Chromosome 6

Chr	Position in a YAC physical map (genetic distance, cM)	Marker name ₁₎	Type of marker ₂₎	Enzyme ₃₎	Amplified band size (bp) in Nipponbare	5' primer sequence	3' primer sequence	Mapping population	Position ₄₎	Comment
6	0-0.9	E30287	STS		225	`5' CAG CTC GTC ATG CAG CAG TG 3'`	`5' AGA GCA AGG AGA GGC AGC AC 3'`	BIL	S15909P/R2869
6	0.9-1.4	S15909	STS		251	`5' ACG TGT CCA AGA TAT CGC AG 3'`	`5' ACT GAG GAA CAG ATC ATC GG 3'`	BIL	R2869
6	3.6	S10372	CAPS	HaeIII,BgiII	1300	`5' CTCCCCGTATTTTGTAACTG 3'`	`5' TGGTAGCATTTAGGGCATCC 3'`	F2	S10372
6	5.1	S2107	STS		211	`5' AGT CCT GGT TGA GCC TCT CG 3'`	`5' CTG CCA CAA TAC GAT TGT CG 3'`	BIL	R1962
6	10.4	R1952	CAPS	SacI	900	`5' CCT TGG CCC TTG AAT AGT TG 3'`	`5' TGC TCG ATT CTG ACA AAG TT 3'`	F2	R1952
6	10.7	R2291	STS		1800	`5' AGA AAG AAT CAG TGG GCA AA 3'`	`5' CAA AAC TTC AAT GCC CAA TG 3'`	F2	R2291	dominant
6	10.7	R1962	CAPS	EcoRI	1000	`5' GCT TGG ATT ATG ACA TTT AG 3'`	`5' TGA AGC AAG GAA CAA ACA 3'`	F2	R1962
6	32.7	R2349	STS		1000	`5' ACG CGG TGC TGT ACT ACA CG 3'`	`5' GCC AAG AAG TGC CTC CCG TA 3'`	F2	R2349
6	37.8	E10125	CAPS	HaeIII	1500	`5' CGG TGG TGT GCC CTA TGG 3'`	`5' GGC GGA CAT GGT CTC TTC AC 3'`	F2	E10125
6	51	R2171	CAPS	PstI,EcoRI,ApaI,XhoI,HaeIII,DraI,XbaI,MspI,HinfI	3000	`5' CTC ATC TAG CTT TCT GCC T 3'`	`5' GTA GTT GGG CTG TAT CAG TT 3'`	F2	R2171
6		C53007	STS		271	`5' CTG CCA AAC AGA CGT CAT CC 3'`	`5' TGC AAA GCC AAT TGT TCA TC 3'`	BIL	R2171/R2123	dominant
6	53.5	R1679	STS		2100	`5' ATG CCT ATC AGA AAT GGT C 3'`	`5' ATA CTC TTT ACA GGT GGT TGA 3'`	F2	R1679	dominant
6	53.5	Y4836L	dCAPS	AciI	100	`5' ACT GAT CCC CCG ATG ATG GTG TTC CG 3'`	`5' TAC GCT GAC GAT CAA AAG TGC ATA ACC A 3'`	F2	Y4836L
6	54.1	S2539	CAPS	HhaI,MboI	2000	`5' GGA CTG AGA TGG AAT GTG CT 3'`	`5' GTA GAG TGA TGA CAA AAT GAC AA 3'`	F2	S2539
6	63.2	R2123	CAPS	PstI	4300	`5' CTA CAA GAG TAC GCA AAG CG 3'`	`5' AGT AGC ACA ACG CAT CAT TC 3'`	F2	R2123
6	68.5	C133A	CAPS	MboI	2000	`5' GTG TTG CGT ACC TTA TAG AC 3'`	`5' AAG CAC AAA TAG CAC ATA GG 3'`	F2	C133A
6	69.6	R2654	STS		1000	`5' AGA TAC AAT GGC GTC CAC CG 3'`	`5' TGG CAC CAG TTT CAA CAT TC 3'`	F2	R2654	dominant
6	72.3-72.6	S2381	STS		185	`5' CCA AAG CAA GTG AAA AAA GC 3'`	`5' TGA AGT CGA ATG GTC TGT AG 3'`	BIL	R437
6	76.5	C214	CAPS	PstI	4000	`5' CCA GGA TTC ATT CTT CAG G 3'`	`5' ACC CGC AAG CAT ACA TCT 3'`	F2	C214
6	80.4-80.7	S20734	STS		225	`5' ACA AGT ACA GAA ACG CCG GG 3'`	`5' TTT TCC TTC ATT GAA CAC CG 3'`	BIL	G122
6	87.5	S10324A	CAPS	EcoT14I,BglII,MvaI	2000	`5' GGA CAA GTA CGT TTC TGA GC 3'`	`5' AGT TGT GGT AGG CAG GTT TC 3'`	F2	S10324A
