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

Structural Analysis of the A Mating Type Locus and Development of the Mating Type Marker of Agaricus bisporus var. bisporus

Karyotyping in Agaricus bisporus is crucial for both the isolation of homokaryotic strains and the confirmation of dikaryon establishment. For the verification of the karyotype, the A mating type loci of two homokaryotic strains, H39 and H97, were analyzed through comparative sequence analysis. The two loci showed major differences in two sequence regions designated as Region 1 and Region 2. H97 had a putative DNA transposon in Region 1 that had target site duplications (TSDs), terminal inverted repeats (TIRs), and a loop sequence, in contrast to H39, which only had the insertional target sequence. Homologous sequences of the transposon were discovered in the two different chromosomes of H97 and in one of H39, all of which have different TSDs but share high sequence homology in TIR. Region 2 shared three consensus sequences between H97 and H39. However, it was only from H97 that a large insertional sequence of unknown origin was discovered between the first and second consensus sequences. The difference in length in Region 1, employed for the verification of the A mating type, resulted in the successful verification of mating types in the heterokaryotic and homokaryotic strains. This length difference enables the discrimination between homo- and heterokaryotic spores by PCR. The present study suggests that the A mating type locus in A. bisporus H97 has evolved through transposon insertion, allowing the discrimination of the mating type, and thus the nuclear type, between A. bisporus H97 and H39.

Nuclear conditions of basidiospores and hyphal cells in the edible mushroom Oudemansiella aparlosarca

Oudemansiella aparlosarca is an edible mushroom possessing medicinal and health benefits. Although there are studies on the cultivation of O. aparlosarca, only a few studies have focused on its genetics and life cycle. Therefore, the main objective of this study was to identify the nuclear conditions of basidiospores and homokaryotic and heterokaryotic hyphal cells and to determine the influence of different nuclear conditions on basidiospore diameter in O. aparlosarca. Two parental strains: strain-55 and strain-81 were used. Staining of basidiospores and hyphal cells in the apical region was performed. We observed the following nuclear conditions: non-nucleate, mononucleate, binucleate, and multinucleate. In both parental strains, binucleate spores were predominant, while the number of non-nucleate spores was the lowest. The diameter of non-nucleate spores was the smallest, being 11.52 µm and 12.15 µm in parental strain-81 and strain-55, respectively, while multinucleate spores had the largest diameter, being 14.78 µm in both parental strains. Both homokaryotic and heterokaryotic strains were identified in isolated single spores from parental strains. Binucleate cells were majorly present in heterokaryotic hyphal cells, and multinucleate cells were predominant in homokaryotic hyphal cells. We conclude that O. aparlosarca contains homokaryotic and heterokaryotic basidiospores, which indicates an amphithallic life cycle. The observed binucleate spores might be the result of post-meiotic mitosis.

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.

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.

Map-based cloning of genes encoding key enzymes for pigment synthesis in Auricularia cornea

