Oryza sativa QTL "CQE2" (plant height)

QTL Accession ID

CQE2

Species

Oryza sativa (Rice) [ GR_tax:013681 ]

Trait Symbol

PTHT

Trait Name

plant height

Published Symbol

Trait Synonym(s)

PH	PHT
height	seedling height

Trait Category

Vigor

Chromosome

Comments

Plant height was measured at 50 days after planting for the middle of the growing phase. Phenotypic effect contributed by Kasalath allele. The means of ten replications per line were used in the data analysis. Chromosomal locations of putative QTLs were determined by single-factor analysis (one-way ANOVA) with the general linear model procedure of QGENE. Two-way ANOVAs for epistatic interaction were also carried out with QGENE at Pd0.01 threshold. The tests were done only with marker loci linked to QTLs with a single-factor P of d0.01 to reduce the likelihood of committing a type-I error.

Map Positions (2)

Oryza sativa Japonica Group (1)

Map Type

Map Set

Name

Map

Position

Ext. Links

Sequence

Gramene Annotated Nipponbare Sequence 2009

BNL6.32

Chr. 1

2,819,089-42,413,852 bp

View Comparative Map

Details

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Oryza sativa (1)

Map Type

Map Set

Name

Map

Position

Ext. Links

QTL

JRGP Nip/Kas F2 QTL 2000

BNL6.32

129.3-176.3 cM

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Details

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QTL DB Map Position (1)

Name	Chromosome	Start	Stop
CQE2	1	129.3	176.3

Associated Markers (144)

