Oryza sativa QTL "EQC0004" (primary branch)

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Oryza sativa QTL "EQC0004" (primary branch)

QTL Accession ID

EQC0004

Species

Oryza sativa (Rice) [ GR_tax:013681 ]

Trait Symbol

PBRNB

Trait Name

primary branch

Published Symbol

pbr1.1

Trait Synonym(s)

NPB	PRB
number of primary branches per panicle	number of primary rachis branches
panicle primary branch number	primary branches per panicle

Trait Category

Anatomy

Chromosome

Comments

The QTL for primary branch pbr1.1 on chromosome 1 is positively correlated with other morphological traits in the F2 population derived from cultivated Oryza sativa and the annual wild species O. nivara. The gene action is partially dominant and phenotypic variance is 9.9%.

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

40,670,383-40,670,766 bp

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Details

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Oryza sativa (Indica Group) x Oryza nivara (1)

Map Type

Map Set

Name

Map

Position

Ext. Links

QTL

USMSU O sativa CL16/O.nivara 80470 SSR QTL 2006

BNL6.32

148-161.5 cM

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QTL DB Map Position (1)

Name	Chromosome	Start	Stop
EQC0004	1	148	161.5

Associated Markers (4)

Direction	Name	Type	Species	Assoc. Type
To	MRG5696	SSR	Oryza sativa	qtl_marker
To	RM529	SSR	Oryza sativa Japonica Group	qtl_marker
To	RM212	SSR	Oryza sativa Indica Group	qtl_marker
To	MRG4921	SSR	Oryza sativa	qtl_marker

Associated Genes (0)

Associated Ontologies (6)

Term Type	Term	Evidence
Trait Ontology	(TO:0000547)	Li-C et al., 2006 (IAGP)
Plant Structure	(PO:0006321 )	Li-C et al., 2006 (SM)
Plant Growth and Development Stage	(PO:0007130 )	Li-C et al., 2006 (SM)
Growth Stage	(GRO:0007044 )	Li-C et al., 2006 (SM)
Environment	(EO:0007403)	Gramene curators, 2007 (IC)
Species Ontology	(GR_tax:013681)	Li-C et al., 2006 (SM)

Database Cross-References (1)

Gramene Literature	Li-C, Zhou-A, Sang-T, "Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara", The New phytologist, 2006, vol. 170, pp. 185-193

SNPs (2)

Chr	Start	Stop	Exp	Num. SNP Positions
chr1	40,670,383	40,670,766	~160K SNPs x 20 accessions (McNally 2...	0
chr1	40,670,383	40,670,766	'1536 chip' - 1311 SNPs x 395 rice ac...	0
chr1	40,670,383	40,670,766	Huang X, et al, Nat Genetics 2010 Nov...	1	Search for SNPs
chr1	40,670,383	40,670,766	RiceDiversity 44K SNP assay, 34 trait...	1	Search for SNPs
chr1	40,670,383	40,670,766	RiceDiversity 44K SNP assay, 34 trait...	0