Chromosome 1

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
1	0.3-5.3	S13774	STS		212	`5' TGA TCA GCT TGG ACG TGG TG 3'`	`5' CAA TGC CCG TAG TCT CTC AG 3'`	BIL	C161/C970
1	9.5	S13048	CAPS	BamHI,EcoRI,HaeIII,XbaI,MspI,HhaI,HapII,AfaI,PshBI	1200	`5' CTC TGG TTT ACT GCA CAT GC 3'`	`5' TCA GTT TCA CCC ACA GCT AC 3'`	F2	S13048
1	10.9	R753	CAPS	AfaI	1200	`5' GAG TTG CAT GAC ATA AAG CC 3'`	`5' GAA CAA AAG GAT GGC AGC AG 3'`	F2	R753
1	12.2-12.8	C1127A	STS		400	`5' GAG CGT CGA GAC CTA CAA GA 3'`	`5' AAC CGC CAA CTA CAC ACT AA 3'`	F2	C1127A	dominant
1	13.1-19.9	C52250	STS		228	`5' AGA TAT GCA GAA GGG TCA GC 3'`	`5' CTT CTT CCA CCA TCT TTG AC 3'`	BIL	R1613
1	20.2	R480B	CAPS	HindIII	4000	`5' CTC CTT CTC CCT CGT CTC CA 3'`	`5' GGT TCT GCT TGC TCC TCT CG 3'`	F2	R480B
1	24.0-25.4	C62003	STS		255	`5' CGG GAG GAA GAT GAC GAT AG 3'`	`5' TAG CTG AAA GTG CCA CAA TC 3'`	BIL	R1944/R1613
1	27.3-28.4	C52409	STS		216	`5' TGT AAC AGC AAT ATA GGA GC 3'`	`5' GTG CAT TTG TTC AGT GAT AC 3'`	BIL	C885
1	28.9	S10057B	CAPS	BamHI,HinfI,HhaI,MboI	3300	`5' TAA CCA GCG GAT GCC ATT GA 3'`	`5' AGA GGG TTC ATT GCG ATT GG 3'`	F2	S10057B
1	37.4-38.8	S13654	STS		171	`5' CAG ACA CGC CAG GTT TGA TG 3'`	`5' AGA ATG CCA CAC CAA CAA TG 3'`	BIL	C955
1	37.8-38.8	E20660	STS		224	`5' CCA AAG CCG AGG AGA AGA AG 3'`	`5' AAG GCC TTC TGG TTC ATG AG 3'`	BIL	C955
1	38.8	C955	CAPS	AfaI	2100	`5' AGG TTA TTC TGT CTC ATT TGT A 3'`	`5' CAG CAA AGT TCC ACC AGG 3'`	F2	C955
1	45.4-46.3	C52190	STS		221	`5' TCT TCA CCG TTT CTT GCA CC 3'`	`5' AAA CCG ATG AAA CGC CAA CC 3'`	BIL	C955/C1211
1	45.6	S11214	CAPS	EcoRI,HaeIII,DraI,XbaI,HinfI,BglI,HhaI,EcoT22I,HapII,AfaI,MspI	2800	`5' GCG ACT TGC TGA TGC TAC CAA C 3'`	`5' ACA TAT CCC CTC CTG CGA CTT TA 3'`	F2	S11214
1	55.4	R210	dCAPS	AluI	119	`5' TGC AGG ATT CTT GGA GAC GTG TTC ATA G 3'`	`5' TAT GAT CCT GAA GGC CCT AGC CAA GCA A 3'`	F2	R210
1	65.8-69.0	R1888	CAPS	HinfI	2000	`5' CCG AAT AAA GGC GAG AAG 3'`	`5' GAG ACA GTA TTA CAG ATG CGG 3'`	F2	R1888
1	73.4	C178	CAPS	HaeIII,MspI,HapII	800	`5' CCC TGT ACC GTC AAG TTC TA 3'`	`5' AAG TGA TTC ATG CCC AGA CC 3'`	F2	C178
1	73.4	E10793	STS		228	`5' AGG ATG CTG CCG ACC AGA AC 3'`	`5' ACA AGA AGC CAA AGG CAA TG 3'`	BIL	C178
1	73.4	C62453	STS		241	`5' TTG GCC TCA ACA CTC AGG TC 3'`	`5' ACA TCC ACA AAT CAC CAT CC 3'`	BIL	R117/C112	dominant
1	73.7-78.0	E51011	STS		192	`5' AGA GTG CAA TTA CCA GGA TG 3'`	`5' CAA GTA ACC AGC AGA GAA CG 3'`	BIL	C178	dominant
1	87.1-87.4	S20243	STS		235	`5' TGC TAC ACC ACA GAC GAA CG 3'`	`5' TAC CAG CAT ACT GCA ATT CC 3'`	BIL	C178/R192�W	dominant
1	87.1-87.4	S13623	STS		200	`5' CTC AAG GCT CGG GGA TAG TC 3'`	`5' ATA ACG CGA CCT GAC ACG AG 3'`	BIL	C178/R1928
1	87.1-87.4	E30745	STS		209	`5' AAG AAG CAG GAG AGT CGT GG 3'`	`5' ATA ATG GAT GGT TCG GTG CC 3'`	BIL	C178/R1928
1	90.9	R1928	CAPS	MvaI	1000	`5' AAT CGG TGG GAG CAG AA 3'`	`5' CTG TGT GCT ATT TGC CTG G 3'`	F2	R1928
1	93.1	S13994	CAPS	BamHI,EcoRI,HhaI,AfaI,PshBI,MboI	1600	`5' ATG GCA GAA ATG GAC TTA TC 3'`	`5' GCA CAT TAC CAG CAT TAC AT 3'`	F2	S13994
1	94.5-95.7	S5756	STS		211	`5' GTA AAG CAT GCG TGC ACA CC 3'`	`5' TTA ATA AGA GGC AAC GGA AC 3'`	BIL	R2635
1	100.4	R2635	CAPS	EcoT14I	2000	`5' AAT CAG CAG ACG GTG GAC TA 3'`	`5' AAC TAA CGC ATC ACG CAG AC 3'`	F2	R2635
1	113.3	C122	CAPS	AfaI	970	`5' TAT GAC CCG ATT CTC CGC AA 3'`	`5' CGA ATG TGG GAT GAT AAG CA 3'`	F2	C122
1	124.8	C137	CAPS	HindIII,HaeIII,DraI,AfaI,HincII	1400	`5' CAT GAC CAA CCG CCT CCT C 3'`	`5' TTA CGC CAT TGC CAC TAG ACC CA 3'`	F2	C137
1	126.2	C1459	STS		2500	`5' CAA GCA GGG GAG GGA GAA GAG GA 3'`	`5' CAG GGT GTG CCG TGT GGT AAA GG 3'`	F2	C1459	dominant
1	132.4	E864	STS		179	`5' CTA CTG CAA AAT GCG TGG TC 3'`	`5' CAC GAG TTG GTG CTT GGT AG 3'`	BIL	R2417
1	136.1	S15628	STS		185	`5' GGA TGA GCT CAC CGA GCA AC 3'`	`5' AGG CTA TAA CAC TGC AGC GG 3'`	BIL	R2417
1	139.9	S13781	CAPS	HindIII	2300	`5' AGT TGA GCA TTG TCC TTT GT 3'`	`5' ACT GTG TGT CTG TAG GTA AGC A 3'`	F2	S13781
1	139.9	R494	STS		4000	`5' GAG AGC GTC CAG ACC AC 3'`	`5' TGA GCA AAC GAG AGA ACA TC 3'`	F2	R494	dominant
1	139.9	R494	STS		206	`5' TGG AGA CGT CGT CTG ACC TC 3'`	`5' AAC GAG AGA ACA TCC CCT CG 3'`	BIL	C813
1	139.9	E60551	STS		195	`5' ATG CGA GTG CTC ATA GAT GG 3'`	`5' GAC AAC TAG GCC TGA ACA TC 3'`	BIL	C813/C86
1	142.4	C1257	CAPS	EcoT14I	400	`5' CCA ACT CTG CCA TCC GTA AG 3'`	`5' TAA ACA TAG CAA GGA ACC AT 3'`	F2	C1257
1	142.9	S10925	CAPS	EcoRI,MvaI	1600	`5' TGC CTC TGT TAT GGC GA 3'`	`5' TAC AAC AAG TAG TTA CAA ATC ACA 3'`	F2	S10925
1	143.7	R3279	CAPS	MboI	1400	`5' ACC TTG AAT GTG TGC TTA TGT A 3'`	`5' GAA TCT CGT CAG CAA GTA GC 3'`	F2	R3279
1	144	E30008	STS		165	`5' CTA GAA TCC AGC GCG CCA AG 3'`	`5' GAC ATC CCT GCA GCC AAC AC 3'`	BIL	C86
1	145	C62329	STS		219	`5' TGT GGT GAA ACG GGC ATA GC 3'`	`5' AAG GAC CGG TGA ACA CGA TG 3'`	BIL	C86
1	145.3	C727A	CAPS	DraI,HinfI	3500	`5' CCA AAC ACC AAC CTC TCC TA 3'`	`5' AGT AAC CCC ACC AAT AAA AC 3'`	F2	C727A
1	146.4	R1764	CAPS	EcoRV	1300	`5' TAT CAT CTA TCA GCC AGC AA 3'`	`5' TTC ACT TAG CAG CAA CAC GG 3'`	F2	R1764
1	146.4	S13471	CAPS	HaeIII	900	`5' CCA CAT ACT CAC TTC TGC TT 3'`	`5' AGG CAC TAC AAC AAT GGC AC 3'`	F2	S13471
1	146.4	S2596	CAPS	EcoT14I,HhaI,MboI	550	`5' ATG TAA AGA GCC TCC AAT CC 3'`	`5' ATG TAA AGA GCC TCC AAT CC 3'`	F2	S2596
1	151	S2523	CAPS	SalI,HhaI	4300	`5' AGG AGA AGA GGA GAG CAA GA 3'`	`5' CAA ACA TCA AGC CCA CAG AG 3'`	F2	S2523
