An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporusxA. bisporus var. burnettii hybrid based on AFLP, SSR and CAPS markers sheds light on the recombination behaviour of the species

Insight into the evolutionary and domesticated history of the most widely cultivated mushroom Agaricus bisporus via mitogenome sequences of 361 global strains

Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate the natural evolutionary history but also the understanding on the evolution going back to the early era of domestication. In this study, we generated the mitochondrial genome sequences of 352 A. bisporus strains and 9 strains from 4 closely related species around the world. The population mitogenomic study revealed all A. bisporus strains can be divided into seven clades, and all domesticated cultivars present only in two of those clades. The molecular dating analysis showed this species origin in Europe on 4.6 Ma and we proposed the main dispersal routes. The detailed mitogenome structure studies showed that the insertion of the plasmid-derived dpo gene caused a long fragment (MIR) inversion, and the distributions of the fragments of dpo gene were strictly in correspondence with these seven clades. Our studies also showed A. bisporus population contains 30 intron distribution patterns (IDPs), while all cultivars contain only two IDPs, which clearly exhibit intron loss compared to the others. Either the loss occurred before or after domestication, that could suggest that the change facilitates their adaptation to the cultivated environment.

Bipolar system of sexual incompatibility and heterothallic life cycle in the basidiomycetes Pachyma hoelen Fr. (Fuling)

The sclerotia of Pachyma hoelen are one of the traditional Chinese medicines and foods that are widely used in East Asian countries. The strains used for cultivation showed bad performance in recent years, and breeding of superior strains has become increasingly important for this fungus. Nevertheless, the mating system and life cycle of P. hoelen were still ambiguous. In this study, the methods for distinguishing between homokaryotic offspring with different mating types were established, as well as confirmation of strain hybridization based on allelic polymorphism at a locus of the rpb2 gene. The bipolar mating system was confirmed according to the mating results of homokaryotic SSIs. The fact that heterokaryotic parents produce homokaryotic meiospores proves that the life cycle is heterothallic. Combining scanning electron microscope observation and DAPI (4',6-diamidino-2-phenylindole) fluorescent staining of hymenium and basidiospores in situ and ex situ, nuclear migration pattern from basidia to spores was revealed. The heterothallic life cycle was verified, revised, and supplemented step by step. This is the first report of systematic research on the mating system, life cycle, and outcrossing of homokaryotic offspring in P. hoelen. It will be helpful for the biological research, strain improvement, and development of the P. hoelen industry.

SNP-Based Genetic Linkage Map and Quantitative Trait Locus Mapping Associated with the Agronomically Important Traits of Hypsizygus marmoreus

White strains of Hypsizygus marmoreus are more difficult to cultivate than are brown strains; therefore, new white strain breeding strategies are required. Accordingly, we constructed the genetic map of H. marmoreus with 1996 SNP markers on 11 linkage groups (LGs) spanning 1380.49 cM. Prior to analysis, 82 backcrossed strains (HM8 lines) were generated by mating between KMCC03106-31 and the progenies of the F1 hybrid (Hami-18 × KMCC03106-93). Using HM8, the first 23 quantitative trait loci (QTLs) of yield-related traits were detected with high limit of detection (LOD) scores (1.98-9.86). The length, thickness, and hardness of the stipe were colocated on LG 1. Especially, length of stipe and thickness of stipe were highly correlated given that the correlation coefficients were negative (-0.39, p value ≤ .01). And a typical biomodal distribution was observed for lightness of the pileus and the lightness of the pileus trait belonged to the LG 8, as did traits of earliness and mycelial growth in potato dextrose agar (PDA) medium. Therefore, results for color traits can be suggested that color is controlled by a multi-gene of one locus. The yield trait was highly negatively correlated with the traits for thickness of the stipe (-0.45, p value ≤ .01). Based on additive effects, the white strain was confirmed as recessive; however, traits of mycelial growth, lightness, and quality were inherited by backcrossed HM8 lines. This new genetic map, finely mapped QTLs, and the strong selection markers could be used in molecular breeding of H. marmoreus.

Genetic Linkage and Physical Mapping for an Oyster Mushroom (Pleurotus cornucopiae) and Quantitative Trait Locus Analysis for Cap Color

Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushroom species because of its gastronomic value and nutraceutical properties. Cap color is an important trait, since consumers prefer dark mushrooms, which are now represented by only a small portion of the commercial varieties. Breeding efforts are required to improve quality-related traits to satisfy various demands of consumers. Here, we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3,449 single nucleotide polymorphism (SNP) markers generated by the 2b-RAD approach. The map contains 11 linkage groups covering 961.6 centimorgans (cM), with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced, resulting in 425 scaffolds (>1,000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to the pseudochromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3,357) were physically localized on 140 scaffolds that were assigned to 11 pseudochromosomes, with a total of 32.5 Mb, representing 92.5% of the whole genome. Six quantitative trait loci (QTL) controlling cap color of P. cornucopiae were detected, accounting for a total phenotypic variation of 65.6%, with the highest value for the QTL on pseudochromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. IMPORTANCE Oyster mushrooms are produced and consumed all over the world. Pleurotus cornucopiae is one of the main oyster mushroom species. Dark-cap oyster mushrooms are becoming more and more popular with consumers, but dark varieties are rare on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae. In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae. The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. As well, the genome characteristics of P. cornucopiae were compared to the closely related species Pleurotus ostreatus. The results provided a basis for understanding the genetic background and marker-assisted breeding of this economically important mushroom species.

Mapping Recombination Landscape and Basidial Spore Number in the Button Mushroom Agaricus bisporus

The button mushroom Agaricus bisporus is represented mainly by two varieties, a secondarily homothallic variety with predominantly two heterokaryotic spores per basidia and a heterothallic variety with predominantly four homokaryotic spored basidium. Both varieties also differ in their recombination landscape with the former showing crossovers (CO) predominantly at chromosome ends whereas the latter has a more evenly distribution of CO over the chromosomes. The two varieties are compatible, and this has been used to study segregation of the basidial spore number (BSN) and the genomic positions of recombination, i.e., the CO landscape, in order to find the underlying genetic determinants. Knowledge on genes controlling CO positions might facilitate either the conservation of favorable allele combinations or the disruption of unwanted allele combinations to reduce linkage drag. For BSN, in total seven QTL were found with the major QTL on chromosome 1 explaining ca. 55% of the phenotypic variation. It appeared, however, difficult to map the recombination landscape. This phenotype can only be assessed in the meiotic offspring of an intervarietal hybrid which is a laborious and difficult task. Nevertheless, this was done, and we were able to map three QTLs for this trait, two on chromosome 1 and one on chromosome 2 not overlapping with the QTL for BSN. The hurdles encountered are discussed and a new strategy is proposed that can solves these. We propose to use two genetically unrelated mapping populations both offspring of a cross between a var. bisporus and a var. burnettii homokaryon and thus segregating both for CO and BSN. Homokaryotic offspring of both populations can be intercrossed without limitation of mating incompatibility and marker homozygosity and the hybrid mushrooms directly used to map BSN. Homokaryotic offspring of these hybrid mushrooms can be genotypes to assess CO positions using next generation sequencing technologies that will solve marker problems encountered, especially for genotyping chromosome ends. This new approach can be a useful strategy for a more efficient breeding strategy for mushrooms in general.

Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus

In heterothallic basidiomycete fungi, sexual compatibility is restricted by mating types, typically controlled by two loci: PR, encoding pheromone precursors and pheromone receptors, and HD, encoding two types of homeodomain transcription factors. We analysed the single mating-type locus of the commercial button mushroom variety, Agaricus bisporus var. bisporus, and of the related variety burnettii. We identified the location of the mating-type locus using genetic map and genome information, corresponding to the HD locus, the PR locus having lost its mating-type role. We found the mip1 and β-fg genes flanking the HD genes as in several Agaricomycetes, two copies of the β-fg gene, an additional HD2 copy in the reference genome of A. bisporus var. bisporus and an additional HD1 copy in the reference genome of A. bisporus var. burnettii. We detected a 140 kb-long inversion between mating types in an A. bisporus var. burnettii heterokaryon, trapping the HD genes, the mip1 gene and fragments of additional genes. The two varieties had islands of transposable elements at the mating-type locus, spanning 35 kb in the A. bisporus var. burnettii reference genome. Linkage analyses showed a region with low recombination in the mating-type locus region in the A. bisporus var. burnettii variety. We found high differentiation between β-fg alleles in both varieties, indicating an ancient event of recombination suppression, followed more recently by a suppression of recombination at the mip1 gene through the inversion in A. bisporus var. burnettii and a suppression of recombination across whole chromosomes in A. bisporus var. bisporus, constituting stepwise recombination suppression as in many other mating-type chromosomes and sex chromosomes.