Color is an important quality attribute of fungi, and a useful marker for classification, genetic, and molecular research. However, there is much debate over which enzymes play key regulatory roles in pigment synthesis pathways among different fungi and even within the same species. Auricularia cornea is the most widely cultivated mushroom in the genus Auricularia; 1.834 million tons of this mushroom were produced in 2016 in China. Thus, systematic studies on its color inheritance and the genes encoding key enzymes for pigment synthesis have high scientific and economic value. In this study, the white strain ACW001 and the purple strain ACP004 of A. cornea were used as dikaryotic parents. Selfing populations of ACW001 and ACP004 were constructed with their monokaryotic strains. The fruiting body color of the two populations was consistent with that of their parents, confirming that the two parents were color homozygotes. All strains in the hybrid population of the two parents produced purple fruiting bodies. A robust hybrid strain (ACW001-33×ACP004-33) was selected from the hybrid population, and 87 monokaryotic strains of ACW001-33×ACP004-33 were obtained as a mapping population. Finally, a testcross population was constructed by crossing the mapping population with the test strain ACW001-9. The color genotype of each monokaryotic strain in the mapping population was identified by a fruiting test. The genomes of the two monokaryotic strains ACW001-33 and ACP004-33 were sequenced, and then simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker primers were developed. Then, 88 pairs of primers that could distinguish the genotypes of the mapping population were used to construct a genetic linkage map. The genetic linkage map consisted of 12 linkage groups (LGs) spanning 1315.2 cM. The color control locus was preliminarily located at 24.5 cM of the 11th LG. Fine-mapping primers were designed based on sequence differences between ACW001-33 and ACP004-33 in the primary location region. Four color control candidate genes were located in an 8.2-kb region of ACW001-33_contig733 and a 9.2-kb region of ACP004-33_contig802. Homologous alignment and prediction of conserved domain analyses indicated that two of the color control candidate genes encoded proteins with unknown function, and the other two, ACP004_g11815 and ACP004_g11816, encoded glutamyl aminotransferases. These two genes were consecutively arranged on ACP004-33_contig802, and were likely to encode key enzymes in the γ-glutamine-4-hydroxy-benzoate (GHB) pigment synthesis pathway. Primers were designed from the flanking sequences of the two genes and used to analyze the testcross population. Products were amplified only from the 30 testcross strains with purple fruiting bodies, confirming the accuracy of the localization results. We discuss the deficiencies and advantages of map-based cloning in fungi vs. plants, and summarize the steps and requirements of the map-based cloning method for fungi. This study has provided novel ideas and methods for locating functional genes in fungi.

Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus)

The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

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.

Insights into the Classical Genetics of Clitopilus passeckerianus - the Pleuromutilin Producing Mushroom

Clitopilus passeckerianus is the fungal species responsible for the production of pleuromutilin, a diterpene antibiotic that is gaining in commercial interest. Production of the antibiotic is constrained by the low titers typically obtained from isolates. We therefore set out to investigate the possibility of using classical breeding techniques coupled with genetic manipulation as a means to develop such fungi. We show that the original production strain of C. passeckerianus is able to fruit under laboratory conditions, giving viable haploid meiotic basidiospores. The derived progeny displayed the typical physiological and genetic characteristics of a tetrapolar mating system. The monokaryon haploids produced pleuromutilin and haploid lines were amenable to genetic manipulation. Together this shows that the basic requirements for a classical breeding approach are present and the tools required to undertake directed genetic engineering on haploid strains are available, demonstrating that strain improvement may be feasible in this fungus.

Asexual but Not Clonal: Evolutionary Processes in Automictic Populations

Many parthenogenetically reproducing animals produce offspring not clonally but through different mechanisms collectively referred to as automixis. Here, meiosis proceeds normally but is followed by a fusion of meiotic products that restores diploidy. This mechanism typically leads to a reduction in heterozygosity among the offspring compared to the mother. Following a derivation of the rate at which heterozygosity is lost at one and two loci, depending on the number of crossovers between loci and centromere, a number of models are developed to gain a better understanding of basic evolutionary processes in automictic populations. Analytical results are obtained for the expected neutral genetic variation, effective population size, mutation-selection balance, selection with overdominance, the spread of beneficial mutations, and selection on crossover rates. These results are complemented by numerical investigations elucidating how associative overdominance (two off-phase deleterious mutations at linked loci behaving like an overdominant locus) can in some cases maintain heterozygosity for prolonged times, and how clonal interference affects adaptation in automictic populations. These results suggest that although automictic populations are expected to suffer from the lack of gene shuffling with other individuals, they are nevertheless, in some respects, superior to both clonal and outbreeding sexual populations in the way they respond to beneficial and deleterious mutations. Implications for related genetic systems such as intratetrad mating, clonal reproduction, selfing, as well as different forms of mixed sexual and automictic reproduction are discussed.

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.

