus, and its expression in response to NaCl stress

Mannitol, a six-carbon sugar alcohol, is the main storage carbon in the button mushroom, Agaricus bisporus. Given the physiological importance of mannitol metabolism in growth, fruit body development, and salt tolerance of A. bisporus, the enzyme responsible for mannitol biosynthesis, NADP-dependent mannitol dehydrogenase (MtDH) (EC 1.1.1.138), was purified to homogeneity, and MtDH cDNA was cloned, sequenced, and characterized. To our knowledge, this represents the first report on the isolation of a cDNA encoding an NADP-dependent mannitol dehydrogenase. The MtDH cDNA contains an open reading frame of 789 bp encoding a protein of approximately 28 kDa. The N-terminal and internal amino acid sequences of the deduced protein exactly matched the ones determined from the purified MtDH subunit, whereas the amino acid composition of the deduced protein was nearly identical to that of the purified MtDH. The MtDH cDNA showed high homology with a plant-induced short-chain dehydrogenase from Uromyces fabae. Phylogenetic analysis based on amino acid sequences from mannitol(-1-phosphate) dehydrogenases indicated a close relationship between the substrate specificity of the enzymes and phylogenetic differentiation. Salt-stressed fruit bodies showed an overall increase in mannitol biosynthesis, as was evident from the increase in MtDH activity, MtDH abundance, and MtDH RNA accumulation. Furthermore, the MtDH transcript level seems to be under developmental control, as MtDH RNA accumulated during maturation of the fruit body.

Geographic variation of Chondrostereum purpureum detected by polymorphisms in the ribosomal DNA

Variation in the ribosomal (rDNA) repeat was analyzed for 107 isolates of the pathogenic fungus Chondrostereum purpureum, collected from Europe, New Zealand, and North America. The rDNA repeat of a representative Canadian isolate of C. purpureum was cloned into the λ vector EMBL-3, and a detailed restriction map was constructed. Variation in the large non-transcribed spacer region of the rDNA was determined for the entire collection of isolates following amplification by the polymerase chain reaction (PCR) and analysis of restriction fragment length polymorphisms (RFLPs). Three distinct nuclear type patterns were identified using the restriction endonuclease HaeIII. Nuclear type I was found in North American, European, and New Zealand isolates. Nuclear type II was only detected in isolates collected from North America, and nuclear type III was observed in isolates collected from both Europe and New Zealand. Nuclear type I was the predominant nuclear type in eastern North America as indicated by a frequency of 0.78, and nuclear type II occurred with a frequency of 0.89 in western North America. Gene flow across the continent was indicated by nearly equal nuclear type distributions (nuclear type I, 0.41; nuclear type II, 0.59) in central North America, but geographic separation has led to unequal nuclear-type distributions across North America. Keywords: Chondrostereum purpureum, biological control, genetic variation, ribosomal DNA.

Isolation of expressed sequence tags of Agaricus bisporus and their assignment to chromosomes

The genome of the cultivated basidiomycete Agaricus bisporus Horst U1 and of its homokaryotic parents has been characterized by using an optimized method of pulsed-field gel electrophoresis. Expressed sequence tags obtained as expressed cDNAs from a primordial tissue-derived cDNA library and a number of previously isolated genes were used to identify the individual chromosomes of the parental lines of Horst U1. The genome consists of 13 chromosomes, and its total size is 31 Mb. For those chromosomes that could not be resolved by contour-clamped homogeneous electric field electrophoresis, the segregation of marker genes was studied in a set of 86 homokaryotic offspring of Horst U1. At least two markers were assigned to each individual chromosome. In this way all individual chromosomes were unequivocally identified. The large size difference observed between the homologous chromosomes IX, harboring the rDNA repeat, was shown to be largely due to a higher copy number of rDNA in parental strain H97 than in parental strain H39.

Transformation of the cultivated mushroom, Agaricus bisporus, to hygromycin B resistance

Application of biotechnology to the cultivated mushroom, Agaricus bisporus, has been hampered thus far by the lack of a transformation system. Here, transformation of both a homo- and a heterokaryotic strain of A. bisporus to hygromycin B resistance is described. Transforming DNA was integrated into the A. bisporus genome and stably maintained throughout vegetative growth. Transformants of the heterokaryotic strain formed transgenic fruiting bodies. Promoters derived from the unrelated ascomycete Aspergillus nidulans and from A. bisporus itself, were able to drive expression of the hygromycin B resistance gene. Expression controlled by a fragment of 265 bp from the A. bisporus GPD promoter was sufficient to generate transformants. However, transformation efficiency was not enhanced by using this homologous promoter.