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.

Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes

Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self-incompatibility loci and fungal mating-type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating-type loci in fungi, sometimes encompassing vast regions of the mating-type chromosomes. The suppression of recombination at mating-type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating-type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating-type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms.

Genetic linkage map construction and quantitative trait loci mapping of agronomic traits in Gloeostereum incarnatum

Gloeostereum incarnatum is an edible medicinal mushroom widely grown in China. Using the whole genome of G. incarnatum, simple sequence repeat (SSR) markers were developed and synthetic primers were designed to construct its first genetic linkage map. The 1,048.6 cm map is composed of 10 linkage groups and contains 183 SSR markers. In total, 112 genome assembly sequences were anchored, representing 16.43 Mb and covering 46.41% of the genome. Selfing populations were used for quantitative trait loci (QTL) targeting, and the composite interval mapping method was used to co-localize the mycelium growth rate (potato dextrose agar and sawdust), growth period, yield and fruiting body length, and width and thickness. The 14 QTLs of agronomic traits had LOD values of 3.20-6.51 and contribution rates of 2.22-13.18%. No linkage relationship was found between the mycelium growth rate and the growth period, but a linkage relationship was observed among the length, width and thickness of the fruiting bodies. Using NCBI's BLAST alignment, the genomic sequences corresponding to the QTL regions were compared, and a TPR-like protein candidate gene was selected. Using whole-genome data, 138 candidate genes were found in four sequence fragments of two SSR markers located in the same scaffold. The genetic map and QTLs established in this study will aid in developing selective markers for agronomic traits and identifying corresponding genes, thereby providing a scientific basis for the further gene mapping of quantitative traits and the marker-assisted selection of functional genes in G. incarnatum breeding programs.

Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends

Agaricus bisporus, the most cultivated edible mushroom worldwide, is represented mainly by the subspecies var. bisporus and var. burnettii. var. bisporus has a secondarily homothallic life cycle with recombination restricted to chromosome ends, while var. burnettii is heterothallic with recombination seemingly equally distributed over the chromosomes. To better understand the relationship between genomic make-up and different lifestyles, we have de novo sequenced a burnettii homokaryon and synchronised gene annotations with updated versions of the published genomes of var. bisporus. The genomes were assembled into telomere-to-telomere chromosomes and a consistent set of gene predictions was generated. The genomes of both subspecies were largely co-linear, and especially the chromosome ends differed in gene model content between the two subspecies. A single large cluster of repeats was found on each chromosome at the same respective position in all strains, harbouring nearly 50% of all repeats and likely representing centromeres. Repeats were all heavily methylated. Finally, a mapping population of var. burnettii confirmed an even distribution of crossovers in meiosis, contrasting the recombination landscape of var. bisporus. The new findings using the exceptionally complete and well annotated genomes of this basidiomycete demonstrate the importance for unravelling genetic components underlying the different life cycles.

A Resequencing-Based Ultradense Genetic Map of Hericium erinaceus for Anchoring Genome Sequences and Identifying Genetic Loci Associated With Monokaryon Growth

Hericium erinaceus has attracted tremendous interest owing to its compelling health-promoting properties. However, breeding of elite cultivars of H. erinaceus is hindered by the lack of a genetic and molecular toolbox. Here, we performed resequencing analysis of 127 F1 single-spore isolates and constructed the first high-resolution genetic map of H. erinaceus. With the use of recombination bins as markers, an ultradense genetic map consisting of 1,174 bins (including 37,082 single-nucleotide polymorphisms) was generated. This newly developed genetic map covered 1,096.5 cM, with an average bin spacing of 0.95 cM. High collinearity between genetic map and H. erinaceus genome assembly was revealed by aligning scaffolds to this genetic map using bin markers as anchors. The application of this newly developed genetic map in quantitative trait locus (QTL) mapping was also elucidated, and four QTLs for monokaryon growth were recovered. One QTL, mgr1, which contributes 12.1% of growth variations, was located near the mating type A (MAT-A) loci. Overall, this newly constructed high-resolution genetic map (or bin map) could be used as reference in future genetic, genomic, and breeding studies on H. erinaceus.

