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.
Labbé
J
J
UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Zhang
X
X
Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6422, USA.|Joint Genome Institute, 2500 Mitchell St, Walnut Creek, CA 94250, USA.
Yin
T
T
Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6422, USA.|Joint Genome Institute, 2500 Mitchell St, Walnut Creek, CA 94250, USA.
Schmutz
J
J
Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304, USA.
Grimwood
J
J
Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304, USA.
Martin
F
F
UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
Tuskan
G A
GA
Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6422, USA.|Joint Genome Institute, 2500 Mitchell St, Walnut Creek, CA 94250, USA.
Le Tacon
F
F
UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France.
D054458:Amplified Fragment Length Polymorphism Analysis; D002874:Chromosome Mapping; D008040:Genetic Linkage; D016681:Genome, Fungal; D055399:Laccaria / Q000235:genetics*; D018598:Minisatellite Repeats; D038821:Mycorrhizae / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D019105:Random Amplified Polymorphic DNA Technique; D011995:Recombination, Genetic; D016415:Sequence Alignment; D013172:Spores, Fungal
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