Ribosomal Intergenic Spacer 1 Based Characterization of Button Mushroom (Agaricus bisporus) Strains

Breeding the button mushroom requires genetic information about its strains. This study was undertaken to genetically characterize four domestically bred button mushroom strains (Saea, Saejung, Saedo, Saeyeon cultivars) and to assess the possibility of using the intergenic spacer 1 (IGS1) region of rDNA as a genetically variable region in the genetic characterization. For the experiment, 34 strains of Agaricus bisporus, two strains of A. bitorquis, and one strain of A. silvaticus, from 17 countries were used. Nucleotide sequence analysis of IGS1 rDNA in these 37 Agaricus strains confirmed that genetic variations exist, not only among the four domestic strains, but also between the four domestic strains and foreign strains. Crossing two different haploid strains of A. bisporus seems to generate genetic variation in the IGS1 region in their off-spring haploid strains. Phylogenetic analysis based on the IGS1 sequence revealed all A. bisporus strains could be differentiated from A. silvaticus and A. bitorquis strains. Five genetic groups were resolved among A. bisporus strains. Saejung and Saeyeon cultivars formed a separate genetic group. Our results suggest that IGS1 could be complementarily applied in the polymorphism analysis of button mushroom.

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.

Unholy marriages and eternal triangles: how competition in the mushroom life cycle can lead to genomic conflict

In the vast majority of sexual life cycles, fusion between single-celled gametes is directly followed by nuclear fusion, leading to a diploid zygote and a lifelong commitment between two haploid genomes. Mushroom-forming basidiomycetes differ in two key respects. First, the multicellular haploid mating partners are fertilized in their entirety, each cell being a gamete that simultaneously can behave as a female, i.e. contributing the cytoplasm to a zygote by accepting nuclei, and a male gamete, i.e. only donating nuclei to the zygote. Second, after gamete union, the two haploid genomes remain separate so that the main vegetative stage, the dikaryon, has two haploid nuclei per cell. Only when the dikaryon produces mushrooms, do the nuclei fuse to enter a short diploid stage, immediately followed by meiosis and haploid spore formation. So in basidiomycetes, gamete fusion and genome mixing (sex) are separated in time. The 'living apart together' of nuclei in the dikaryon maintains some autonomy for nuclei to engage in a relationship with a different nucleus. We show that competition among the two nuclei of the dikaryon for such 'extramarital affairs' may lead to genomic conflict by favouring genes beneficial at the level of the nucleus, but deleterious at that of the dikaryon.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

The good, the bad and the tasty: The many roles of mushrooms

Fungi are often inconspicuous in nature and this means it is all too easy to overlook their importance. Often referred to as the "Forgotten Kingdom", fungi are key components of life on this planet. The phylum Basidiomycota, considered to contain the most complex and evolutionarily advanced members of this Kingdom, includes some of the most iconic fungal species such as the gilled mushrooms, puffballs and bracket fungi. Basidiomycetes inhabit a wide range of ecological niches, carrying out vital ecosystem roles, particularly in carbon cycling and as symbiotic partners with a range of other organisms. Specifically in the context of human use, the basidiomycetes are a highly valuable food source and are increasingly medicinally important. In this review, seven main categories, or 'roles', for basidiomycetes have been suggested by the authors: as model species, edible species, toxic species, medicinal basidiomycetes, symbionts, decomposers and pathogens, and two species have been chosen as representatives of each category. Although this is in no way an exhaustive discussion of the importance of basidiomycetes, this review aims to give a broad overview of the importance of these organisms, exploring the various ways they can be exploited to the benefit of human society.

