Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences.
In this study, an in silico approach was developed to identify homologies existing between livestock microsatellite flanking sequences and GenBank nucleotide sequences. Initially, 1955 bovine, 1570 porcine and 1121 chicken microsatellites were downloaded and the flanking sequences were compared with the nr and dbEST databases of GenBank. A total of 74 bovine, 44 porcine and 37 chicken microsatellite flanking sequences passed our criteria and had at least one significant match to human genomic sequence, genes/expressed sequence tags (ESTs) or both. GenBank annotation and BLAT searches of the UCSC human genome assembly revealed that 38 bovine, 13 porcine and 17 chicken microsatellite flanking sequences were highly similar to known human genes. Map locations were available for 67 bovine, 44 porcine and 21 chicken microsatellite flanking sequences, providing useful links in the comparative maps of humans and livestock. In support of our approach, 112 alignments with both microsatellite and match mapping information were located in the expected chromosomal regions based on previously reported syntenic relationships. The development of this in silico mapping approach has significantly increased the number of genes and EST sequences anchored to the bovine, porcine and chicken genome maps and the number of links in various human-livestock comparative maps.
Farber
C R
CR
Department of Animal Science, University of California, Davis, CA, USA.
Medrano
J F
JF
D000818:Animals; D002417:Cattle / Q000235:genetics*; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D034421:Sus scrofa / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics