Skip to main content

Table 3 The proportion of variance explained for each annotation class across all dairy traits

From: Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Class Fat Milk Protein Fat Percent Protein Percent Fertility
Antisense RNA 0.4 (0.15)* 0.48 (0.17)* 0.43 (0.15)* 0.6 (0.23)* 0.59 (0.2)* 0.02 (0)
Long noncoding RNA 0.28 (0) 0.34 (−0.01) 0.29 (0) 0.5 (−0.05)* 0.53 (−0.04)* 0.02 (0)
miRNA Target Sites 0.31 (0.04)* 0.37 (0.03)* 0.32 (0.04)* 0.5 (−0.02)* 0.53 (0) 0.02 (0)
Splice Sites 0.32 (0.03)* 0.39 (0.03)* 0.34 (0.03)* 0.49 (0.06)* 0.51 (0.07)* 0.01 (0)
Missense Deleterious 0.24 (−0.01) 0.31 (− 0.01) 0.26 (− 0.01) 0.41 (0.02)* 0.41 (− 0.01) 0.01 (0)
Missense Tolerated 0.27 (0) 0.34 (0) 0.28 (0) 0.5 (0.03)* 0.49 (0) 0.02 (0)
Synonymous 0.27 (0) 0.35 (0) 0.29 (0.01) 0.51 (0) 0.53 (0) 0.02 (0)
CDS 0.28 (0) 0.36 (0) 0.29 (0) 0.53 (0.01) 0.56 (0.01) 0.02 (0)
TFBS 0.37 (0.09)* 0.44 (0.09)* 0.39 (0.08)* 0.52 (0.11)* 0.52 (0.1)* 0.01 (0)
3’ UTR 0.27 (0.01) 0.34 (0.01) 0.28 (0.01) 0.48 (−0.01) 0.48 (−0.02) 0.02 (0)
5’ UTR 0.28 (0.03)* 0.34 (0.03)* 0.29 (0.02)* 0.45 (0.08)* 0.45 (0.06)* 0.01 (0)
Upstream 5 k 0.29 (0) 0.36 (0) 0.3 (0) 0.59 (0) 0.58 (−0.03) 0.02 (0)
Downstream 5 k 0.29 (0) 0.37 (0) 0.3 (0) 0.6 (0.01) 0.59 (−0.02) 0.02 (0)
DNA Methylated 0.28 (0) 0.34 (0.00) 0.29 (0) 0.54 (−0.03)* 0.57 (0) 0.02 (0)
  1. In brackets is the difference in the variance explained (heritability, h2) between the actual variance explained in that class and the mean variance explained by five random permutation sets. An asterisk indicates a significant difference between the variance explained by that class and the random permuted test. DNA methylated represents methylated regions in bovine placenta [23]. 3 prime and 5 prime untranslated regions (UTR) are represented as 3’ UTR and 5’ UTR, respectively. CDS represents the coding sequence of an exon. Transcription factor binding sites (TFBS) were from Bickhart D.M et al. [47]. Downstream 5 k and Upstream 5 k represent all variants that are found within 5 kilobases either upstream of a gene transcription start site (TSS) or downstream of a gene transcription termination site (TTS)
\