Genome sequence, comparative analysis, and population genetics of the domestic horse

Abstract

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Figure 1. Major findings of the genome analysis

(a) Analysis of the primary centromeric constriction of ECA11: 26,000,000–30,000,000; (i) ChIP-on-chip analysis with antibodies against centromeric proteins (CENP-A and CENP-C) shows two regions (136 and 99kb) bound by kinetochore proteins; (ii) there are no un-captured and few captured gaps; (iii) a normal fraction of bases in repeat sequences; (iv) no satellite tandem repeats (v) no protein coding sequences are present nearby (vi) normal levels of non-coding conserved elements (29 eutherians). (b) Horse LD is intermediate between human and dog. (c) Horses exhibit more long-range across-breed haplotype sharing than dogs. Haplotypes have the same color across breeds, haplotypes in < 5% of all individuals (light gray), haplotypes in > 5% of all individuals but a single breed (dark gray). Data show LD regions of ECA18 (first 100kb) and dog chromosome 12 (first 100kb) which are representative. Full data are in Table S11.