QTL analysis of back fat thickness and carcass pH in an F2 intercross between Landrace and Korean native pigs

In this study, we conducted a genome-wide linkage analysis to identify the quantitative trait loci (QTL) that influence back fat thickness and carcass pH in an F2 intercross between Landrace and Korean native pigs. Eight phenotypes related with back fat thickness and carcass pH were measured in more than 960 F2 progeny. All experimental animals were subjected to genotypic analysis using 173 microsatellite markers located throughout the pig genome. The GridQTL program, based on the least squares regression model, was used to perform the QTL analysis. We identified 22 genome-wide significant QTL in 9 chromosomal regions (SSC1, 2, 5, 6, 7, 8, 12, 15, and 16) and 29 suggestive QTL in 16 chromosomal regions (SSC2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, and X). On SSC5, we detected a QTL affecting back fat thickness that accounted for 4.8 % of the phenotypic variance, which was the highest test statistic (F-ratio = 50.3 under the additive model, nominal P value = 2.5 × 10−12) observed in this study. Additionally, we showed that there were significant QTL on SSC16 affecting carcass pH traits. In conclusion, the QTL identified in this study together with associated positional candidate genes could play an important role in determining the genetic structure underlying the variation of back fat thickness and carcass pH in pigs.