Indigenous and introduced populations ofAgaricus bisporus, the cultivated button mushroom, in eastern and western Canada: implications for population biology, resource management, and conservation of genetic diversity

Agaricus bisporus is known from field collections in several parts of southern Canada and the border states of Washington and Idaho. In Ontario, the species is associated with urban horticultural sites, agricultural areas, and thoroughfares. In British Columbia, Washington, and Idaho, the species is less well documented but occurs in habitats similar to those in Ontario. All studied isolates from these two regions were genotypically similar to those collected in Europe and also to a representative sample of cultivar isolates believed to be of European origin. In contrast, a population from forests of Picea in the Rocky Mountains of Alberta had genotypes that are very different from European and cultivar groups, including the putatively introduced populations in other parts of Canada. To a lesser extent, the Albertan individuals also differed from three other isolated natural populations, two in California and one in Israel. Two of 35 isolates from Alberta had nuclear genotypes that were partially or entirely consistent with European ancestry, indicating that foreign (probably cultivar) germ plasm has become established in the native habitat. Thirty of 35 isolates from the Alberta field sample had one of six mitochondrial DNA (mtDNA) haplotypes known only from Alberta; the remaining five had an mtDNA type known from cultivar strains. However, nuclear genotypic similarity to other Albertan or European-cultivar isolates was not significantly correlated with presence or absence of this latter mtDNA type. The genetic diversity represented by the previously unknown Albertan population, and to a lesser extent by the heirloom varietal lineages and their derivatives that have become established in Ontario, British Columbia, Washington, and Idaho, is an important resource for breeders of this valuable fungal crop species. Threats to resource populations of this species, and possible responses, are discussed. Key words: Agaricus bisporus, mushroom population biology, resource management, germ plasm conservation, genetic diversity, microphylogeny.

Uniparental Mitochondrial Transmission in the Cultivated Button Mushroom, Agaricus bisporus

A uniparental mitochondrial (mt) transmission pattern has been previously observed in laboratory matings of the cultivated mushroom Agaricus bisporus on petri dishes. In this study, four sets of specific matings were further examined by taking mycelial plugs from the confluent zone of mated homokaryons and inoculating these plugs into rye grain for laboratory fruiting and for fruiting under industrial conditions. Examination of the mt genotype of each individual fruit body for mt-specific restriction fragment length polymorphisms further confirmed that the mt genome was inherited uniparentally. The vegetative radial growth and the fruiting activity of two pairs of intraspecific heterokaryons, each pair carrying the same combination of nuclear genomes but different mt genotypes, were compared. Our results suggested that the mt genotype did not appreciably affect radial growth or fruiting activity. The failure to recover both heterokaryons, each carrying either parental mt genotype in any given cross, therefore clearly indicated that in matings of A. bisporus , the mt genome from one of the parental homokaryons is either selectively excluded in the newly formed heterokaryon or selectively eliminated in the immediate heterokaryotic mitotic progeny of the newly formed heterokaryon.

Inheritance of Strain Instability (Sectoring) in the Commercial Button Mushroom, Agaricus bisporus

The button mushroom, Agaricus bisporus , is a commercially important cultivated filamentous fungus. During the last decade, the button mushroom industry has depended mainly on two strains (or derivatives of these two strains). Using one of these highly successful strains (strain U1) we examined the phenomenon of strain instability, specifically, the production of irreversible sectors. Three “stromatal” and three “fluffy” sectors were compared with a healthy type U1 strain and with a wild-collected isolate. Compost colonization and fruit body morphology were examined. The main objective of this study, however, was to examine the meiotic stability of the sectored phenotype. Single basidiospores were isolated and subjected to a grain bioassay in which the ability to produce sectors was measured. Our results were as follows: (i) basidiospore cultures obtained from a wild-collected isolate showed no tendency to produce sectors; (ii) approximately 5% of the basidiospore cultures obtained from healthy type U1 strains produced irreversible sectors in the grain bioassay; (iii) the five primary sectors examined produced basidiospore cultures, half of which produced normal-looking growth in the grain bioassay and half of which produced some degree of sectoring; and (iv) the one sectored isolate that represented the F2 generation gave ratios similar to the 1:1 ratio observed for the F1 cultures.