1	155	S13528	STS		217	`5' AGC ACA TTC GGC AGT TTC TC 3'`	`5' GCA CGC CAT ACA ACA GCC TC 3'`	BIL	C86/R2414
1	157.6	R2414	CAPS	AfaI	2000	`5' CTC TAA GCC GGT ACA GGG 3'`	`5' AGT CAC TTT CAA TCA TAT ACG A 3'`	F2	R2414
1	159.6	R3203	CAPS	ScaI,AfaI	1600	`5' ATG AAC TAT GTC CGA CTG CT 3'`	`5' GTC AAA CAA GTC ACG AGA TG 3'`	F2	R3203
1	167.2	R503	STS		400	`5' TGG GGC TGT ACA TCG CGT 3'`	`5' AGT TTA ACG GAT CGG TAC GG 3'`	F2	R503	dominant
1	169.5	S10581	CAPS	AfaI	1100	`5' CTG GAG AGA ACT ACG AAA CA 3'`	`5' ACA AAT TAG CTT TCT TCC AC 3'`	F2	S10581
1	181.8	C112	CAPS	MvaI	2200	`5' TTC CTT TCC TGC TTT TCT CA 3'`	`5' TAC AGG CAG TCA CAC ACT CA 3'`	F2	C112
1	5.6	C970	NP		1100	`5' CAA GAT AGT GGA TGC TGG AG 3'`	`5' TAC AGT CCA TTC CTC AAA G 3'`
1	24	R1944	NP		2000	`5' GGG GTG TCA TTC CTC TCC 3'`	`5' TTA GCA AGT CCA AAC ATT AC 3'`
1	49.6	R2151S	NP		1900	`5' ACG CAG GCA CAC AAA CAC AGA GA 3'`	`5' GAT CAG CGC CGA TGA AAC GAG 3'`
1	58.1	R1712	NP		650	`5' CGG CGT GGT GTC CTG CTC 3'`	`5' CGT CGT TGA TCA TCG TCT CTG TG 3'`
1	71.2	R1903	NP		1300	`5' CTC CTT CTT GGG CTT CTC CT 3'`	`5' TCC ATC AAT CTC AGC CGT CC 3'`
1	123.2	C1162	NP		1100	`5' GTG GTT GGT CAT CAA TGG AT 3'`	`5' TTT CGA GTT CAC CAG TTT CC 3'`
1	126.2-126.5	C3057	NP		650	`5' AAC ACA CTC GCC TCG CCT CCT TT 3'`	`5' TCA GAA CTC AAC GGG CAC AAC CA 3'`
1	132	R37	NP		300	`5' CGA GAA CAC CGA CTA CCT G 3'`	`5' AGC ACT TCT GTT GCA TCA TAA C 3'`
1	135.8	C836	NP		4000	`5' ATG CCA CCT CTT CCT CAC GAA CC 3'`	`5' AGG CGC CAC CAC AGA ACG A 3'`
1	139.9	R2648	NP		4000	`5' GGT TTA GTT GGT GAT GGG 3'`	`5' CTC GTA GGT TCC AGC AGA 3'`
1	142.9	S10346	NP		500	`5' GTT TGC TGT GAT TGC TCT AA 3'`	`5' TGG ACT TCT CAA CAA CAT TT 3'`
1	143.7	C283	NP		630	`5' TCT GCT AAC ACT GAC ACC GT 3'`	`5' AAT CTG CTT TCC TCG TCT CG 3'`
1	143.7	C713	NP		310	`5' CCT TGT TCC ACT ATT CTG CT 3'`	`5' CCT TTC CAT CCT TGT AGT AA 3'`
1	143.7	S10846	NP		1200	`5' CCT TGA TCT TCT TAC CGG AC 3'`	`5' CCA TCC AGT ACA TCT CAC AA 3'`
1	143.7	C434	NP		280	`5' CAC GCT TAT TGA ACA TTG AT 3'`	`5' GGG ATA AAT GAT GCC AGA TG 3'`
1	145	S12805	NP		580	`5' GCC AAC AGA CTC ATT TCC AA 3'`	`5' TGG TCA AAT TAT CTC CCC TA 3'`
1	146.4	C86	NP		280	`5' CTC AGA CCA GAC CTC AGA AG 3'`	`5' CAT ACA CCG CAG TTC CAT AG 3'`
1	146.4	R1403	NP		500	`5' AGC ACC ACC TCC TTC TCT CA 3'`	`5' GCA ATG GCA CAG CAG ATA CA 3'`
1	163.5	C742	NP		580	`5' CAC CCT TGG ACT CTT TCT GC 3'`	`5' AGT GCC ATT TAG TGC CTT CT 3'`
1	176.3	R117	NP		1200	`5' ATT GGA GGT TCT TTG ACG AT 3'`	`5' GCA CAA GAT TTA TTT ATG AAG G 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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