Table 2.
Variation of LD extent, and percentage of genome covered
| Chromosome | Whole Genome | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | |||
| Physical Size (Mbp) | 301 | 237 | 232 | 241 | 217 | 169 | 176 | 175 | 156 | 150 | 2,058 | |
| Genetic Size (cM) | 268 | 211 | 188 | 150 | 205 | 129 | 148 | 182 | 145 | 139 | 1766 | |
| Physical LD extent (kbp) in low recombination regions | 306 | 491 | 846 | 808 | 658 | 418 | 547 | 497 | 899 | 815 | 629 | |
| Genetic LD Extent (cM) in high recombination regions | 0.062 | 0.027 | 0.033 | 0.022 | 0.031 | 0.019 | 0.012 | 0.038 | 0.023 | 0.019 | 0.029 | |
| Percent of physical genome covered | 50 K | 81% | 72% | 76% | 77% | 74% | 67% | 71% | 73% | 71% | 71% | 74% |
| 600 K | 98% | 88% | 91% | 89% | 90% | 84% | 81% | 90% | 87% | 84% | 89% | |
| GBS | 92% | 81% | 84% | 83% | 83% | 77% | 77% | 81% | 79% | 76% | 82% | |
| ALL | 98% | 90% | 92% | 90% | 91% | 87% | 83% | 92% | 88% | 85% | 90% | |
| Percent of genetic map covered | 50 K | 72% | 41% | 44% | 38% | 41% | 32% | 24% | 46% | 32% | 27% | 42% |
| 600 K | 96% | 71% | 76% | 68% | 72% | 62% | 47% | 78% | 63% | 53% | 71% | |
| GBS | 86% | 58% | 61% | 53% | 61% | 48% | 37% | 63% | 48% | 40% | 58% | |
| ALL | 97% | 74% | 78% | 72% | 74% | 65% | 51% | 81% | 66% | 57% | 74% | |
Genetic and Physical LD extent were obtained by adjusting Hill and Weir model’s on 100 different sets of 500,000 loci randomly sampled in high (> 0.5 cM / Mbp) and low (< 0.5 cM / Mbp) recombination regions, respectively. The value represented the average across these 100 sets. The percentage of genome coverage was estimated using markers with MAF > 5% and E(r2K) = 0.1, for each technology and for the three technologies combined (ALL: GBS + 600 K + 50 K)