Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 2-6 generations

Bailey et al.

Abstract:

Whole genome sequences (WGS) of 185 North American Thoroughbred horses were 
compared to quantify the number and frequency of variants, diversity of mitotypes, 
and autosomal runs of homozygosity (ROH). Of these samples, 82 were born between 
1965 and 1986 (Group 1); the remaining 103, selected based on pedigree diversity, 
were born between 2000 and 2020 (Group 2).  Over 14.3 million autosomal variants were 
identified with 4.5 to 5.0 million found per horse.  Mitochondrial sequences associated 
the North American Thoroughbreds with 9 of 17 clades previously identified among diverse 
breeds, with 34 unique mitochondrial haplotypes observed.  Individual coefficients of 
inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2).  When SNP 
arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH.
WGS-based estimates of inbreeding were highly correlated (r>0.98) with SNP array-based 
estimates, but only moderately correlated (r=0.40) with inbreeding based on 5-generation 
pedigrees.  On average, Group 1 horses had more heterozygous variants (P<0.001), more total 
variants (P<0.001), and lower individual inbreeding (FROH; P<0.001) than horses in Group 2.
However, the distribution of numbers of variants, homozygosity and extent of ROH overlapped 
among all horses such that it was not possible to identify the group origin of any single 
horse using these measures.  Consequently, the Thoroughbred population would be better 
monitored by investigating changes in specific variants, rather than relying on broad measures 
of diversity/inbreeding.  The WGS for these 185 horses is publicly available for comparison to 
other populations and as a foundation for modeling changes in population structure, breeding 
practices, or the appearance of deleterious variants.



If you need to load the EquCab3 genome with the male specific Y chromosome, copy the link below and use if to "Load Genome from URL..."

(IGV version 2.17 or greater))Variant Call Format File for 185 North American Thoroughbreds.(naTbredDiversity.vcf.gz)(naTbredDiversity.vcf.gz.tbi)

(IGV less than version 2.17)Variant Call Format File for 185 North American Thoroughbreds.(naTbredDiversity.vcf.gz)(naTbredDiversity.vcf.gz.tbi)