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GrainGenes Marker Report: HVM40

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Locus	HVM40
Type	Microsatellite
Synonym	Correct name HVM040 Synonym HVM40
Chromosome	4 (4H) 4H
Chromosome Arm	4HS
Map	Barley-consensus-2003-4H 6 [ Show all 26 ]
	[ Show Nearby Loci ]
QTL with Locus Marker	QAa.HaMo-4H [ Show all 15 ]
Map Data	Barley consensus 2003 [ Show all 26 ]
Species	Hordeum vulgare Hordeum vulgare subsp. spontaneum
Probe	HVM40 Liu Z-W et al. (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theoretical and Applied Genetics 93:869-876.
Reference	Sato K et al. (2009) A high-density transcript linkage map of barley derived from a single population. Heredity 103:110-117. [ Show all 7 ]
Data Source	Langridge, Peter J.
Remark	[ Hide all but 1 of 8 ] Number of populations contributing to the placement of HVM40 in the Barley, Consensus 2006 DArT maps = 5 Bin on the 'Barley, Integrated, Marcel 2009' Map Set : 'chromosome_kleinhofs & graner BIN nb.subBIN nb' Mapping population(s) used for locus placement on the 'Barley, Integrated, Marcel 2009' Map Set = L94 x Vada, Vada x SusPtrit, Steptoe x Morex, Oregon Wolfe Barleys Loci in 'Barley, Consensus 2006, Marcel' mapped in population(s) : L94 x Vada; Oregon Wolfe Dom x Rec; Vada x SusPtrit; Steptoe x Morex Locus in 'Barley, Consensus 2007, SSR' mapped in population(s) : L94 x Vada, SusPtrit x Vada, Steptoe x Morex, OWBrecessive x OWBdominant Insert contains repeat (GA)6(GT)4(GA)7 Polymorphic Information Content (PIC) = 0.58 Developing laboratory = VPISU (MA Saghai Maroof)
Probe	HVM40
Locus	HVM40 [ Show all 6 ]
Reference	Hearnden PR et al. (2007) A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theoretical and Applied Genetics 115:383-391. Varshney RK et al. (2007) A high density barley microsatellite consensus map with 775 SSR loci. Theoretical and Applied Genetics 114:1091. Liu Z-W et al. (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theoretical and Applied Genetics 93:869-876.
Remarks	Insert contains repeats (GA)6, (GT)4, and (GA)7.
Type	PCR SSR
PCR primers	5' CGATTCCCCTTTTCCCAC 3' 5' ATTCTCCGCCGTCCACTC 3' CGATTCCCCTTTTCCCAC ATTCTCCGCCGTCCACTC
SSR size	0.160
Amplification Conditions	The 'touchdown' PCR comprised 48 cycles of 94oC for 1 min denaturing and 72oC for 1 min extension. Annealing (30 s) temperatures were progressively decreased by 1oC every second cycle from 64oC to 55oC. Annealing conditions of 1 min at 55oC were maintained during the final 30 cycles. The reaction ended with a 5-min extension at 72oC.
Insert Enzyme	TaqI
Source Species	Hordeum vulgare
Source Germplasm	Old ZZ (barley)
DNA Origin	Size-fractionated genomic library screened with synthetic dinucleotide repeats (CA)10 and (GA)10.