Table 1.
Yield, filtering and mapping summary of the next generation sequencing data of six horses from different breeds.
The depth of coverage and mapping metrics show a descent quality of the 6 genomes sequencing and genome coverage.
Table 2.
Genotype categories of SNPs and INDELs and counts of CNVs and SVs in the six horses.
Fig 1.
Circos plot summarizing the genetic variants detected in each horse.
The pattern of variation across the genomes of the six horses reveals structurally diverse regions important for immunity and olfactory reception at chromosomes 12 and 20 in all six horses. From the inside out, each plot shows two endpoints of the inter- (orange) and intra- (blue) chromosomal translocations. Intrachromosomal translocations > 5 MB are in dark blue. The yellow ring shows the copy number variations (green = normal, blue = loss, red = gain). The histogram (in orange) shows the density of SNPs detected using 1MB windows.
Fig 2.
RT-qPCR results of the LATH CNV region for seven horses belonging to different breeds, a thoroughbred (TB), a Percheron (PER) and an American Miniature (AMH), and an Arabian (ARB), a Tennessee Walking Horse (TWH), a Mangalarga Marchador (MM) and a Native Mongolian Chakouyi (CH).
The Y axis represents the copy number and the X axis, represents horses from different breeds. The results are shown for different primers in the order they appear in in the genome are shown, starting with BPIFB4 to BPIFA1. The results show statistically significant difference in copy number variation between horses for BPIFB4 (a) and BPIFA1 (d) two genes that flank LATH (c) in the EquCab 2.0 assembly.
Table 3.
Real-time quantitative PCR primers.