Skip to main content

Table 2 Summary of studies.

From: Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping

Study Type Loci Type of locia Loci effects Additional effects Model Comments
LABayes [7] LA multiple multi-markerb fixed, additive sex + generation Bayesian only every tenth marker used
LDBayes [8] LD multiple single marker random, additive - Bayesian  
LDLA1 [9] LD multiple single marker fixed, additive +dominance polygenic mixed model, REMLc and FSd markers selected by allele frequency difference in high/low offspring per sire
  LDLA single haplotype (2) random, additive polygenic variance component, REML markers selected by allele frequency difference in high/low offspring per sire
LDmulti [10] LD multiple single marker fixed, additive +dominance +epistasis pre-correction for polygenic + sex + generation linear regression, least squares and FS mixed model, REML used for pre-correction
LDHap [11] LD single haplotype (10e) fixed, additive pre-correction for polygenic + sex + generation phylogeny building, cluster analysisf mixed model, MLg for pre-correction, maximum in 10 cM interval
  LD single single marker fixed, additive polygenic + sex + generation mixed model, ML maximum in 5 cM interval, explored epistasis
LDLA2 [12] LA two single marker random, additive polygenic variance component, REML only marker data from last two generations used
  LDLA single haplotype (10) random, additive polygenic variance component, REML only marker data from last two generations used, only on most significant region per chromosome from LA
  LD single haplotype (3) random, additive polygenic variance component, REML only marker data from last two generations used, only on most significant region per chromosome from LA
  1. aIn brackets is the number of markers in a haplotype. bProbability of QTL genotype is conditional on all marker data (at reduced 1 cM density) for the chromosome. cRestricted maximum likelihood. dForward selection. eAt least 10 markers used. fUsing Blossoc [16]. gMaximum likelihood.