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Volvariella volvacea is an important crop in Southeast Asia, but erratic fruiting presents a serious challenge for its production and breeding. Efforts to explain inconsistent fruiting have been complicated by the multinucleate nature, typical lack of clamp connections, and an incompletely identified sexual reproductive system. In this study, we addressed the life cycle of V. volvacea using whole genome sequencing, cloning of MAT loci, karyotyping of spores, and fruiting assays. Microscopy analysis of spores had previously indicated the possible coexistence of heterothallic and homothallic life cycles. Our analysis of the MAT loci showed that only MAT-A, and not MAT-B, controlled heterokaryotization. Thus, the heterothallic life cycle was bipolar. Karyotyping of single spore isolates (SSIs) using molecular markers supported the existence of heterokaryotic spores. However, most SSIs were clearly not heterokaryotic, yet contained structural variation (SV) markers relating to both alleles of both parents. Heterokaryons from crossed, self-sterile homokaryons could produce fruiting bodies, agreeing with bipolar heterothallism. Meanwhile, some SSIs with two different MAT-A loci also produced fruiting bodies, which supported secondary homothallism. Next, SSIs that clearly contained only one MAT-A locus (homothallism) were also able to fruit, demonstrating that self-fertile SSIs were not, per definition, secondary homothallic, and that a third life cycle or genetic mechanism must exist. Finally, recombination between SV markers was normal, yet 10 out of 24 SV markers showed 1:2 or 1:3 distributions in the spores, and large numbers of SSIs contained doubled SV markers. This indicated selfish genes, and possibly partial aneuploidy.

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.

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.

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.

Genetic and Biochemical Characterization of Monokaryotic Progeny Strains of Button Mushroom (Agaricus bisporus)

To promote the selection of promising monokaryotic strains of button mushroom (Agaricus bisporus) during breeding, 61 progeny strains derived from basidiospores of two different lines of dikaryotic parental strains, ASI1038 and ASI1346, were analyzed by nucleotide sequencing of the intergenic spacer I (IGS I) region in their rDNA and by extracellular enzyme assays. Nineteen different sizes of IGS I, which ranged from 1,301 to 1,348 bp, were present among twenty ASI1346-derived progeny strains, while 15 different sizes of IGS I, which ranged from 700 to 1,347 bp, were present among twenty ASI1038-derived progeny strains. Phylogenetic analysis of the IGS sequences revealed that different clades were present in both the ASI10388- and ASI1346-derived progeny strains. Plating assays of seven kinds of extracellular enzymes (β-glucosidase, avicelase, CM-cellulase, amylase, pectinase, xylanase, and protease) also revealed apparent variation in the ability to produce extracellular enzymes among the 40 tested progeny strains from both parental A. bisporus strains. Overall, this study demonstrates that characterization of IGS I regions and extracellular enzymes is useful for the assessment of the substrate-degrading ability and heterogenicity of A. bisporus monokaryotic strains.

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.

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 variation and combining ability analysis of bruising sensitivity in Agaricus bisporus

Advanced button mushroom cultivars that are less sensitive to mechanical bruising are required by the mushroom industry, where automated harvesting still cannot be used for the fresh mushroom market. The genetic variation in bruising sensitivity (BS) of Agaricus bisporus was studied through an incomplete set of diallel crosses to get insight in the heritability of BS and the combining ability of the parental lines used and, in this way, to estimate their breeding value. To this end nineteen homokaryotic lines recovered from wild strains and cultivars were inter-crossed in a diallel scheme. Fifty-one successful hybrids were grown under controlled conditions, and the BS of these hybrids was assessed. BS was shown to be a trait with a very high heritability. The results also showed that brown hybrids were generally less sensitive to bruising than white hybrids. The diallel scheme allowed to estimate the general combining ability (GCA) for each homokaryotic parental line and to estimate the specific combining ability (SCA) of each hybrid. The line with the lowest GCA is seen as the most attractive donor for improving resistance to bruising. The line gave rise to hybrids sensitive to bruising having the highest GCA value. The highest negative SCA possibly indicates heterosis effects for resistance to bruising. This study provides a foundation for estimating breeding value of parental lines to further study the genetic factors underlying bruising sensitivity and other quality-related traits, and to select potential parental lines for further heterosis breeding. The approach of studying combining ability in a diallel scheme was used for the first time in button mushroom breeding.

