title: 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 test indicated that only one QTL was responsible for this trait in SSC1. The linkage disequilibrium (LD) drop test result for the condition of the reported potential causative mutation (c.575T > C missense mutation of NR6A1) indicated that this mutation was probably not the underlying mutation that affected lumbar number in our study. As the first trial of imputed whole-genome sequence GWAS in swine, this approach can be also powerful to investigate complex traits in pig like in human and cattle.
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China.
authors.forename: Guorong
authors.initials: G
authors.lastname: Yan
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, 450002, Zhengzhou, P.R. China.
authors.forename: Ruimin
authors.initials: R
authors.lastname: Qiao
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China.
authors.forename: Wenshui
authors.initials: W
authors.lastname: Xin
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China. bioducklily@hotmail.com.
authors.forename: Zhiyan
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, P.R. China.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D001947:Breeding; D002874:Chromosome Mapping; D005787:Gene Frequency; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008159:Lumbar Vertebrae / Q000033:anatomy & histology; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D013552:Swine