Construction of a genetic linkage map of Lentinula edodes based on SSR, SRAP and TRAP markers

Genetic mapping is a basic tool for eukaryotic genomic research. It allows the localization of genes or quantitative trait loci (QTLs) and map-based cloning. In this study, we constructed a linkage map based on DNA samples from a commercial strain L808, including two parental monokaryons and 93 single spore isolates considered with segregating to 1:1:1:1 at four mating types (A₁B₁, A₁B₂, A₂B₁ and A₂B₂). Using Simple Sequence Repeats (SSR), Sequence Related Amplified Polymorphism (SRAP), Target Region Amplified Polymorphism (TRAP) molecular markers, 182 molecular markers and two mating factors were located on 11 linkage groups (LGs). The total length of the map was 948.083 centimorgan (cM), with an average marker interval distance of 4.817 cM. Only two gaps spanning more than 20 cM was observed. The probability of 20 cM, 10 cM, 5 cM genetic distance cover one marker was 99.68%, 94.36%, 76.43% in our genetic linkage map, respectively. This is the first linkage map of Lentinula edodes using SSR markers, which provides essential information for quantitative trait analyses and improvement of genome assembly.

Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)

We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (M_AF) and the average number of alleles (N_A) were 0.50 and 5.47, respectively. The average number of genotypes (N_G), observed heterozygosity (H_O), expected heterozygosity (H_E), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson's correlation coefficient showed that M_AF was negatively correlated with N_G (-0.683), N_A (-0.600), H_O (-0.584), and PIC (-0.941). N_G, N_A, H_O, and PIC were positively correlated with other polymorphic parameters except for M_AF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

Background

Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Developing saturated genetic linkage and physical maps is a start for applying genetic and molecular approaches to accelerate the precise breeding programs.

Results

Here we present a genetic linkage map for P. tuoliensis constructed by using 115 haploid monokaryons derived from a hybrid strain H6. One thousand one hundred and eighty-two SNP markers developed by 2b–RAD (type IIB restriction-site associated DNA) approach were mapped to 12 linkage groups. The map covers 1073 cM with an average marker spacing of 1.0 cM. The genome of P. tuoliensis was de novo sequenced as 40.8 Mb and consisted of 500 scaffolds (>500 bp), which showed a high level of colinearity to the genome of P. eryngii var. eryngii. A total of 97.4% SNP markers (1151) were physically localized on 78 scaffolds, and the physical length of these anchored scaffolds were 33.9 Mb representing 83.1% of the whole genome. Mating type loci A and B were mapped on separate linkage groups and identified physically on the assembled genomes. Five putative pheromone receptors and two putative pheromone precursors were identified for the mating type B locus.

Conclusions

This study reported a first genetic linkage map integrated with physical mapping of the de novo sequenced genome and the mating type loci of an important cultivated mushroom in China, P. tuoliensis. The de novo sequenced and annotated genome, assembled using a 2b–RAD generated linkage map, provides a basis for marker-assisted breeding of this economic important mushroom species.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4421-z) contains supplementary material, which is available to authorized users.

Construction of a genetic linkage map and QTL mapping of agronomic traits in Auricularia auricula-judae

Auricularia auricula-judae is a traditional edible fungus that is cultivated widely in China. In this study, a genetic linkage map for A. auricula-judae was constructed using a mapping population consisting of 138 monokaryons derived from a hybrid strain (A119-5). The monokaryotic parent strains A14-5 and A18-119 were derived from two cultivated varieties, A14 (Qihei No. 1) and A18 (Qihei No. 2), respectively. In total, 130 simple sequence repeat markers were mapped. These markers were developed using the whole genome sequence of A. auricula-judae and amplified in A14-5, A18- 119, and the mapping population. The map consisted of 11 linkage groups (LGs) spanning 854 cM, with an average interval length of 6.57 cM. A testcross population was derived from crossing between the monokaryon A184-57 (from the wild strain A184 as a tester strain) and the mapping population. Important agronomic trait-related QTLs, including mycelium growth rate on potato dextrose agar for the mapping population, mycelium growth rate on potato dextrose agar and sawdust for the testcross population, growth period (days from inoculation to fruiting body harvesting), and yield for the testcross population, were identified using the composite interval mapping method. Six mycelium growth raterelated QTLs were identified on LG1 and LG4, two growth period-related QTLs were identified on LG2, and three yieldrelated QTLs were identified on LG2 and LG6. The results showed no linkage relationship between mycelium growth rate and growth period. The present study provides a foundation for locating genes for important agronomic characteristics in A. auricula-judae in the future.

Developments in breeding of Agaricus bisporus var. bisporus: progress made and technical and legal hurdles to take

True breeding of button mushrooms has hardly been done in the last decades, despite this species being one of the most cultivated mushrooms worldwide. Research done in the last 20 years has identified and characterised new germplasm and improved our understanding of the genetic base for some traits. A substantial collection of wild-collected strains is now available and partly characterised for a number of important traits such as disease resistance and yield. Most of the variations found in a number of important agronomic traits have a considerable heritability and are thus useful for breeding. Genetic marker technology has also developed considerably for this mushrooms in the last decade and used to identify quantitative trait loci (QTL) for important agronomic traits. This progress has, except for one example, not resulted so far into new commercially varieties. One of the reasons lies in the typical life cycle of the button mushroom Agaricus bisporus var. bisporus which hampers breeding. Joint investment is needed to solve technical problems in breeding. Special attention is needed for the protection of new varieties. Due to its typical life cycle, it is very easy to generate so called "look-a-likes" from protected cultivars by screening fertile single spore cultures. A consensus has been reached within the mushroom (breeding) industry to consider this method as the generation of essentially derived varieties as defined in plant breeding.

Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms)

The demand for button mushrooms of high quality is increasing. Superior button mushroom varieties require the combination of multiple traits to maximize productivity and quality. Very often these traits are correlated and should, therefore, be evaluated together rather than as single traits. In order to unravel the genetic architecture of multiple traits of Agaricus bisporus and the genetic correlations among traits, we have investigated a total of six agronomic and quality traits through multi-trait QTL analyses in a mixed-model. Traits were evaluated in three heterokaryon sets. Significant phenotypic correlations were observed among traits. For instance, earliness (ER) correlated to firmness (FM), cap color, and compost colonization, and FM correlated to scales (SC). QTLs of different traits located on the same chromosomes genetically explains the phenotypic correlations. QTL detected on chromosome 10 mainly affects three traits, i.e., ER, FM and SC. It explained 31.4 % phenotypic variation of SC on mushroom cap (heterokaryon Set 1), 14.9 % that of the FM (heterokaryon Set 3), and 14.2 % that of ER (heterokaryon Set 3). High value alleles from the wild parental line showed beneficial effects for several traits, suggesting that the wild germplasm is a valuable donor in terms of those traits. Due to the limitations of recombination pattern, we only made a start at understanding the genetic base for several agronomic and quality traits in button mushrooms.

A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus

The button mushroom (Agaricus bisporus) is one of the world's most cultivated mushroom species, but in spite of its economic importance generation of new cultivars by outbreeding is exceptional. Previous genetic analyses of the white bisporus variety, including all cultivars and most wild isolates revealed that crossing over frequencies are low, which might explain the lack of introducing novel traits into existing cultivars. By generating two high quality whole genome sequence assemblies (one de novo and the other by improving the existing reference genome) of the first commercial white hybrid Horst U1, a detailed study of the crossover (CO) landscape was initiated. Using a set of 626 SNPs in a haploid offspring of 139 single spore isolates and whole genome sequencing on a limited number of homo- and heterokaryotic single spore isolates, we precisely mapped all COs showing that they are almost exclusively restricted to regions of about 100kb at the chromosome ends. Most basidia of A. bisporus var. bisporus produce two spores and pair preferentially via non-sister nuclei. Combined with the COs restricted to the chromosome ends, these spores retain most of the heterozygosity of the parent thus explaining how present-day white cultivars are genetically so close to the first hybrid marketed in 1980. To our knowledge this is the first example of an organism which displays such specific CO landscape.

Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated.

Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii

Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes.

The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens.

Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map

Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi.

Biocontrol Activity of Bacillus subtilis Isolated from Agaricus bisporus Mushroom Compost Against Pathogenic Fungi

Bacillus subtilis strain B154, isolated from Agaricus bisporus mushroom compost infected by red bread mold, exhibited antagonistic activities against Neurospora sitophila. Antifungal activity against phytopathogenic fungi was also observed. The maximum antifungal activity was reached during the stationary phase. This antifungal activity was stable over a wide pH and temperature range and was not affected by proteases. Assay of antifungal activity in vitro indicated that a purified antifungal substance could strongly inhibit mycelia growth and spore germination of N. sitophila. In addition, treatment with strain B154 in A. bisporus mushroom compost infected with N. sitophila significantly increased the yield of bisporus mushrooms. Ultraviolet scan spectroscopy, tricine sodium dodecyl sulfate-polyacrylamide gel electrophoresis, matrix-associated laser desorption ionization time-of-flight mass spectrometry, and electrospray ionization tandem mass spectrometry analyses revealed a molecular weight consistent with 1498.7633 Da. The antifungal compound might belong to a new type of lipopeptide fengycin.

Quantitative trait locus mapping for bruising sensitivity and cap color of Agaricus bisporus (button mushrooms)

White button mushrooms discolor after mechanical damage of the cap skin. This hampers the development of a mechanical harvest system for the fresh market. To unravel the genetic basis for bruising sensitivity, two haploid populations (single spore cultures) were generated derived from crosses between parental lines differing in discoloration after mechanical damage (bruising sensitivity). The haploids were crossed with different homokaryotic tester lines to generate mushrooms and allow assessment of the bruising sensitivity in different genetic backgrounds. Bruising sensitivity appears to be a polygenic highly heritable trait (H(2): 0.88-0.96) and a significant interaction between genotypes and tester lines and genotypes and flushes was found. Using SNP markers evenly spread over all chromosomes, a very low recombination was found between markers allowing only assignment of QTL for bruising sensitivity to chromosomes and not to sub-regions of chromosomes. The cap color of the two parental lines of population 1 is white and brown respectively. A major QTL for bruising sensitivity was assigned to chromosome 8 in population 1 that also harbors the main determinant for cap color (brown versus white). Splitting offspring in white and non-white mushrooms made minor QTL for bruising sensitivity on other chromosomes (e.g. 3 and 10) more prominent. The one on chromosome 10 explained 31% phenotypic variation of bruising sensitivity in flush 2 in the subpopulations of population 1. The two parental lines of population 2 are both white. Major QTL of bruising sensitivity were detected on chromosome 1 and 2, contributing totally more than 44% variation of the bruising sensitivity in flush 1 and 54% variation of that in flush 2. A considerable consistency was found in QTL for bruising sensitivity in the different populations studied across tester lines and flushes indicating that this study will provide a base for breeding cultivars that are less sensitive for bruising allowing the use of mechanical harvest and automatic postharvest handling for produce for the fresh market. The low recombination between homologous chromosomes, however, underlines the need to introduce a normal recombination pattern found in a subspecies of the button mushroom.