Direction	Name	Type	Species	Assoc. Type
To	ABC161	RFLP	Hordeum vulgare	qtl_marker
To	ABC261	RFLP	Hordeum vulgare	qtl_marker
To	ABG499	RFLP	Hordeum vulgare	qtl_marker
To	C1000	RFLP	Oryza sativa	qtl_marker
To	C10205S	RFLP	Oryza sativa	qtl_marker
To	C11019S	RFLP	Oryza sativa	qtl_marker
To	C11234S	RFLP	Oryza sativa	qtl_marker
To	C1127	RFLP	Oryza sativa	qtl_marker
To	C12266S	RFLP	Oryza sativa	qtl_marker
To	C12309S	RFLP	Oryza sativa	qtl_marker
To	C1257	RFLP	Oryza sativa	qtl_marker
To	C1282	RFLP	Oryza sativa	qtl_marker
To	C1310S	RFLP	Oryza sativa	qtl_marker
To	C1335	RFLP	Oryza sativa	qtl_marker
To	C1385S	RFLP	Oryza sativa	qtl_marker
To	C1439	RFLP	Oryza sativa	qtl_marker
To	C1482	RFLP	Oryza sativa	qtl_marker
To	C191	RFLP	Oryza sativa	qtl_marker
To	C1979	RFLP	Oryza sativa	qtl_marker
To	C225	RFLP	Oryza sativa	qtl_marker
To	C2340	RFLP	Oryza sativa	qtl_marker
To	C250	RFLP	Oryza sativa	qtl_marker
To	C283	RFLP	Oryza sativa	qtl_marker
To	C3120	RFLP	Oryza sativa	qtl_marker
To	C3125	RFLP	Oryza sativa	qtl_marker
To	C346	RFLP	Oryza sativa	qtl_marker
To	C434	RFLP	Oryza sativa	qtl_marker
To	C547	RFLP	Oryza sativa	qtl_marker
To	C555	RFLP	Oryza sativa	qtl_marker
To	C60583S	RFLP	Oryza sativa	qtl_marker
To	C61337S	RFLP	Oryza sativa	qtl_marker
To	C63135S	RFLP	Oryza sativa	qtl_marker
To	C713	RFLP	Oryza sativa	qtl_marker
To	C727	RFLP	Oryza sativa	qtl_marker
To	C742	RFLP	Oryza sativa	qtl_marker
To	C813	RFLP	Oryza sativa	qtl_marker
To	C836	RFLP	Oryza sativa	qtl_marker
To	C86	RFLP	Oryza sativa	qtl_marker
To	R2417	RFLP	Oryza sativa	qtl_marker
To	L685	RFLP	Oryza sativa	qtl_marker
To	L694	RFLP	Oryza sativa	qtl_marker
To	Y4564L	RFLP	Oryza sativa	qtl_marker
To	R2882	RFLP	Oryza sativa	qtl_marker
To	R37	RFLP	Oryza sativa	qtl_marker
To	C30040	RFLP	Oryza sativa	qtl_marker
To	R3347	RFLP	Oryza sativa	qtl_marker
To	R758	RFLP	Oryza sativa	qtl_marker
To	S14591	RFLP	Oryza sativa	qtl_marker
To	R655	RFLP	Oryza sativa	qtl_marker
To	S10271	RFLP	Oryza sativa	qtl_marker
To	S2245	RFLP	Oryza sativa	qtl_marker
To	G1087	RFLP	Oryza sativa	qtl_marker
To	E30358S	RFLP	Oryza sativa	qtl_marker
To	S12776S	RFLP	Oryza sativa	qtl_marker
To	PSR578	RFLP	Triticum aestivum	qtl_marker
To	R2347	RFLP	Oryza sativa	qtl_marker
To	Y6185L	RFLP	Oryza sativa	qtl_marker
To	E30143S	RFLP	Oryza sativa	qtl_marker
To	L669	RFLP	Oryza sativa	qtl_marker
To	R1623S	RFLP	Oryza sativa	qtl_marker
To	S13781	RFLP	Oryza sativa	qtl_marker
To	Y8008L	RFLP	Oryza sativa	qtl_marker
To	R2648	RFLP	Oryza sativa	qtl_marker
To	R494	RFLP	Oryza sativa	qtl_marker
To	L825	RFLP	Oryza sativa	qtl_marker
To	S14403	RFLP	Oryza sativa	qtl_marker
To	S721	RFLP	Oryza sativa	qtl_marker
To	G370	RFLP	Oryza sativa	qtl_marker
To	R836	RFLP	Oryza sativa	qtl_marker
To	R2125	RFLP	Oryza sativa	qtl_marker
To	S10346	RFLP	Oryza sativa	qtl_marker
To	S10925	RFLP	Oryza sativa	qtl_marker
To	M324	RFLP	Zea mays subsp. mays	qtl_marker
To	umc184	RFLP	Zea mays subsp. mays	qtl_marker
To	Y6302R	RFLP	Oryza sativa	qtl_marker
To	R3265	RFLP	Oryza sativa	qtl_marker
To	S10846	RFLP	Oryza sativa	qtl_marker
To	R578	RFLP	Oryza sativa	qtl_marker
To	E60580S	RFLP	Oryza sativa	qtl_marker
To	R3279	RFLP	Oryza sativa	qtl_marker
To	E20351S	RFLP	Oryza sativa	qtl_marker
To	S12805	RFLP	Oryza sativa	qtl_marker
To	Y2929R	RFLP	Oryza sativa	qtl_marker
To	S13491S	RFLP	Oryza sativa	qtl_marker
To	E50125S	RFLP	Oryza sativa	qtl_marker
To	R1403	RFLP	Oryza sativa	qtl_marker
To	E10026S	RFLP	Oryza sativa	qtl_marker
To	L610	RFLP	Oryza sativa	qtl_marker
To	R1764	RFLP	Oryza sativa	qtl_marker
To	S13471	RFLP	Oryza sativa	qtl_marker
To	S2596	RFLP	Oryza sativa	qtl_marker
To	E1458S	RFLP	Oryza sativa	qtl_marker
To	PSR78	RFLP	Triticum aestivum	qtl_marker
To	E30867	RFLP	Oryza sativa	qtl_marker
To	C12740	RFLP	Oryza sativa	qtl_marker
To	C10491	RFLP	Oryza sativa	qtl_marker
To	C30021	RFLP	Oryza sativa	qtl_marker
To	S2523	RFLP	Oryza sativa	qtl_marker
To	L819	RFLP	Oryza sativa	qtl_marker
To	L543	RFLP	Oryza sativa	qtl_marker
To	R2625	RFLP	Oryza sativa	qtl_marker
To	G1133	RFLP	Oryza sativa	qtl_marker
To	S13312	RFLP	Oryza sativa	qtl_marker
To	Y3653R	RFLP	Oryza sativa	qtl_marker
To	R2018	RFLP	Oryza sativa	qtl_marker
To	G2200	RFLP	Oryza sativa	qtl_marker
To	L1082	RFLP	Oryza sativa	qtl_marker
To	R2657	RFLP	Oryza sativa	qtl_marker
To	S1008	RFLP	Oryza sativa	qtl_marker
To	PSR170	RFLP	Triticum aestivum	qtl_marker
To	R2414	RFLP	Oryza sativa	qtl_marker
To	G6001	RFLP	Oryza sativa	qtl_marker
To	gosvp1-B	RFLP	Oryza sativa	qtl_marker
To	S10526	RFLP	Oryza sativa	qtl_marker
To	R1545	RFLP	Oryza sativa	qtl_marker
To	G7001	RFLP	Oryza sativa	qtl_marker
To	G7002	RFLP	Oryza sativa	qtl_marker
To	G7003	RFLP	Oryza sativa	qtl_marker
To	S11062	RFLP	Oryza sativa	qtl_marker
To	SPS	RFLP	Oryza sativa	qtl_marker
To	E3256S	RFLP	Oryza sativa	qtl_marker
To	R3203	RFLP	Oryza sativa	qtl_marker
To	S10304	RFLP	Oryza sativa	qtl_marker
To	R2833	RFLP	Oryza sativa	qtl_marker
To	S877	RFLP	Oryza sativa	qtl_marker
To	S1046	RFLP	Oryza sativa	qtl_marker
To	G54	RFLP	Oryza sativa	qtl_marker
To	E1181S	RFLP	Oryza sativa	qtl_marker
To	S2672	RFLP	Oryza sativa	qtl_marker
To	Y3553R	RFLP	Oryza sativa	qtl_marker
To	E2071S	RFLP	Oryza sativa	qtl_marker
To	R503	RFLP	Oryza sativa	qtl_marker
To	PSR858	RFLP	Triticum aestivum	qtl_marker
To	S10581	RFLP	Oryza sativa	qtl_marker
To	L726	RFLP	Oryza sativa	qtl_marker
To	S21582S	RFLP	Oryza sativa	qtl_marker
To	G5005	RFLP	Oryza sativa	qtl_marker
To	R117	RFLP	Oryza sativa	qtl_marker
To	Y2320L	RFLP	Oryza sativa	qtl_marker
To	S10712	RFLP	Oryza sativa	qtl_marker
To	PSR156	RFLP	Triticum aestivum	qtl_marker
To	E61984S	RFLP	Oryza sativa	qtl_marker
To	Y2929L	RFLP	Oryza sativa	qtl_marker
To	Y2320R	RFLP	Oryza sativa	qtl_marker