Karyotype polymorphism and chromosomal rearrangement in populations of the phytopathogenic fungus, Ascochyta rabiei

The fungus Ascochyta rabiei is the causal agent of Ascochyta blight of chickpea and the most serious threat to chickpea production. Little is currently known about the genome size or organization of A. rabiei. Given recent genome sequencing efforts, characterization of the genome at a population scale will provide a framework for genome interpretation and direction of future resequencing efforts. Electrophoretic karyotype profiles of 112 isolates from 21 countries revealed 12-16 chromosomes between 0.9 Mb and 4.6 Mb with an estimated genome size of 23 Mb-34 Mb. Three general karyotype profiles A, B, and C were defined by the arrangement of the largest chromosomes. Approximately one-third of isolates (group A) possessed a chromosome larger than 4.0 Mb that was absent from group B and C isolates. The ribosomal RNA gene (rDNA) cluster was assigned to the largest chromosome in all except four isolates (group C) whose rDNA cluster was located on the second largest chromosome (3.2 Mb). Analysis of progeny from an in vitro sexual cross between two group B isolates revealed one of 16 progeny with an rDNA-encoding chromosome larger than 4.0 Mb similar to group A isolates, even though a chromosome of this size was not present in either parent. No expansion of the rDNA cluster was detected in the progeny, indicating the increase in chromosome size was not due to an expansion in number of rDNA repeats. The karyotype of A. rabiei is relatively conserved when compared with published examples of asexual ascomycetes, but labile with the potential for large scale chromosomal rearrangements during meiosis. The results of this study will allow for the targeted sequencing of specific isolates to determine the molecular mechanisms of karyotype variation within this species.

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.

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.

Consequences of reproductive mode on genome evolution in fungi

An organism's reproductive mode is believed to be a major factor driving its genome evolution. In theory, sexual inbreeding and asexuality are associated with lower effective recombination levels and smaller effective population sizes than sexual outbreeding, giving rise to reduced selection efficiency and genetic hitchhiking. This, in turn, is predicted to result in the accumulation of deleterious mutations and other genomic changes, for example the accumulation of repetitive elements. Empirical data from plants and animals supporting/refuting these theories are sparse and have yielded few conclusive results. A growing body of data from the fungal kingdom, wherein reproductive behavior varies extensively within and among taxonomic groups, has provided new insights into the role of mating systems (e.g., homothallism, heterothallism, pseudohomothallism) and asexuality, on genome evolution. Herein, we briefly review the theoretical relationships between reproductive mode and genome evolution and give examples of empirical data on the topic derived to date from plants and animals. We subsequently focus on the available data from fungi, which suggest that reproductive mode alters the rates and patterns of genome evolution in these organisms, e.g., protein evolution, mutation rate, codon usage, frequency of genome rearrangements and repetitive elements, and variation in chromosome size.

A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme

A novel approach is presented to map avirulence gene Avr1 in the basidiomycete Cronartium quercuum f.sp. fusiforme, the causal agent of fusiform rust disease in pines. DNA markers tightly linked to resistance gene Fr1 in loblolly pine tree 10-5 were used to classify 10-5 seedling progeny as either resistant or susceptible. A single dikaryotic isolate (P2) heterozygous at the corresponding Avr1 gene was developed by crossing Fr1 avirulent isolate SC20-21 with Fr1 virulent isolate NC2-40. Bulk basidiospore inoculum derived from isolate P2 was used to challenge the pine progeny. The ability to unambiguously marker classify 10-5 progeny as resistant (selecting for virulence) or susceptible (non-selecting) permitted the genetic mapping of the corresponding Avr1 gene by bulked segregant analysis. Using this approach, 14 genetic markers significantly linked to Avr1 were identified and placed within the context of a genome-wide linkage map produced for isolate P2 using samples from susceptible seedlings.

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.

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

A genetic linkage map for the edible basidiomycete Agaricus bisporus was constructed from 118 haploid homokaryons derived from an intervarietal A. bisporus var. bisporus x A. bisporus var. burnettii hybrid. Two hundred and thirty-one AFLP, 21 SSR, 68 CAPS markers together with the MAT, BSN, PPC1 loci and one allozyme locus (ADH) were evenly spread over 13 linkage groups corresponding to the chromosomes of A. bisporus. The map covers 1156cM, with an average marker spacing of 3.9cM and encompasses nearly the whole genome. The average number of crossovers per chromosome per individual is 0.86. Normal recombination over the entire genome occurs in the heterothallic variety, burnettii, contrary to the homothallic variety, bisporus, which showed adaptive genome-wide suppressed recombination. This first comprehensive genetic linkage map for A. bisporus provides foundations for quantitative trait analyses and breeding programme monitoring, as well as genome organisation studies.

A genetic linkage map of Pleurotus pulmonarius based on AFLP markers, and localization of the gene region for the sporeless mutation

In the cultivation of edible mushrooms, including Pleurotus pulmonarius (Fr.) Quel., the enormous number of spores produced by fruiting bodies can adversely affect mushroom growers' health, mushroom cultivation facilities, and the genetic diversity of natural populations. In this study, we constructed a primary genetic linkage map and identified the locus associated with the sporulation-deficient (sporeless) mutation of P. pulmonarius using 150 progeny isolates derived from a cross between sporeless and wild-type isolates. Based on the segregation of 300 AFLP markers, two mating-type factors, and the sporeless trait, a linkage map was generated consisting of 12 linkage groups. The map covered a total genetic distance of 971 cM, with an average marker interval of 5.2 cM. The gene region responsible for the sporeless mutation was located in linkage group II including 40 AFLP markers and the A mating-type factor locus. Of these markers, the nearest marker to the sporeless locus was located 1.4 cM away. Construction of this P. pulmonarius genetic linkage map and identification of markers that are closely linked to the sporeless locus will facilitate marker-assisted selective breeding of a sporeless strain with economically important traits.

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.

A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies

A genetic linkage map for the ectomycorrhizal basidiomycete Laccaria bicolor was constructed from 45 sib-homokaryotic haploid mycelial lines derived from the parental S238N strain progeny. For map construction, 294 simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers were employed to identify and assay loci that segregated in backcross configuration. Using SNP, RAPD and SSR sequences, the L. bicolor whole-genome sequence (WGS) assemblies were aligned onto the linkage groups. A total of 37.36 Mbp of the assembled sequences was aligned to 13 linkage groups. Most mapped genetic markers used in alignment were colinear with the sequence assemblies, indicating that both the genetic map and sequence assemblies achieved high fidelity. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 13 linkage groups spanning 812 centiMorgans (cM) at an average distance of 2.76 cM between markers (range 1.9-17 cM). The WGS and the present linkage map represent an initial step towards the identification and cloning of quantitative trait loci associated with development and functioning of the ectomycorrhizal symbiosis.

Construction of a genetic linkage map of the fungal pathogen of banana Mycosphaerella fijiensis, causal agent of black leaf streak disease

A genetic linkage map of the fungal plant pathogen Mycosphaerella fijiensis, causal agent of black leaf streak disease of banana was developed. A cross between the isolates CIRAD86 (from Cameroon) and CIRAD139A (from Colombia) was analyzed using molecular markers and the MAT locus. The genetic linkage map consists of 298 AFLP and 16 SSR markers with 23 linkage groups, containing five or more markers, covering 1,879 cM. Markers are separated on average by around 5.9 cM. The MAT locus was shown to segregate in a 1:1 ratio but could not be successfully mapped. An estimate of the relation between physical size and genetic distance was approximately 39.0 kb/cM. The estimated total haploid genome size was calculated using the genetic mapping data at 4,298.2 cM. This is the first genetic linkage map reported for this important foliar pathogen of banana. The great utility of the map will be for anchoring contigs in the genome sequence, evolutionary studies in comparison with other fungi, to identify quantitative trait loci (QTLs) associated with aggressiveness or oxidative stress resistance and with the recently available genome sequence, for positional cloning.