Further characterization of a large inverted repeat in the mitochondrial genomes of Agaricus bisporus (= A. brunnescens) and related species

The mitochondrial (mt) genome of Agaricus bisporus Ag50 (a heterokaryon) is a 136-kilobase (kb) circular molecule which contains a pair of large inverted repeats (IRs). Two large BAMHI fragments (B1 and B2) which contain the IR regions were further mapped. The repeated regions were determined to be approximately 7.7 kb in length. The mt small ribosomal RNA (S rRNA) gene is located adjacent to one of the repeated regions. Orientational isomers, generated by homologous recombination between the repeated regions, were not observed in mtDNA extractions from Ag50 mycelium (liquid culture) or from Ag50 fruit bodies. We also did not observe any orientational isomers in Ag50HA or Ag50HB, two homokaryons somatically isolated from Ag50. DNA homologous to the Ag50 mt repeated regions was observed in ten other isolates of Agaricus including four isolates of A. bisporus, two isolates of A. subperonatus, two isolates of A. subfloccosus, one isolate of A. bitorquis, and one isolate of A. pattersonae. The repeated regions and the small unique regions in two other heterokaryotic strains of A. bisporus, Ag2 and Ag85, were physically mapped. The repeated regions in these two strains are also in the inverted forms. Restriction endonuclease mapping indicated that the two copies of the IR in Ag85 were not identical.

Meiotic behavior and linkage relationships in the secondarily homothallic fungus Agaricus bisporus

This study followed the transmission of 64 segregating genetic markers to 52 haploid offspring, obtained from both homokaryotic and heterokaryotic meiospores, of a cross (AG 93b) of Agaricus bisporus, the commonly cultivated "button mushroom." The electrophoretic karyotypes of the AG 93b component nuclei were determined concurrently (n = 13). Eleven distinct linkage groups were identified by two-point analysis. DNA-DNA hybridization showed that nine of these corresponded to unique chromosome-sized DNAs. Two other chromosomal DNAs were marked with nonsegregating markers, including the rDNA repeat. Two remaining chromosomes remained unmarked but hybridized to repeated-sequence probes. Cross 93b had an essentially conventional meiosis in which both independent assortment and joint segregation of markers occurred, but in which crossing over was infrequent over much of the mapped genome. The 48 homokaryotic spore-offspring had overall crossover frequencies that were similar to, but possibly slightly less than, those of three homokaryon constituents of heterokaryotic spore-offspring. These daa provide support for our earlier cytogenetic model of sporogenesis in A. bisporus, that explains why heterokaryotic spore-offspring usually appear to exhibit no recombination. No evidence favoring an alternative, mitotic model of sporogenesis was found. The resulting genetic map appears to survey the genome extensively and for the first time permits localization of loci determining economically important traits in this fungal crop species. Large differences in the vigor of homokaryotic offspring were correlated with the inheritance of certain chromosome segments and were also often associated with significant departures from Mendelian segregation ratios.

Investigation of Mitochondrial Transmission in Selected Matings between Homokaryons from Commercial and Wild-Collected Isolates of Agaricus bisporus (= Agaricus brunnescens )

Ten heterokaryons of Agaricus bisporus (= Agaricus brunnescens ) were shown to carry four different mitochondrial (mt) genotypes by analysis of mt restriction fragment length polymorphisms (RFLPs). Fifteen homokaryons derived from these strains were used to investigate mt inheritance in A. bisporus. One hundred eighty-nine pairings were performed in 25 different combinations. Pairings in 15 different combinations produced heterokaryons on the basis of nuclear RFLP analyses and/or fruiting trials. The mt genotype of each new intraspecies hybrid was examined by using mt RFLPs as genetic markers. Our results suggest the following. (i) Recombination between the mt genomes was not a common event. (ii) From most individual pairings, all heterokaryons carried the same mt genotype. (iii) Heterokaryons carrying either of the two possible mt genotypes were observed in certain crosses after modification of the pairing procedure. A biparental transmission pattern was demonstrated for some crosses, but there appears to be a preference for one of the mt genotypes to predominate in any specific pairing.

