GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data.

ABSTRACT: Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R²) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip.

SUBMITTER: Wang X 

PROVIDER: S-EPMC9656588 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature