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GrainGenes Reference Report: PPS-125-1236

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Reference	PPS-125-1236
Title	Sequence haplotypes revealed by sequence-tagged site fine mapping of the Ror1 gene in the centromeric region of barley chromosome 1H
Journal	Plant Physiology
Year	2001
Volume	125
Pages	1236-1247
Author	Collins NC [ Show all 6 ]
Abstract	Summary: We describe the development of polymerase chain reaction-based, sequence-tagged site (STS) markers for fine mapping of the barley (Hordeum vulgare) Ror1 gene required for broad-spectrum resistance to powdery mildew (Blumeria graminis f. sp. hordei). After locating Ror1 to the centromeric region of barley chromosome 1H using a combined amplified fragment length polymorphism/restriction fragment-length polymorphism (RFLP) approach, sequences of RFLP probes from this chromosome region of barley and corresponding genome regions from the related grass species oat (Avena spp.), wheat, and Triticum monococcum were used to develop STS markers. Primers based on the RFLP probe sequences were used to polymerase chain reaction-amplify and directly sequence homologous DNA stretches from each of four parents that were used for mapping. Over 28,000 bp from 22 markers were compared. In addition to one insertion/deletion of at least 2.0 kb, 79 small unique sequence polymorphisms were observed, including 65 single nucleotide substitutions, two dinucleotide substitutions, 11 insertion/deletions, and one 5-bp/10-bp exchange. The frequency of polymorphism between any two barley lines ranged from 0.9 to 3.0 kb, and was greatest for comparisons involving an Ethiopian landrace. Haplotype structure was observed in the marker sequences over distances of several hundred basepairs. Polymorphisms in 16 STSs were used to generate genetic markers, scored by restriction enzyme digestion or by direct sequencing. Over 2,300 segregants from three populations were used in Ror1 linkage analysis, mapping Ror1 to a 0.2- to 0.5-cM marker interval. We discuss the implications of sequence haplotypes and STS markers for the generation of high-density maps in cereals
External Databases	Pubmed: 11244105
Keyword	[ Hide all but 1 of 64 ] avena barley blumeria graminis cell-death chain chromosome conferring resistance development digestion dinucleotide direct sequencing distance dna dna polymorphism enzyme ethiopian exchange fine mapping fine-mapping fragment length polymorphism frequencies gene generation genetic markers genome graminis haplotype high-density hordei hordeum vulgare interval landrace line linkage linkage analysis map mapping marker mildew mlo resistance nucleotide nucleotide substitution oat pcr-based markers polymerase polymorphism population powdery mildew powdery mildew resistance primer probes recombination rates resistance rflp rust resistance sequence sequence tagged site single sp structure sts sts marker substitution triticum monococcum

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