Query (optional)   in Class  All Allele Author Colleague Collection Assembly Gene Gene Class Gene Product Germplasm Image Journal Keyword Library Locus Map Map Data Marker Pathology Polymorphism Probe Protein QTL Rearrangement Reference Sequence Species Trait Trait Study Two Point Data  

---

GrainGenes Reference Report: PMB-48-529

[Submit comment/correction]

Reference	PMB-48-529
Title	Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare)
Journal	Plant Molecular Biology
Year	2002
Volume	48
Pages	529-537
Author	Kanazin V [ Show all 6 ]
Abstract	Summary: The least ambiguous genetic markers are those based on completely characterized DNA sequence polymorphisms. Unfortunately, assaying allele states by allele sequencing is slow and cumbersome. The most desirable type of genetic marker would be unambiguous, inexpensive to assay and would be assayable singly or in parallel with hundreds of other markers (multiplexable). In this report we sequenced alleles at 54 barley (Hordeum vulgare ssp. vulgare) loci, 38 of which contained single-nucleotide polymorphisms (SNPs). Many of these 38 loci contained multiple polymorphisms, and a total of 112 polymorphisms were scored in five barley genotypes. The polymorphism data set was analyzed both by using the individual mutations as cladistic characters and by reducing data for each locus to haplotypes. We compared the informativeness of these two approaches by consensus tree construction and bootstrap analysis. Both approaches provided similar results. Since some of the loci sequenced contained insertion/deletion events and multiple point mutations, we thought that these multiple-mutated loci might represent old alleles that predated the divergence of barley from H. spontaneum. We evaluated sequences from a sample of H. spontaneum accessions from the Eastern Mediterranean, and observed similar alleles present in both cultivated barley and H. spontaneum, suggesting either multiple domestication events or multiple transfers of genes between barley and its wild ancestor
Keyword	[ Hide all but 1 of 47 ] 40 accessions allele assay barley barley genotypes bootstrap cultivated barley data set discovery divergence dna dna sequence domestication events gene genetic marker genotype haplotype hordeum hordeum vulgare human genome isozyme locus map marker microarray multiple mutation old pcr point mutation point mutations polymerase chain-reaction polymorphism primer extension sequence sequencing single-nucleotide polymorphism snp spontaneum state states tagged sites stss transfer tree wild

GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.