The first linkage map of the plant-pathogenic basidiomyceteTyphula ishikariensis

Speckled snow mold, caused by the basidiomycete Typhula ishikariensis Imai, is one of the most prominent winter diseases on perennial grasses and cereal crops in the northern hemisphere. The first linkage map of T. ishikariensis was constructed using a population of 93 sibling monokaryons derived from a single dikaryotic hybrid isolate that was created by a hyphal fusion of two monokaryotic parental isolates. The parental isolates were produced from a pathogenic dikaryotic isolate collected from a golf course in Wisconsin. The two parents exhibit significant differences in the production of aerial mycelium and sclerotia, and in their aggressiveness on creeping bentgrass ( Agrostis stolonifera L.). A total of 251 loci were mapped, comprising 89 inter-simple sequence repeat (ISSR) and 160 random amplified polymorphic DNA (RAPD) markers along with 2 phenotype-based mating-type (MAT) loci. The MAT loci were mapped on linkage groups (LGs) 1 and 7. The markers were evenly distributed over 7 LGs, covering 436 cM with an average marker interval of 2.2 cM. Seven chromosomes were cytologically observed using germ tube bursting methods with acetocarmine staining. This reference linkage map of T. ishikariensis should provide a framework for the mapping of quantitatively controlled traits such as fungal growth, survival, and virulence/avirulence under low temperatures. The map should also be utilized for studying the genome organization of the cold-loving plant-pathogenic Typhula spp. and for comparative genome analysis among fungal taxa.

Genetic analyses of a hybrid cross between serotypes A and D strains of the human pathogenic fungus Cryptococcus neoformans

Cryptococcus neoformans has two varieties, var. grubii and var. neoformans, that correspond to serotypes A and D, respectively. Molecular phylogenetic analyses suggest that these two varieties have diverged from each other for approximately 18 million years. The discovery of pathogenic serotype AD hybrid strains in nature indicates that intervariety mating in C. neoformans occurs in the natural environment. However, little is known about the genetic consequences of hybridization in C. neoformans. Here, we analyzed a hybrid population of 163 progeny from a cross between strains of serotypes A (CDC15) and D (JEC20), using 114 codominant nuclear PCR-RFLP markers and 1 direct PCR marker. These markers were distributed on all 14 chromosomes of the sequenced strain JEC21 that was isogenic to one of the parents (JEC20) in our cross. Our analyses identified that of the 163 progeny, 5 were heterozygous at all 115 loci, 1 was completely homozygous and identical to one of the parents (CDC15), and the remaining 157 each contained at least 1 heterozygous locus. Because all 163 progeny inherited mitochondria from the MATa parent JEC20, none of the progeny had a genotype identical to either of the two parents or to a composite of the two parents. All 115 nuclear loci showed three different genotypes in the progeny population, consistent with Mendelian segregation during meiosis. While the linkage analysis showed independent reassortment among loci on different linkage groups, there were significant differences in recombination frequencies among chromosomes and among regions within certain chromosomes. Overall, the linkage-map length from this hybrid cross was much shorter and the recombination frequency much lower than those constructed using serotype D strains, consistent with suppressed recombination in the intervariety cross between strains of serotypes A and D. We discuss the implications of our results in our understanding of the speciation and evolution of the C. neoformans species complex.

Development of a molecular genetic linkage map for Colletotrichum lindemuthianum and segregation analysis of two avirulence genes

A framework genetic map was developed for the fungal pathogen Colletotrichum lindemuthianum, the causal agent of anthracnose of common bean (Phaseolus vulgaris L.). This is the first genetic map for any species within the family Melanconiaceae and the genus Colletotrichum and provides the first estimate of genome length for C. lindemuthianum. The map was generated using 106 haploid F1 progeny derived from crossing two Mexican C. lindemuthianum isolates differing in two avirulence genes (AvrclMex and AvrclTO). The map comprises 165 AFLP markers covering 1,897 cM with an average spacing of 11.49 cM. The markers are distributed over 19 major linkage groups containing between 5 and 25 markers each and the genome length was estimated to be approximately 3,241 cM. The avirulence genes AvrclMex and AvrclTO segregate in a 1:1 ratio supporting the gene for gene hypothesis for the incompatible reaction between C. lindemuthianum and P. vulgaris, but could not be incorporated into the genetic map. This initial outline map forms the basis for the development of a more detailed C. lindemuthianum linkage map, which would include other types of molecular markers and allow the location of genes previously isolated and characterized in this species.