DNA amplification polymorphisms of the cultivated mushroom Agaricus bisporus

Single 10-bp primers were used to generate random amplified polymorphic DNA (RAPD) markers from commercial and wild strains of the cultivated mushroom Agaricus bisporus via the polymerase chain reaction. Of 20 primers tested, 19 amplified A. bisporus DNA, each producing 5 to 15 scorable markers ranging from 0.5 to 3.0 kbp. RAPD markers identified seven distinct genotypes among eight heterokaryotic strains; two of the commercial strains were shown to be related to each other through single-spore descent. Homokaryons recovered from protoplast regenerants of heterokaryotic strains carried a subset of the RAPD markers found in the heterokaryon, and both of the haploid nuclei from two heterokaryons were distinguishable. RAPD markers also served to verify the creation of a hybrid heterokaryon and to analyze meiotic progeny from this new strain: most of the basidiospores displayed RAPD fingerprints identical to that of the parental heterokaryon, although a few selected slow growers were homoallelic at a number of loci that were heteroallelic in the parent, suggesting that they represented rare homokaryotic basidiospores; crossover events between a RAPD marker locus and its respective centromere appeared to be infrequent. These results demonstrate that RAPD markers provide an efficient alternative for strain fingerprinting and a versatile tool for genetic studies and manipulations of A. bisporus.

DNA Polymorphisms in Lentinula edodes , the Shiitake Mushroom

DNA restriction fragment length polymorphisms (RFLPs) were examined in Lentinula edodes strains. Genomic DNA from strain 70 was cloned in plasmid vector pUC19, and 18 random clones containing low-copy DNA sequences were used to probe seven strains in Southern DNA-DNA hybridizations. Each cloned fragment revealed DNA polymorphism. An RFLP genotype was determined for each strain and the genetic relatedness was assessed. The coefficients of genetic similarity among the seven strains ranged from 0.43 to 0.90. The inheritance of RFLP markers was examined in single spore isolates. Homokaryons displayed a loss of polymorphic bands compared with the parent dikaryon. Hybrids constructed by crossing compatible homokaryons displayed the inheritance of RFLP markers from each parent homokaryon.

Inheritance of restriction fragment length polymorphisms in Agaricus brunnescens

The cultivated mushroom, Agaricus brunnescens, is secondarily homothallic; most basidia produce only two basidiospores, each of which receives two of the four post meiotic nuclei. The segregation of restriction fragment length polymorphisms (RFLPs) detected by four plasmid probes carrying single-copy nuclear DNA of Agaricus was followed in seven parental strains including commercial, wild-collected, and artificially synthesized heterokaryons. Of a total of 367 single-spore progeny examined, 351 (95.6%) were heteroallelic at all RFLP loci heteroallelic in the respective parents. Of the 16 segregant isolates, ten (2.7% of the total) were homoallelic at all segregating loci assayed, suggesting that these isolates were most probably derived from rare spores that had received only a single postmeiotic nucleus. Some of these ten isolates had recombinant genotypes. Only five isolates (1.4% of the total) showed homoallelism at one of the loci heteroallelic in the parent, while remaining heteroallelic at other loci. These five genotypes suggest that a crossover had occurred between a marker locus and its respective centromere. Taken together, the results suggest that meiosis in A. brunnescens is accompanied by low levels of recombination and that nonsister nuclei are preferentially incorporated into basidiospores after meiosis II.

DNA polymorphisms in commercial and wild strains of the cultivated mushroom, Agaricus bisporus

DNA from the cultivated mushroom, Agaricus bisporus, was cloned into the bacteriophage lambda vector EMBL3 creating a partial genomic library. Ten random clones from the library were used to probe for restriction fragment length polymorphisms (RFLPs). Six of the ten probes detected polymorphisms and were used to demonstrate variation in wild and cultivated strains of the mushroom. These results suggest that RFLPs could form a basis for genetic finger-printing and subsequent strain protection in A. bisporus. In single spore progeny, RFLPs were used to demonstrate normal meiotic segregation and to differentiate between homokaryons and heterokaryons. RFLPs therefore have great potential in the development of the genetics and breeding of this commercially important species.

Detection of DNA "fingerprints" of cultivated rice by hybridization with a human minisatellite DNA probe

A human minisatellite DNA probe detects several restriction fragment length polymorphisms in cultivars of Asian and African rice. Certain fragments appear to be inherited in a Mendelian fashion and may represent unlinked loci. The hybridization patterns appear to be cultivar-specific and largely unchanged after the regeneration of plants from tissue culture. The results suggest that these regions of the rice genome may be used to generate cultivar-specific DNA fingerprints. The demonstration of similarity between a human minisatellite sequence and polymorphic regions in the rice genome suggests that such regions also occur in the genomes of many other plant species.