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To answer this, we compared the distribution of matrilineally-inherited mitochondrial DNA (mtDNA) markers retrieved from Lokomotiv skeletal remains against various lines of archaeological evidence.
The QTL location for relevant traits and the physical positions of microsatellite markers retrieved from ArkDB (http://www.thearkdb.org) and PigQTL (http://www.animalgenome.org/cgi-bin/QTLdb/SS/index) were integrated, to obtain connections between QTL and candidate regions found from GWA studies.
The current version of MoccaDB provides information regarding Coffea EST and genomic SSR markers retrieved from 11 published studies as well as original data (table 1).
Both for markers retrieved from publications and for those designed and/or tested in this study, a maximum of available transferability-associated information was stored in the database: transferability status, amplification quality, information on the polymorphism (number and sizes of alleles within a given species, polymorphism information content (PIC) value).
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For this purpose, 2 gene based markers (Pina-D1, Pinb-D1), 23 Simple Sequence Repeat (SSR) markers and 63 Expressed Sequence Tag (EST) markers were retrieved from GrainGenes database 2.0 (http://wheat.pw.usda.gov).
After being identified as candidate markers, the fasta sequences of the markers were retrieved from each genome.
Apart from new markers developed from public BAC sequences, all SSR markers were retrieved from the Maize Genetics and Genomics Database (http://www.maizegdb.org) (Additional file 1) and synthesized by Invitrogen (Beijing, China).
A total of 332 full-length soybean P450 genes and 378 pseudogenes with Glyma location markers were retrieved from the database.
The physical position of each RFLP marker was retrieved from the Rice Annotation Project Database (RAP-DB) http://rapdb.dna.affrc.go.jp/[ 19].
Primer sequences for each marker were retrieved from NCBI's UniSTS database (http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists) and each forward primer was labeled on the 5′ end with one of the two fluorescent dyes 6-FAM or HEX.
Physical positions of the SSR markers and centromeric markers (cent1 cent10) were retrieved from MaizeGDB to project centromere positions on our genetic map.
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