Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 64

variation patterns for each species. The Arabidopsis 1,001 project and genome-wide
variation study is one of the few available information web sites so far contain-
ing this information. Therefore, the demand is rapidly increasing for high through-
put and cost-effective platforms for comprehensive variation analysis studies (also
called 'variome' analysis). Complete genome resequencing information are already
being realized as a direct solution to 'variome' analysis in species whose reference
genome sequence data are already available; the URL list for the web sites used for
variation analysis are detailed below and URL listed in Table 2.3 .
DArT P/L
Diversity Array Technology (DArT) is a high throughput genotyping system that
was developed based on microarrays (Jaccoud et al. 2001 ; Wenzl et al. 2007 ). In
various crop species such as wheat, barley and sorghum, DArT markers have been
used with other conventional molecular markers to construct dense genetic maps
and/or to perform genetic association studies (Crossa et al. 2007 ; Peleg et al. 2008 ;
Mace et al. 2009 ). This genotype technology web site describes DNA variations us-
ing SNP, as well as other molecular markers; and also described is information on
DNA methylation.
Gene Chip Array
In barley and wheat, Affymetrix GeneChip Arrays have been used to show nucle-
otide polymorphisms based on the differential hybridization of GeneChip probes
(Rostoks et al. 2005 ; Bernardo et al. 2009 ). The Affimetrix site includes a spe-
cific Medicago chip and a miRNA site. The Illumina GoldenGate Assay allows
the simultaneous analysis of up to 1,536 SNPs in 96 samples, and has been used to
analyse genotypes of segregating populations in order to construct genetic maps of
SNPs in crops such as barley, wheat and soybean (Hyten et al. 2008 ; Akhunov et al.
2009 ; Close et al. 2009 ).
SNP Genotyping
The University of California, Davis site contains a number of options for high
throughput genotyping. It operates a commercial division where SNP genotyping
can be performed using Illumina technology and GoldenGate Assay.
Analysis of Variation
Comprehensive gene family data sets are usually produced by computer programs,
including a sequence similarity search, and then a step for building clusters of EST