An integrated genetic approach prioritizes closely linked candidate genes underlying an open-field behavior QTL on...

Although numerous QTL associated with complex economic and behavioral traits in chickens have been identified across the genome, the specific functional variants underlying these QTL remain poorly understood. We previously identified a QTL region associated with open-field (OF) behavior on chicken chromosome 1 in an F2 population derived from a cross between Oh-Shamo (OSM), a native Japanese chicken breed with aggressive behavior, and the White Leghorn T line (WL-T), which exhibits docile behavior. In this study, we aimed to identify candidate genes for this OF QTL using an integrated genetic approach combining QTL remapping, transcriptome analysis, haplotype frequency analysis, and association analysis. QTL remapping in the F2 population using the first principal component (PC1) scores derived from 4 OF traits affected by this QTL revealed a complex logarithm of odds (LOD) profile, identifying a 95% confidence interval (CI) spanning approximately 23 Mb and containing 297 genes. RNA sequencing of F2 individuals with extreme PC1 scores, followed by expression validation using reverse transcription quantitative PCR in the parental and F1 populations, reduced the number of candidate genes from 297 to 13. Subsequent haplotype frequency and correlation analyses prioritized G2 and S-phase expressed protein 1 (GTSE1) as the strongest candidate gene underlying the OF QTL region on chromosome 1, with IQ motif and ubiquitin domain containing (IQUB), and inner mitochondrial membrane peptidase subunit 2 (IMMP2L) representing additional candidate genes. Furthermore, multiple regression analysis suggested that these 3 genetically linked genes are associated with variation in OF behavior. These findings demonstrate the utility of an integrated genetic approach for prioritizing closely linked candidate genes within a broad QTL region exhibiting a complex LOD profile and provide new insights into the genetic architecture of OF behavior in chickens.