BcSNPdb: Bovine Coding Region Single Nucleotide Polymorphisms Located Proximal to Quantitative Trait Loci

• Published in: BMB reports Vol. 40; no. 1; pp. 95 - 99
• Main Authors: Moon, S.J. (Seoul National University, Seoul, Republic of Korea), Shin, H.D. (SNP Genetics Inc., Seoul, Republic of Korea), Cheong, H.S. (SNP Genetics Inc., Seoul, Republic of Korea), Cho, H.Y. (SNP Genetics Inc., Seoul, Republic of Korea), Namgoong, S. (SNP Genetics Inc., Seoul, Republic of Korea), Kim, E.M. (SNP Genetics Inc., Seoul, Republic of Korea), Han, C.S. (SNP Genetics Inc., Seoul, Republic of Korea), Sung, S.S. (Seoul National University, Seoul, Republic of Korea), Kim, H.B. (Seoul National University, Seoul, Republic of Korea), E-mail: heebal@snu.ac.kr
• Format: Journal Article
• Language: English
• Published: Korea (South) 31.01.2007
• Subjects: Amino Acid Substitution; Animals; Base Sequence; bovine single nucleotide polymorphism; Cattle - genetics; Chromosome Mapping - methods; Databases, Genetic; GENE; GENES; non-synonymous SNP; Open Reading Frames - genetics; Polymorphism, Single Nucleotide; QTL; Quantitative Trait Loci
• ISSN: 1225-8687; 1976-6696; 0219-1024
• DOI: 10.5483/bmbrep.2007.40.1.095

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth greater than 3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498.