Mapping of expressed sequence tags from a porcine early embryonic cDNA library.
The goal of this study was to identify and map genes expressed during the elongation phase of embryogenesis in swine. Expressed sequence tags were analysed from a previously described porcine cDNA library prepared from elongating swine embryos. Average insert length of randomly selected clones was approximately 600 bp, with a range from < 100 to > 2500 bp. Single-pass, coding strand sequences from 1132 independent clones were compared with the GenBank non-redundant (nr) database via BLASTN analysis to identify potential porcine homologous of known genes. Among these sequences, 781 (69%) showed significant (score > 300) homology to non- mitochondrial sequences previously deposited in GenBank. Sequences matching interleucin 1 beta and thymosin beta 10 were most frequently observed (24 and 18 clones, respectively), in addition to matches with 310 other distinct genes. No significant match in the GenBank nr database was obtained for 303 sequences. Analysis demonstrated that 151 (50%) had open reading frames (ORF) extending at least 50 codons from the first base of the clone insert. Genetic markers were developed and used to map a subset of 17 genes, selected on the basis of function or of the ability to design primers that successfully amplified porcine genomic DNA, to 10 different porcine chromosomes, providing a set of mapped markers corresponding to genes expressed during conceptus elongation.
Smith
T P
TP
US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Spur 18D, PO Box 166, Clay Center, NE 68933, USA. marc.usda.gov
Fahrenkrug
S C
SC
Rohrer
G A
GA
Simmen
F A
FA
Rexroad
C E
CE
Keele
J W
JW
D000483:Alleles; D000818:Animals; D001755:Blastocyst / Q000378:metabolism; D002874:Chromosome Mapping; D019992:Databases as Topic; D020224:Expressed Sequence Tags; D018507:Gene Expression Regulation, Developmental; D005838:Genotype; D006801:Humans; D008126:Lod Score; D018895:Microsatellite Repeats / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D013552:Swine / Q000196:embryology* / Q000235:genetics*