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We eliminated 162 loci because they had identical map positions to other loci (n = 151) or did not map to any LG (n = 11).
The high homology between FLcDNAs (27%) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151 233 FLcDNAs on each of the seven barley chromosomes.
Connecting map positions to GO terms requires synchronizing several information sources, including livestock maps, human sequence annotated GO terms, and GO databases.
Output data were filtered for pairwise comparisons containing significantly associated loci, and perl was used to add LGs and map positions to the data.
Sato et al. (submitted for publication) assigned linkage map positions to 2890 non-redundant 3′ ESTs, providing the densest, reliable barley map available.
We then explored three available gene-based mapping datasets: Illumina OPA-SNPs [ 28], Single Feature Polymorphisms (R. Wise, unpublished data) and TDMs [ 22] to help assign genetic map positions to the 55 genes.
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Berg et al. [33] characterized this FAT1 QTL and refined its map position to a 3.3 cM interval between the RXRG and SDHC genes.
For the remaining 16 markers, the median distance was calculated from the marker's map position to the respective gene in the genome sequence.
Šimková et al. (2008) mapped 162 SNP loci, including 40 loci with hitherto unknown map position to barley chromosome 1H using a pilot oligonucleotide pool assay.
For the purpose of QTL analysis, clusters of markers were removed to leave only one marker at each locus (taken as the map position to one decimal place).
Harhay and Keele [ 31] used GO and GO-annotated human sequence to link livestock EST with function; mapping the EST can extend their procedures to relate map position to function.
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