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Publicly available genotype data for almost four million markers were downloaded from the HapMap [30].
Sequences of the SSR, RFLP and new SNP markers were downloaded in FASTA format from NCBI.
Informative DNA markers were downloaded from the Mouse Genome Database (DXMit114, DXMit96 and DXMit41)., Custom DNA markers were also designed in-house around novel SSLPs between CAST and SWR alleles in the region of Gct4 (Table S1 ).
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From the Arabidopsis Information Resource (TAIR), information on SSLP markers was downloaded; and from the Monsanto Arabidopsis Polymorphism and Ler Sequence Collection [16], polymorphism information was obtained to generate polymorphic makers.
Sequences for each marker were downloaded from HADB and aligned using Clustal X [ 61].
Sequences of each marker were downloaded from H fwADB and aligned using Clustal X [ 96].
To determine syntenic relationships between date palm, oil palm and coconut, markers from coconut were downloaded from GENBANK (http://www.ncbi.nlm.nih.gov) selecting only microsatellite DNA markers with significant (~500 bp) surrounding sequence.
First, all sequences involving the five markers of Asteraceae were downloaded from GenBank.
For most of the markers, nucleotide sequences were downloaded from GenBank databases and stored in the database.
Genomic or EST sequences from which these markers were developed were downloaded from databases located at MELOGEN (http://www.melogen.upv.es/), GenBank (http://www.ncbi.nih.gov/) or at ICUGI (http://www.icugi.org/) websites.
In order to define the starting and ending point of each IL-bin on the tomato genome, edge molecular marker sequences (MMs) were downloaded.
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