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Constructing A Genetic Map for C. briggsae

We constructed a high-density genetic map by genotyping single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) made from C. briggsae strains AF16 (reference) and HK104.

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Current Release (v3.3)

Our most recent version of the map (v3.3) was constructed using genotype data for 400 SNPs. It includes 149 of the largest ultracontigs in the cb25.agp8 sequence assembly, covering approximately 85% of the genome, and was published in the July 2007 issue of PLoS Biology.

Publication to Cite

Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, and Waterston RH. (2007) Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny. PLoS Biol 5(7): e167

SNP Discovery

In the initial SNP discovery, each of 13,632 whole-genome shotgun reads from the C. briggsae HK104 strain was aligned against the reference genome sequence using CrossMatch. Substitution discrepancies (SNPs) with quality values higher than 35 were mapped back to the reference genome. Over 20,000 high quality discrepancies between HK104 and the AF16 reference were observed. Subsequent SNP discovery passes have made use of Polybayes, ssaha-SNP, and other programs.

Genotyping

Four hundred SNPs were genotyped by FP-TDI in two crosses of RILs: AF16 X HK104, and AF16 X VT847. Due to a high degree of monomorphism in the second cross, only data from the AF16 X HK104 cross were used to construct the map.

Map Construction

After quality control, genotype data were assembled in a text file ordered by SNP and RI line. This file was imported into Map Manager QTX (b20, www.mapmanager.org) which was used to assemble the genetic map.

Physical map coordinates

Physical map coordinates for the PCR primers bounding the SNPs in our genetic map were obtained by BLASTing the primer sequences to these C. briggsae genome assemblies on Wormbase:

assembly_type	nomenclature	FTP directory
super-contig	c003400901.Contig1	/pub/wormbase/genomes/briggsae/assembly/cb25.agp8
ultra-contig	cb25.fpc0006	/pub/wormbase/genomes/briggsae/assembly/cb25.agp8
chromosome	chrI	/pub/wormbase/genomes/briggsae/assembly/cb3

Important: Our draft genetic map of C. briggsae is a work in progress. Our current data set does not provide enough scientific evidence to finalize this version of the map. Use at your own risk. By accessing any of the files below, you agree to adhere to our data access policy.