title: Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6.
abstract: On pig chromosome 6, the SW71 microsatellite is located in the region corresponding to several quantitative trait loci (QTL), such as those for intramuscular fat content and for body weight at 4 weeks of age. The genomic sequence of approximately 909 kb was obtained from seven BAC clones encompassing the SW71 region corresponding to human 18q11.21-q11.22. By searching the NCBI GenBank using BLASTX and BLASTN, this 909-kb segment was found to contain eight genes, RAB31, TXNDC2, VAPA, APCDD1, NAPG, FAM38B, C18orf30, and C18orf58, and one putative gene (DN119777). The average G + C content in the sequence of this contig was 45.75% and 33 CpG islands were detected. CpG islands were scattered throughout the region in which most of the putative genes were located. Dense CpG islands of approximately 840 bp were observed, including within the 5' UTR and exon 1 of the orthologs of the RAB31, VAPA, APCDD1, and NAPG genes. Comparative analysis of conserved segments of six species showed that K(a)/K(s) ratios of the TXNDC2 gene in collinear and rearranged segments were significantly different at 4.1 and 1.3, respectively. In conclusion, we demonstrated the genomic organization of pig chromosome 6, including the gene order surrounding SW71, which provides important information for comparative mapping. Moreover, the genes revealed in this study may be positional candidate genes associated with QTL on chromosome 6 that affect fat deposition in pigs.
authors.affiliation: Division of Animal Genomics and Bioinformatics, National Livestock Research Institute, Rural Development Administration, Omokchun-dong 564, Kwonsun-gu, Suwon, Korea.
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.forename: Eung-Woo
authors.initials: EW
authors.lastname: Park
authors.forename: Sunjin
authors.initials: S
authors.lastname: Moon
authors.forename: Hye-Sook
authors.initials: HS
authors.lastname: Park
authors.forename: Hyung-Yong
authors.initials: HY
authors.lastname: Kim
authors.forename: Gil-Won
authors.initials: GW
authors.lastname: Jang
authors.forename: Bong-Hwan
authors.initials: BH
authors.lastname: Choi
authors.forename: H Y
authors.initials: HY
authors.lastname: Chung
authors.forename: Ji-Woong
authors.initials: JW
authors.lastname: Lee
authors.forename: Il-Cheong
authors.initials: IC
authors.lastname: Cheong
authors.forename: Sung-Jong
authors.initials: SJ
authors.lastname: Oh
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.forename: Dong-Sang
authors.initials: DS
authors.lastname: Suh
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
mesh_terms: D050154:Adiposity / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D017931:DNA Primers; D016678:Genome; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D040641:Quantitative Trait Loci; D013552:Swine / Q000235:genetics*
chemical_list: D017931:DNA Primers