Haplotype analysis within quantitative trait locus affecting intramuscular fat content on porcine chromosome

摘要

Previous results of fine mapping for quantitative trait loci affecting intramuscular fat content identified a 3.0-Mb chromosome interval on porcine chromosome 7, which contains at least 9 genes, based on the pig genome assembly. Therefore, we proposed these nine genes ( LOC100154481 , LOC100155711 , LOC100155276 , SPATA7 , PTPN21 , ZCH14 , EML5 , TTC8 , and FOXN3 ) as positional candidate genes. The coding exons of the nine genes were characterized, and 45 polymorphisms were detected in F₂ Duroc × Meishan population. Within the nine genes, 10 non-synonymous substitutions and 1 insertion were genotyped among three European breeds (Landrace, Large White, and Duroc) and 1 Chinese breed (Meishan). Genotyping data was used to perform the haplotype analysis. Polymorphisms were found in all the studied genes, except ZCH14 . We surveyed the frequency of 33 haplotypes that formed non-synonymous substitutions in four breeds. One of them was distributed widely in the Landrace, Large White, and Meishan breeds, but not in Duroc. Each breed had different major haplotypes.