Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA libraries.
Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.
Lee
Seung-Hwan
SH
Animal Genomics & Bioinformatics Division, National Livestock Research Institute, RDA, Suwon 441-350, Korea.
Park
Eung-Woo
EW
Cho
Yong-Min
YM
Lee
Ji-Woong
JW
Kim
Hyoung-Yong
HY
Lee
Jun-Heon
JH
Oh
Sung-Jong
SJ
Cheong
Il-Cheong
IC
Yoon
Du-Hak
DH
D000818:Animals; D001483:Base Sequence; D002417:Cattle; D018076:DNA, Complementary / Q000235:genetics*; D020224:Expressed Sequence Tags; D015723:Gene Library; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide
D018076:DNA, Complementary