Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs.

ABSTRACT: Resequencing a number of individuals of various breeds as reference population and imputing the whole-genome sequences of individuals that were genotyped with medium-density chips to perform an association study is a very efficient strategy. Previously, we performed a genome-wide association study (GWAS) of lumbar number using 60K SNPs from the porcine Illumina chips in 418 Sutai pigs and did not detect any significant signals. Therefore, we imputed the whole-genome sequences of 418 Sutai individuals from 403 deeply resequenced reference individuals and performed association tests. We identified a quantitative trait locus (QTL) for lumbar number in SSC1 with a P value of 9.01E-18 that was close to the potential causative gene of NR6A1. The result of conditioning on the top SNP association

SUBMITTER: Yan G 

PROVIDER: S-EPMC5429657 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature