A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

BMC Genomics

Table 2 List of validated snip-SNPs by RFLP assays.

Chr	SNP id	Location (cM)	Ultra_contig	RE	DNA fragments in AF16 (bp)		DNA fragments in HK104 (bp)		Validation type
					Expected	Observed	Expected	Observed
1	cb15251	13.45	cb25.fpc4321	DraI	747	700	332 and 415	310 and 400	*
	cb55627	21.82	cb25.fpc3441	HindIII	691	691	251 and 440	270 and 440	*
	cb55670	21.82	cb25.fpc3441	DraI	312 and 437	749	749	312 and 437	**
	cb650	43.93	cb25.fpc4140	SacI	689	689	257 and 432	257 and 432	*
	(bhP27)
2	cb41028	11.88-13.1	cb25.fpc0011	DraI	332 and 419	332 and 400	751	800	*
	cb43091	21.28-26.58	cb25.fpc0058	HindIII	748	800	365 and 383	383 and 383	*
	cb64777	27.92-33.95	cb25.fpc4206	DraI	325 and 424	325 and 400	749	749	*
3	cb20723	12.46	cb25.fpc4153	DraI	20, 196, 220 and 311	230, 311 and 390	20, 196 and 531	230 and 800	**
	cb54953	21.77	cb25.fpc2976	HindIII	751	800	368 and 383	380 and 400	*
	cb40003	31.14	cb25.fpc0002	DraI	685	PCR failure	208 and 477	800
4	cb8971	7.88	cb25.fpc4250	DraI	750	PCR failure	337 and 413	350 and 413
	cb48850	20.02	cb25.fpc1570	HindIII	750	780	314 and 436	350 and 500	*
	cb56202	37.52-41.16	cb25.fpc3835	DraI	60, 190 and 489	60, 190 and 500	60 and 679	60 and 800	*
5	cb39304	20.98-22.23	cb25.fpc4126	HindIII	742	790	286 and 456	310 and 470	*
	cb39354	20.98-22.23	cb25.fpc4126	DraI	751	PCR failure	269 and 482	PCR failure
	cb62	17.07-17.74	cb25.fpc4470	DraI	54, 295 and 400	PCR failure	54 and 695	800
	bdP3	unknown	cb25.fpc0156	DraI	907	907	227 and 680	227 and 680	*
x	cb20148	9.52	cb25.fpc0045	DraI	660	PCR failure	171 and 489	PCR failure
	cb40232	20.1-20.71	cb25.fpc0003	HindIII	237 and 473	300 and 473	710	850	*
	cb6050	24.07	cb25.fpc4403	DraI	750	PCR failure	270 and 480	290 and 510

The snip-SNPs are arranged by chromosome and location. The corresponding ultracontigs are also listed. The expected and observed DNA fragments refer to products based on in silico analysis and actual experiments, respectively. The bdP3 location is unknown because the corresponding contig is unassembled. The validation type column marks snip-SNPs that were consistent with prediction (*) and those that differed significantly (**). RE: Restriction enzyme used to digest PCR amplified products.

ISSN: 1471-2164