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

Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.

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

Genome ◽

10.1139/g09-021 ◽

2009 ◽

Vol 52 (5) ◽

pp. 438-446 ◽

Cited By ~ 16

Author(s):

Yasuhito Okuda ◽

Shigeyuki Murakami ◽

Teruyuki Matsumoto

Keyword(s):

Linkage Map ◽

Mating Type ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Natural Populations ◽

Aflp Markers ◽

Gene Region ◽

Pleurotus Pulmonarius ◽

Type Factor ◽

Enormous Number

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.

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The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species

10.1101/365676 ◽

2018 ◽

Author(s):

Di Wu ◽

Jennifer Koch ◽

Mark Coggeshall ◽

John Carlson

Keyword(s):

North America ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

De Novo ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Fraxinus Pennsylvanica ◽

Green Ash ◽

Entire Genome

AbstractGreen ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n=46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid invasion of emerald ash borer (EAB, Agrilus planipennis) from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few resources for genetic studies and improvement of green ash are available. In this study, a total of 5,712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al. 2015; Lane et al. 2016). A first genetic linkage map of green ash was constructed from 91 individuals in a full-sib family, combining 2,719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1,201 markers in 23 linkage groups spanning 2008.87cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds (LOD) of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.

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A Combined Amplified Fragment Length Polymorphism and Randomly Amplified Polymorphism DNA Genetic Linkage Map of Mycosphaerella graminicola, the Septoria Tritici Leaf Blotch Pathogen of Wheat

Genetics ◽

10.1093/genetics/161.4.1497 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1497-1505

Author(s):

Gert H J Kema ◽

Stephen B Goodwin ◽

Sonia Hamza ◽

Els C P Verstappen ◽

Jessica R Cavaletto ◽

...

Keyword(s):

Molecular Markers ◽

Linkage Map ◽

Mating Type ◽

Genetic Linkage ◽

Rapd Markers ◽

Genetic Linkage Map ◽

Mycosphaerella Graminicola ◽

Septoria Tritici ◽

Biological Traits ◽

Linkage Groups

Abstract An F1 mapping population of the septoria tritici blotch pathogen of wheat, Mycosphaerella graminicola, was generated by crossing the two Dutch field isolates IPO323 and IPO94269. AFLP and RAPD marker data sets were combined to produce a high-density genetic linkage map. The final map contained 223 AFLP and 57 RAPD markers, plus the biological traits mating type and avirulence, in 23 linkage groups spanning 1216 cM. Many AFLPs and some RAPD markers were clustered. When markers were reduced to 1 per cluster, 229 unique positions were mapped, with an average distance of 5.3 cM between markers. Because M. graminicola probably has 17 or 18 chromosomes, at least 5 of the 23 linkage groups probably will need to be combined with others once additional markers are added to the map. This was confirmed by pulsed-field gel analysis; probes derived from 2 of the smallest linkage groups hybridized to two of the largest chromosome-sized bands, revealing a discrepancy between physical and genetic distance. The utility of the map was demonstrated by identifying molecular markers tightly linked to two genes of biological interest, mating type and avirulence. Bulked segregant analysis was used to identify additional molecular markers closely linked to these traits. This is the first genetic linkage map for any species in the genus Mycosphaerella or the family Mycosphaerellaceae.

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Physical mapping of the human pseudo-autosomal region; comparison with genetic linkage map.

The EMBO Journal ◽

10.1002/j.1460-2075.1988.tb03081.x ◽

1988 ◽

Vol 7 (8) ◽

pp. 2369-2376 ◽

Cited By ~ 68

Author(s):

C. Petit ◽

J. Levilliers ◽

J. Weissenbach

Keyword(s):

Linkage Map ◽

Physical Mapping ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Autosomal Region

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Genome Sequence Analysis of Auricularia heimuer Combined with Genetic Linkage Map

Journal of Fungi ◽

10.3390/jof6010037 ◽

2020 ◽

Vol 6 (1) ◽

pp. 37

Author(s):

Ming Fang ◽

Xiaoe Wang ◽

Ying Chen ◽

Peng Wang ◽

Lixin Lu ◽

...

Keyword(s):

Sequence Analysis ◽

Linkage Map ◽

Genome Sequence ◽

Mating Type ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Genetic Linkage Analysis ◽

Type Locus ◽

Genome Sequence Analysis ◽

Mating Type Locus

Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis. By combining the genome sequence analysis with the genetic linkage map, the mating-type locus of A. heimuer was located on scaffold45 and consisted of two subunits, α and β. Each subunit consisted of a pair of homeodomain mating-type protein genes HD1 and HD2. The mapping revealed conserved synteny at the whole mating-type loci and mirror symmetry relations near the β subunit between A. heimuer and Exidia glandulosa. This study proposed the potential for the bioethanol production by consolidated bioprocessing of A. heimuer. It will promote understanding of the lignocellulose degradation system and facilitate more efficient conversion of the agricultural wastes used for mushroom cultivation. It also will advance the research on the fruiting body development and evolution of A. heimuer.

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Genetic linkage and physical mapping for an oyster mushroom Pleurotus cornucopiae and QTL analysis for the trait cap color

Applied and Environmental Microbiology ◽

10.1128/aem.00953-21 ◽

2021 ◽

Author(s):

Yan Zhang ◽

Wei Gao ◽

Anton Sonnenberg ◽

Qiang Chen ◽

Jinxia Zhang ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

De Novo ◽

Agronomic Traits ◽

Snp Markers ◽

Biological Efficiency ◽

Solid Base ◽

Marker Assisted Breeding ◽

Oyster Mushrooms

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 mushrooms species for its gastronomic value and nutraceutical properties. Cap color is an important trait since consumers prefer dark colored mushrooms, which are now only represented by a small portion of the commercial varieties. Breeding efforts are greatly 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 3449 SNP markers generated by 2b-RAD approach. The map contains 11 linkage groups covering 961.6 cM (centimorgan) with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced resulting in 425 scaffolds (>1000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to pseudo-chromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3357) were physically localized on 140 scaffolds that were assigned to 11 pseudo-chromosomes with a total of 32.5 Mb representing 92.5% of the whole genome. Six QTL controlling cap color of P. cornucopiae were detected explaining a total phenotypic variation of 65.6% with the highest value for the QTL on pseudo-chromosome 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 over the world. Pleurotus cornucopiae is one of the main oyster mushrooms species. Dark cap oyster mushrooms are more and more popular to a consumer’s preferences, but dark varieties are rare to see 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. Besides, the genome characteristics of P. cornucopiae was compared to its closely related species P . ostreatus . The results provided a basis for understanding the genetic background and marker-assisted breeding of this economic important mushroom species.

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