6	87.5	S1437	CAPS	MspI,HapII	1200	`5' ATG CTT CTC TTT CGG TGA TT 3'`	`5' CAG GAC CCA AGA AAC CAA CT 3'`	F2	S1437
6	96.5-100.0	R3879	STS		250	`5' CAC TAA TCA AGC CAC TTC GG 3'`	`5' CGA AAC TTG TTT TCC TTC CC 3'`	BIL	C358
6	109.5	C11635	STS		236	`5' AGG AAA ACC GTA GCG TAG AC 3'`	`5' GGC TTT CAG CAA TTC ACT GG 3'`	BIL	C556
6	113.1	C962	STS		1800	`5' GTG TCC ATC TCC TCC TCG TC 3'`	`5' TAG CAG AAG AGA GCC CGA AA 3'`	F2	C962	dominant
6	113.4	R2071	CAPS	HinfI,SacI,ScaI,HincII,MboI	2000	`5' TAA CTC ATT GCC TTT TGC C 3'`	`5' CTT CCA TTT CCT TGA TTC AG 3'`	F2	R2071
6	5.1-6.0	C952	NP			`5' AGG GAA GGA GCA AAG TGA AG 3'`	`5' AAC CAA GGG CTA TCA GAG GC 3'`
6	9.8	C1496	NP		870	`5' TGT GGT TAA GGT AGT TTC CC 3'`	`5' CTT GCA CTA GAT AAT TGC GC 3'`
6	11.5	C764	NP		1300	`5' AAG CGG AGG ATC TCT ATT GC 3'`	`5' CGG GCA CTA CCA TTG TAA AG 3'`
6	13.5	C226A	NP		840	`5' ATG TGG GGT AAG CCT CAA GC 3'`	`5' GCC TGC TGC TGC CTC AAT GG 3'`
6	13.5	R845	NP		550	`5' AAA TCG CTC ATT AGC CTG CC 3'`	`5' ATC ATG GTC AGT TGG TCA CC 3'`
6	54.1	C235	NP			`5' AGC GAG GAG TCA AGG AG 3'`	`5' AGA CAA CAT CCG ATA GAT AA 3'`
6	64.9	R538	NP		800	`5' CCT AGA TAT TGG ACC AGA AAG A 3'`	`5' CAT CGG CAG TAA AAT AGC AT 3'`
6	65.8	C574	NP		610	`5' CAA CTC CAC CGC TCC CAA TC 3'`	`5' GAT GAA ACC GGC AAC CAA AC 3'`
6	67.7	C81	NP		600	`5' ACG ACA AAC ACC ACA AGC 3'`	`5' TAT TTA CAA CAT CAT CAT TCC A 3'`
6	79	C829	NP		400	`5' GGA TCT GTG CCG CAA GTA TG 3'`	`5' CCA GGT CAA ATA AAC AGC AA 3'`
6	91.9	R2549	NP		1300	`5' ATG GCA GCG ATG AAC AAT GA 3'`	`5' GAC AGA CAA GGG CGA AGG A 3'`
6	100.8	C882	NP		900	`5' ATC TCC TCC TCC TCC TCC TC 3'`	`5' AGG CTT CTG GCA CAC AAA AC 3'`
6	103	R276	NP		2100	`5' TCA GCA ATG GCA TCT CAC AG 3'`	`5' CAC GAT GAC CAC AAC GAT TC 3'`
6	107.3	C556	NP		700	`5' ATG AGT GGG TGA AGG TTG AG 3'`	`5' TGT GGT AGG AGA GGC GAG AT 3'`
6	122.8	R1394B	NP		800	`5' AGG CTT AGT GTC GCA ATC TC 3'`	`5' CGT GTA TGC TGA ACT GTC TT 3'`

1) Polymorphism between Nipponbare and Kasalath were revealed by STS, CAPS, or dCAPS. NP indicates that no polymorphism was detected between Nipponbare and Kasalath. 2) Restriction enzymes used for CAPS and dCAPS to detect polymorphism between Nipponbare and Kasalath. No digestion is needed for STS markers. 3) Gel electrophoresis images of each marker can be linked at the "marker mane" column. 4) Chromosomal location of each marker is shown by either the RFLP marker co-segregated or the interval of flanking RFLP markers on the previously reported linkage map (Harushima et al. 1998, Lin et al.1998).

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