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GrainGenes Marker Report: HVM3

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Locus	HVM3
Type	Microsatellite
Synonym	Correct name HVM003 Synonym HVM3
Chromosome	4H 5H
Chromosome Arm	4HL
Map	[ Hide all but 1 of 13 ] Barley-consensus-2003-5H 31.4 Hordeum-Consensus2005-SNP-4H 51.993 Hordeum-Consensus2006-DArT-4H 65.6 Hordeum-Graner2-4H 61.1 Hordeum-LiHs-SNP-4H 44.46 Hordeum-LxHs-4H 45 Hordeum-OWB-2004-4H 48.1 Hordeum-OWB-2005-4H 49.4 Hordeum-OWB-4H 53.1 Hordeum-OWB-SNP-4H 55.4 Hordeum-QTLConsensus-Abiotic-4H 51.99 Hordeum-QTLConsensus-Agronomic-4H 51.99 Hv-HNxH602-4H 96.3
	[ Show Nearby Loci ]
Map Data	Barley consensus 2003 [ Show all 13 ]
Species	Hordeum vulgare Hordeum vulgare subsp. spontaneum
Probe	HVM3 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. Wenzl P et al. (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits BMC Genomics 7:206. Rostoks N et al. (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Molecular Genetics and Genomics 274:515-527.
Data Source	Langridge, Peter J.
Remark	Number of populations contributing to the placement of HVM3 in the Barley, Consensus 2006 DArT maps = 1
Probe	HVM3
Locus	HVM3 HVM0003 HVM003 HVM03 HVM03-4H
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. Fu YB et al. (2007) Microsatellite variation in Avena sterilis oat germplasm Theoretical and Applied Genetics 114:1029-1038. Saghai Maroof MA et al. (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proceedings of the National Academy of Sciences, USA 91:5466-5470.
Remarks	Insert contains repeat (AT)29. In 369 Avena sterilis accessions there were 3 alleles of size 138-142 bp, PIC = negative.
Type	Genomic PCR SSR
PCR primers	5' ACACCTTCCCAGGACAATCCATTG 3' 5' AGCACGCAGAGCACCGAAAAAGTC 3' ACACCTTCCCAGGACAATCCATTG AGCACGCAGAGCACCGAAAAAGTC
SSR size	0.188
Amplification Conditions	PCR comprised one cycle of 94oC for 3 min, 55oC for 2 min, and 72oC for 1.5 min, followed by 30 cycles of 94oC for 1 min, 55oC for 2 min, and 72oC for 1.5 min.
Sequence	M55449
Insert Enzyme	TaqI
Source Gene Class	Ribulose bisphosphate carboxylase activase
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.