Associated Genes (0)

Associated Ontologies (9)

Term Type	Term	Evidence
Trait Ontology	(TO:0000207)	Ishimaru-K et al., 2001 (IAGP)
Plant Structure	(PO:0009047)	Ishimaru-K et al., 2001 (SM)
	(PO:0009006)	Gramene curators, 2007 (IC)
Plant Growth and Development Stage	(PO:0007134)	Ishimaru-K et al., 2001 (SM)
	(PO:0007130)	Gramene curators, 2007 (IC)
Growth Stage	(GRO:0007139)	Ishimaru-K et al., 2001 (SM)
	(GRO:0007140)	Ishimaru-K et al., 2001 (SM)
Environment	(EO:0007403)	Gramene curators, 2007 (IC)
Species Ontology	(GR_tax:013681)	Ishimaru-K et al., 2001 (SM)

Database Cross-References (1)

Gramene Literature	Ishimaru-K, Yano-M, Aoki-N, Ono-K, Hirose-T, Lin-S-Y, Monna-L, Sasaki-T, Ohsugi-R, "Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags", Theoretical and applied genetics, 2001, vol. 102- (6/7-)., pp. 793-800

SNPs (188,356)

Chr	Start	Stop	Exp	Num. SNP Positions
chr1	2,819,089	42,413,852	~160K SNPs x 20 accessions (McNally 2...	25,049	Search for SNPs
chr1	2,819,089	42,413,852	'1536 chip' - 1311 SNPs x 395 rice ac...	140	Search for SNPs
chr1	2,819,089	42,413,852	Huang X, et al, Nat Genetics 2010 Nov...	78,834	Search for SNPs
chr1	2,819,089	42,413,852	RiceDiversity 44K SNP assay, 34 trait...	78,834	Search for SNPs
chr1	2,819,089	42,413,852	RiceDiversity 44K SNP assay, 34 trait...	5,499	Search for SNPs

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