Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction

摘要: Abstract This study investigated the effect on reliability of genomic prediction when a small number significant variants from single marker analysis based whole genome sequence data were added to regular 54k nucleotide polymorphism (SNP) array data. The extra markers selected with aim augmenting custom low-density Illumina BovineLD SNP chip (San Diego, CA) used in Nordic countries. single-marker was done breed-wise all 16 index traits included breeding goals for Holstein, Danish Jersey, and Red cattle plus total merit itself. Depending trait's economic weight, 15, 10, or 5 quantitative trait loci (QTL) per breed 3 tag each QTL. After removing duplicate (same more than one breed) filtering high pairwise linkage disequilibrium assaying performance array, 1,623 QTL inclusion chip. Genomic analyses performed French Holstein animals using either BLUP Bayesian variable selection model. When model including analysis, increased by up 4 percentage points production animals, Reds, Holstein. Smaller gains 1 point observed mastitis, but only 0.5 increase seen fertility. accuracies generally higher compared approach, increases relatively smaller included. Results this indicate that can be genome-wide association studies alongside set.