Evidence for amphithallism and broad geographical hybridization potential among Agaricus subrufescens isolates from Brazil, France, and Thailand

Agaricus subrufescens is a cultivated edible and medicinal mushroom. Its known geographical distribution encompasses the Americas, Europe, Oceania, and Asia. The objective of this study was to assess mating compatibility and interfertility of strains originating from Brazil, France, and Thailand. Progeny of each strain were analyed with codominant molecular markers. Multilocus genotype tests revealed that the three strains were amphithallic with percentages of heterokaryotic single spore progenies of 75% for the Thai strain and around 40% for the Brazilian and French strains. In mating tests A. subrufescens had a multiallelic unifactorial system of sexual incompatibility. The three parent strains were interfertile based on experimental pairings of single-spore isolates, the recovery of hybrid heterokaryons from compatible matings, and the ability of hybrids to produce mushrooms and fertile spores. This biological approach supports the inclusion of the European strains within the species and the extension of the geographical distribution range to Asia. Our data should help to develop breeding strategies and to better manage and exploit the diversity existing in A. subrufescens.

Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina

The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring.

Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes

The most saturated linkage map for Lentinula edodes to date was constructed based on a monokaryotic population of 146 single spore isolates (SSIs) using sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), insertion-deletion (InDel) markers, and the mating-type loci. Five hundred and twenty-four markers were located on 13 linkage groups (LGs). The map spanned a total length of 1006.1 cM, with an average marker spacing of 2.0 cM. Quantitative trait loci (QTLs) mapping was utilized to uncover the loci regulating and controlling the vegetative mycelium growth rate on various synthetic media, and complex medium for commercial cultivation of L. edodes. Two and 13 putative QTLs, identified respectively in the monokaryotic population and two testcross dikaryotic populations, were mapped on seven different LGs. Several vegetative mycelium growth rate-related QTLs uncovered here were clustered on LG4 (Qmgr1, Qdgr1, Qdgr2 and Qdgr9) and LG6 (Qdgr3, Qdgr4 and Qdgr5), implying the presence of main genomic areas responsible for growth rate regulation and control. The QTL hotspot region on LG4 was found to be in close proximity to the region containing the mating-type A (MAT-A) locus. Moreover, Qdgr2 on LG4 was detected on different media, contributing 8.07 %-23.71 % of the phenotypic variation. The present study provides essential information for QTL mapping and marker-assisted selection (MAS) in L. edodes.

Genetic linkage mapping in fungi: current state, applications, and future trends

Genetic mapping is a basic tool for eukaryotic genomic research. Linkage maps provide insights into genome organization and can be used for genetic studies of traits of interest. A genetic linkage map is a suitable support for the anchoring of whole genome sequences. It allows the localization of genes of interest or quantitative trait loci (QTL) and map-based cloning. While genetic mapping has been extensively used in plant or animal models, this discipline is more recent in fungi. The present article reviews the current status of genetic linkage map research in fungal species. The process of linkage mapping is detailed, from the development of mapping populations to the construction of the final linkage map, and illustrated based on practical examples. The range of specific applications in fungi is browsed, such as the mapping of virulence genes in pathogenic species or the mapping of agronomically relevant QTL in cultivated edible mushrooms. Future prospects are finally discussed in the context of the most recent advances in molecular techniques and the release of numerous fungal genome sequences.

Relationship between yield components and partial resistance to Lecanicillium fungicola in the button mushroom, Agaricus bisporus, assessed by quantitative trait locus mapping

Dry bubble, caused by Lecanicillium fungicola, is one of the most detrimental diseases affecting button mushroom cultivation. In a previous study, we demonstrated that breeding for resistance to this pathogen is quite challenging due to its quantitative inheritance. A second-generation hybrid progeny derived from an intervarietal cross between a wild strain and a commercial cultivar was characterized for L. fungicola resistance under artificial inoculation in three independent experiments. Analysis of quantitative trait loci (QTL) was used to determine the locations, numbers, and effects of genomic regions associated with dry-bubble resistance. Four traits related to resistance were analyzed. Two to four QTL were detected per trait, depending on the experiment. Two genomic regions, on linkage group X (LGX) and LGVIII, were consistently detected in the three experiments. The genomic region on LGX was detected for three of the four variables studied. The total phenotypic variance accounted for by all QTL ranged from 19.3% to 42.1% over all traits in all experiments. For most of the QTL, the favorable allele for resistance came from the wild parent, but for some QTL, the allele that contributed to a higher level of resistance was carried by the cultivar. Comparative mapping with QTL for yield-related traits revealed five colocations between resistance and yield component loci, suggesting that the resistance results from both genetic factors and fitness expression. The consequences for mushroom breeding programs are discussed.

Quantitative trait locus mapping of yield-related components and oligogenic control of the cap color of the button mushroom, Agaricus bisporus

As in other crops, yield is an important trait to be selected for in edible mushrooms, but its inheritance is poorly understood. Therefore, we have investigated the complex genetic architecture of yield-related traits in Agaricus bisporus through the mapping of quantitative trait loci (QTL), using second-generation hybrid progeny derived from a cross between a wild strain and a commercial cultivar. Yield, average weight per mushroom, number of fruiting bodies per m(2), earliness, and cap color were evaluated in two independent experiments. A total of 23 QTL were detected for 7 yield-related traits. These QTL together explained between 21% (two-flushes yield) and 59% (earliness) of the phenotypic variation. Fifteen QTL (65%) were consistent between the two experiments. Four regions underlying significant QTL controlling yield, average weight, and number were detected on linkage groups II, III, IV, and X, suggesting a pleiotropic effect or tight linkage. Up to six QTL were identified for earliness. The PPC1 locus, together with two additional genomic regions, explained up to 90% of the phenotypic variation of the cap color. Alleles from the wild parent showed beneficial effects for some yield traits, suggesting that the wild germ plasm is a valuable source of variation for several agronomic traits. Our results constitute a key step toward marker-assisted selection and provide a solid foundation to go further into the biological mechanisms controlling productive traits in the button mushroom.

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

In this study, three molecular marker systems including sequence related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and inter-simple sequence repeats (ISSR) were screened to select polymorphisms of 24 main commercial strains of Lentinula edodes cultivated widely in China. Twenty-nine sequence characterized amplified region (SCAR) markers were developed to set up a dendrogram using UPMGA based on nucleotide sequences of some SRAP, RAPD, and ISSR polymorphic fragments. The grouping showed that the 24 strains were apparently clustered into five groups at a level of 0.68 similarity coefficient, and those that have similar breeding background clustered preferentially into the same subgroup. Results also revealed that the 24 strains had a low level of genetic diversity, and the breeding source of L. edodes should be broadened by exploiting wild types and introducing exotic strains. In addition, the tested strains of L. edodes could be clearly distinguished and identified from others by using different combinations of SCAR primers. Thus, results of this work demonstrated that SCAR was an excellent genetic marker system to characterize and investigate genetic diversity of L. edodes. Furthermore, this provided an alternative method to identify the genetic relationship of different strains of other fungi.

Construction of a genetic linkage map based on amplified fragment length polymorphism markers and development of sequence-tagged site markers for marker-assisted selection of the sporeless trait in the oyster mushroom (Pleurotus eryngii)

A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Quél. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection.

Quantitative genetics to dissect the fungal-fungal interaction between Lecanicillium verticillium and the white button mushroom Agaricus bisporus

Lecanicillium fungicola (formerly Verticillium fungicola) is responsible for dry bubble disease in the white button mushroom Agaricus bisporus. Selection for resistance to this pathogen raises an important challenge for mushroom breeders. We have investigated the inheritance of resistance to dry bubble under artificial inoculation in three independent experiments, using a progeny of 89 hybrids derived from an intervarietal A. bisporus var. bisporus×A. bisporus var. burnettii cross. Overall, phenotypic correlations were highly significant between the different experiments. Principal component analysis, together with analysis of variance results stated that the disease reactions were accurately assessed using the percentage of bubbles (PB) and the percentage of spotty cap mushrooms (PS) separately rather than with the combination of both. An original contribution of this study lies in the effective use of area under the disease-progress curve (AUDPC) to describe the dry bubble resistance. The continuous phenotypic distribution observed for the resistance traits suggested that tolerance to dry bubble was under polygenic control. Heritability estimates for either PB or AUDPC were high (0.67-0.86) while it was inconsistent for PS (0.33-0.68) suggesting a strong impact of the environment on this latter trait. Earliness and latent period were found highly correlated with disease incidence. The earliest strains appeared to be the most resistant ones. These results contribute to disentangle the complex fungal-fungal A. bisporus / L. fungicola interaction and to provide genetic basis as a prerequisite for mushroom breeding program.