We recently investigated fine-scale recombination rate variability in the domestic horse1 using high-density genotyping data from the MNEc2M SNP array2 and the EquCab2 reference genome assembly3. Recent completion of EquCab34 has resulted in an overall higher-quality assembly which includes inversions and translocations relative to EquCab2. Further, thousands of SNPs on the MNEc2M array, previously mapped to unplaced contigs in EquCab2, now map to equine chromosomes (ECA) 1-31 and ECAX in EquCab35. The purpose of this report is to update the domestic horse recombination map to EquCab3 coordinates to ensure its continued usefulness to the equine genome research community.
Our dataset consists of previously generated SNP genotypes of 485 horses from 32 breeds2. Genomic coordinates for these data were originally based on the EquCab2 reference build3; therefore, we performed probe-based remapping to EquCab35, producing a final set of 1,820,349 biallelic SNP genotypes, which we phased using BEAGLE6. We generated recombination maps as described previously1. Briefly, we sampled 40 haplotypes 100 times per chromosome from the dataset described above and estimated population recombination rates (4Ner) using LDhat7, taking the average across random samples. For 12 individual breeds (Arabian, Belgian, Franches-Montagnes, French Trotter, Icelandic, Lusitano, Maremmano, Morgan, Quarter Horse, Standardbred, Thoroughbred, and Welsh Pony), we created breed-specific maps following the same procedure. Using these recombination rate estimates, we predicted recombination hotspots with LDhot8. Finally, we converted recombination rates from 4Ner to centimorgans (cM) with effective population size estimates generated previously1. More details are provided in the Supplemental Methods.
The equine genome recombination map updated to EquCab3 spans 2,794.81 centimorgans (cM) over 2.41 Gb. As a result, the average genome-wide recombination rate is 1.16 cM/Mb. This is lower than our previous estimate of 1.24 cM/Mb1. Table 1 and Supplemental Figure S1 contain a summary of chromosomal recombination rates and fine-scale rates by chromosome, respectively. In all cases, the estimated rate across individual chromosomes is lower in EquCab3 than in EquCab21 (Supplemental Table S1). The median width of predicted recombination hotspot regions is 3.1 kb, with an overall range of 1-10 kb. Hotspots now account for approximately 155.3 Mb, or 6% of the equine genome, and 1,416.9 cM, or 50.6% of the genetic map length, both of which are reductions from previous estimates. In predicted hotspot regions, the mean recombination rate is 9.1 cM/Mb, roughly 8 times the genome-wide average. Breed-specific maps are summarized in Supplemental Table S2. Overall, differences between the updated recombination map and our previous map appear to reflect improvements in the equine genome assembly and provide an improved means for investigating the basis of equine genome structure and function.
Table 1.
Physical distance, genetic distance, average recombination rate, and hotspot count by chromosome in the updated recombination map.
| Genetic length (cM) |
Physical length (Mb) |
Mean rate (cM/Mb) |
Hotspots | |
|---|---|---|---|---|
| Genome | 2,794.81 | 2,408.75 | 1.16 | 42,243 |
| ECA1 | 190.98 | 188.25 | 1.01 | 2,962 |
| ECA2 | 134.22 | 121.34 | 1.11 | 1,969 |
| ECA3 | 129.48 | 121.35 | 1.07 | 1,987 |
| ECA4 | 112.60 | 109.46 | 1.03 | 1,843 |
| ECA5 | 102.97 | 96.75 | 1.06 | 1,737 |
| ECA6 | 94.92 | 87.22 | 1.09 | 1,594 |
| ECA7 | 113.78 | 100.78 | 1.13 | 1,764 |
| ECA8 | 101.07 | 97.55 | 1.04 | 1,544 |
| ECA9 | 91.71 | 85.75 | 1.07 | 1,435 |
| ECA10 | 105.89 | 85.15 | 1.24 | 1,505 |
| ECA11 | 91.71 | 61.66 | 1.49 | 1,088 |
| ECA12 | 71.06 | 36.98 | 1.92 | 858 |
| ECA13 | 57.88 | 43.78 | 1.32 | 902 |
| ECA14 | 99.99 | 94.59 | 1.06 | 1,547 |
| ECA15 | 95.74 | 92.85 | 1.03 | 1,601 |
| ECA16 | 94.46 | 88.94 | 1.06 | 1,497 |
| ECA17 | 88.09 | 80.71 | 1.09 | 1,463 |
| ECA18 | 84.47 | 82.62 | 1.02 | 1,414 |
| ECA19 | 75.39 | 62.67 | 1.20 | 1,106 |
| ECA20 | 92.01 | 65.22 | 1.41 | 1,281 |
| ECA21 | 68.05 | 58.94 | 1.15 | 1,051 |
| ECA22 | 53.25 | 50.92 | 1.05 | 954 |
| ECA23 | 57.68 | 55.56 | 1.04 | 917 |
| ECA24 | 57.52 | 48.27 | 1.19 | 842 |
| ECA25 | 46.27 | 40.27 | 1.15 | 695 |
| ECA26 | 62.31 | 43.12 | 1.45 | 741 |
| ECA27 | 46.72 | 40.25 | 1.16 | 755 |
| ECA28 | 54.21 | 47.34 | 1.15 | 828 |
| ECA29 | 51.13 | 34.77 | 1.47 | 705 |
| ECA30 | 42.94 | 31.39 | 1.37 | 597 |
| ECA31 | 34.27 | 26.00 | 1.32 | 1,079 |
| ECAX | 192.04 | 128.20 | 1.50 | 1,982 |
Supplementary Material
Acknowledgements
Support for this work came from United States Department of Agriculture National Institute of Food and Agriculture project 2012-67,015-19,432, Minnesota Agricultural Experiment Station Multistate project MIN-62-090, and National Animal Genome Project (NRSP-8) through the equine genome coordinator: USDA-NRSP8 (2013-2018) horse-technical-committee coordinator funds. Support for SKB: National Institutes of Health National Research Service Award 5F30OD023369.
Footnotes
Data Availability
Recombination maps and hotspots are available at https://osf.io/e72ah.
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