title: Development and implementation of high-throughput SNP genotyping in barley.
abstract: BACKGROUND
  High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource.
  
  
  RESULTS
  Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM.
  
  
  CONCLUSIONS
  The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.
authors: Department of Botany & Plant Sciences, University of California (UCR), Riverside, CA, 92521, USA. timothy.close@ucr.edu
authors: Timothy J
authors: TJ
authors: Close
authors: Prasanna R
authors: PR
authors: Bhat
authors: Stefano
authors: S
authors: Lonardi
authors: Yonghui
authors: Y
authors: Wu
authors: Nils
authors: N
authors: Rostoks
authors: Luke
authors: L
authors: Ramsay
authors: Arnis
authors: A
authors: Druka
authors: Nils
authors: N
authors: Stein
authors: Jan T
authors: JT
authors: Svensson
authors: Steve
authors: S
authors: Wanamaker
authors: Serdar
authors: S
authors: Bozdag
authors: Mikeal L
authors: ML
authors: Roose
authors: Matthew J
authors: MJ
authors: Moscou
authors: Shiaoman
authors: S
authors: Chao
authors: Rajeev K
authors: RK
authors: Varshney
authors: Péter
authors: P
authors: Szucs
authors: Kazuhiro
authors: K
authors: Sato
authors: Patrick M
authors: PM
authors: Hayes
authors: David E
authors: DE
authors: Matthews
authors: Andris
authors: A
authors: Kleinhofs
authors: Gary J
authors: GJ
authors: Muehlbauer
authors: Joseph
authors: J
authors: DeYoung
authors: David F
authors: DF
authors: Marshall
authors: Kavitha
authors: K
authors: Madishetty
authors: Raymond D
authors: RD
authors: Fenton
authors: Pascal
authors: P
authors: Condamine
authors: Andreas
authors: A
authors: Graner
authors: Robbie
authors: R
authors: Waugh
mesh_terms: D000483:Alleles; D008040:Genetic Linkage; D005819:Genetic Markers; D005821:Genetic Techniques; D005838:Genotype; D001467:Hordeum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers