Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6.
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.
Lee
Kyung-Tai
KT
Division of Animal Genomics and Bioinformatics, National Livestock Research Institute, Rural Development Administration, Omokchun-dong 564, Kwonsun-gu, Suwon, Korea.
Park
Eung-Woo
EW
Moon
Sunjin
S
Park
Hye-Sook
HS
Kim
Hyung-Yong
HY
Jang
Gil-Won
GW
Choi
Bong-Hwan
BH
Chung
H Y
HY
Lee
Ji-Woong
JW
Cheong
Il-Cheong
IC
Oh
Sung-Jong
SJ
Kim
Heebal
H
Suh
Dong-Sang
DS
Kim
Tae-Hun
TH
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*
D017931:DNA Primers