Table 3.
Haplotypes inferred at each region and the fraction of chromosomes carrying each haplotype
|
Frequency
|
||||||
|---|---|---|---|---|---|---|
| Region | Haplotype | AK | BM | GR | LB | PK |
| 1 | GGTICAC | 0.09 | — | 0.78 | 0.33 | 0.20 |
| AGTICAC | — | 0.83 | 0.10 | 0.25 | 0.08 | |
| GGCDTTT | 0.12 | — | 0.10 | — | 0.58 | |
| GCTICAC | 0.38 | 0.18 | 0.03 | 0.20 | — | |
| GCCDTTT | 0.41 | — | — | — | — | |
| 2 | GCTCTTC | — | 0.08 | 0.30 | 0.53 | 0.60 |
| GGTCTTT | 0.12 | — | 0.60 | 0.23 | 0.10 | |
| ACATCCT | — | 0.78 | — | — | — | |
| ATATCCT | 0.68 | — | — | — | 0.15 | |
| ACTCTTC | — | 0.03 | 0.10 | 0.08 | 0.05 | |
| 3 | CATITC | 0.65 | 0.28 | 0.73 | 0.50 | 0.80 |
| GGCDGT | 0.24 | 0.73 | 0.28 | 0.28 | 0.20 | |
| 4 | CCTTATC | 0.47 | 0.38 | 0.20 | 0.13 | 0.55 |
| CCCGTCT | 0.09 | 0.15 | 0.05 | 0.38 | 0.30 | |
| AACGTCT | — | 0.13 | 0.65 | 0.40 | — | |
| CCCGACT | 0.26 | — | — | — | 0.15 | |
| AATTATC | — | 0.35 | — | — | — | |
| 5 | CADCAATAG | 0.09 | 0.45 | 0.15 | 0.28 | 0.60 |
| CAITATCCA | 0.35 | 0.05 | 0.40 | 0.25 | — | |
| GGITATCCA | 0.03 | 0.43 | 0.23 | 0.30 | — | |
| GGITCTCCA | 0.38 | — | — | — | 0.30 | |
| CAITCTCCA | 0.09 | 0.03 | 0.23 | 0.03 | 0.10 | |
| 6 | TCGIGCTT | — | 0.55 | — | — | 0.55 |
| CTADATTT | — | 0.33 | 0.40 | 0.28 | — | |
| CCGIGCTT | 0.62 | — | — | — | — | |
| CTADATCC | 0.12 | — | 0.10 | 0.30 | — | |
| CTAIGCTT | 0.06 | — | 0.05 | — | 0.30 | |
| CTAIGCTC | — | — | 0.30 | — | 0.08 | |
| TCGDATCC | — | — | 0.05 | 0.28 | — | |
| CCGIGCCC | 0.18 | 0.10 | — | — | — | |
| 7 | GCAAGATTA | — | 0.50 | 0.35 | 0.15 | — |
| GCGGGGCCG | 0.56 | — | — | — | 0.25 | |
| AGAGCACTA | — | 0.33 | 0.23 | — | — | |
| GCAGGGCCG | 0.06 | — | 0.10 | 0.28 | — | |
| AGAGCACCG | — | — | — | 0.03 | 0.35 | |
| GCGGGACTA | — | — | — | — | 0.28 | |
| AGGGCACCG | — | 0.10 | 0.03 | 0.10 | 0.03 | |
| 8 | GIGA | 0.59 | — | 0.40 | 0.75 | 0.70 |
| GDAG | 0.32 | 0.65 | 0.13 | — | 0.08 | |
| AIGA | — | — | 0.20 | 0.08 | 0.23 | |
| AIGG | — | 0.33 | — | — | — | |
| 9 | CCAATGG | 0.53 | 0.33 | 0.30 | 0.28 | 0.55 |
| TATGCTC | — | 0.20 | 0.45 | 0.43 | 0.33 | |
| TCTGCGC | 0.18 | — | 0.10 | 0.05 | 0.05 | |
| TATGCGC | — | 0.23 | — | 0.10 | — | |
| CCTGCGC | — | 0.23 | 0.03 | — | 0.05 | |
| CATGCGC | 0.18 | — | 0.05 | 0.08 | — | |
| 10 | ADTT | 0.32 | 0.18 | 0.18 | 0.28 | 0.88 |
| ADTG | 0.18 | 0.38 | 0.38 | 0.30 | — | |
| GIAT | 0.06 | 0.28 | 0.25 | 0.20 | 0.05 | |
| GDAT | 0.12 | 0.13 | 0.15 | 0.20 | 0.08 | |
Haplotypes that are observed on <5% of all chromosomes are not shown. Alleles for insertion/deletion polymorphisms are: (I) inserted; (D) deleted sequence. Note that the second marker in region 2 is a triallelic SNP. Haplotypes were inferred for these 10 regions since they contain at least four SNPs of ≥0.2 MAF in all breeds, and the SNPs span a distance of at least 9 kb. (AK) Akita; (BM) Bernese Mountain Dog; (GR) Golden Retriever; (LB) Labrador Retriever; (PK) Pekingese.