DOI: 10.5061/dryad.v4126t4
title: Data from: Multi-trait single-step genomic prediction accounting for heterogeneous (co)variances over the genome

description: Widely used genomic prediction models may not properly account for
 heterogeneous (co)variance structure across the genome. Models such as
 BayesA and BayesB assume locus-specific variance, which are highly
 influenced by the prior for (co)variance of single nucleotide polymorphism
 (SNP) effect, regardless of the size of data. Models such as BayesC or
 GBLUP assume a common (co)variance for a proportion (BayesC) or all
 (GBLUP) of the SNP effects. In this study, we propose a multi-trait
 Bayesian whole genome regression method (BayesN0), which is based on
 grouping a number of predefined SNPs to account for heterogeneous
 (co)variance structure across the genome. This model was also implemented
 in single-step Bayesian regression (ssBayesN0). For practical
 implementation, we considered multi-trait single-step SNPBLUP models,
 using (co)variance estimates from BayesN0 or ssBayesN0. Genotype data were
 simulated using haplotypes on first five chromosomes of 2,200 Danish
 Holstein cattle, and phenotypes were simulated for two traits with
 heritabilities 0.1 or 0.4, assuming 200 QTL. We compared prediction
 accuracy from different prediction models and different region sizes (one
 SNP, 100 SNPs, one chromosome or whole genome). In general, highest
 accuracies were obtained when 100 adjacent SNPs were grouped together. The
 ssBayesN0 improved accuracies over BayesN0, and using (co)variance
 estimates from ssBayesN0 generally yielded higher accuracies than using
 (co)variance estimates from BayesN0, for the 100 SNPs region size. Our
 results suggest that it could be a good strategy to estimate (co)variance
 components from ssBayesN0, and then to use those estimates in genomic
 prediction using multi-trait single-step SNPBLUP, in routine genomic
 evaluations.
description: chromosome ID and
 base-pair position for SNPs Chromosome ID and
 base-pair position for (11,154) SNPs. The order is the same as in the
 genotype files. First column is the chromosome ID, and second column is
 the base-pair position chrInfo.txt
 
 repl1.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl2.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl3.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl4.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl5.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl6.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl7.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl8.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl9.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl10.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl11.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl12.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl13.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl14.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl15.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl16.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl17.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl18.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl19.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.   
 repl20.zip
 Compressed file
 including genotypes (genoData_X, where X is the replicate number), and
 pedigree (ped0-ped5) for 6 generations (13,200 individuals). The ID of
 individuals in the genotype file are 1 to 13,200, and pedigree files
 include individual, sire and dam ID respectively.