Table 2.
ROH peaks indicated by single nucleotide polymorphisms (SNP) occurring in an ROH in more than 40% of the individuals of the respective goat population
| Breed | Start SNP | End SNP | Chr1 | nSNP | From2 | To2 | Annotated genes3 |
|---|---|---|---|---|---|---|---|
| Barki | snp30392-scaffold335-200469 | snp30397-scaffold335-418126 | 12 | 6 | 50,047,521 | 50,253,456 | RNF17 |
| snp54264-scaffold828-29085 | snp15260-scaffold1625-7565 | 18 | 15 | 60,120,713 | 61,158,064 | ||
| Boer | snp27343-scaffold2904-5676 | ilmnseq_rs119103308 | 18 | 15 | 15,731,287 | 16,105,667 | SPG7, CPNE7, SPATA2L, ZNF276, TCF25, MC1R |
| snp31127-scaffold3444-44647 | GoatD01.018893 | 18 | 22 | 60,178,927 | 61,711,572 | ||
| QTLSaanen19.36_O | QTLSaanen19.47_O | 19 | 22 | 26,676,012 | 27,087,979 | PHF23, GABARAP, TMEM95, SPEM1, FGF11, TNFSF12, TNFSF13, CD68, SOX15 | |
| 6_5343525_AF-PAKI | 6_5343525_AF-PAKI | 6 | 1 | 5,343,525 | 5,343,525 | ||
| snp18690-scaffold189-404920 | snp18687-scaffold189-286736 | 6 | 4 | 5,426,581 | 5,545,798 | ||
| snp17777-scaffold1844-103982 | Random2.2 K-637 | 6 | 7 | 6,514,342 | 6,755,014 | ||
| ilmnseq_rs669256409 | snp58095-scaffold94-5505002 | 6 | 16 | 70,744,246 | 70,834,128 | KIT | |
| Damascus | ilmnseq_rs662787102 | ilmnseq_rs635694893 | 6 | 5 | 71,146,873 | 71,150,677 | KDR |
| Egyptian Nubian | snp5758-scaffold1202-226615 | snp15101-scaffold1613-34525 | 13 | 10 | 41,738,246 | 42,085,766 | CST3, CST7 |
| snp56019-scaffold873-331410 | snp59699-scaffold99-95183 | 18 | 22 | 15,776,603 | 16,198,866 | MC1R | |
| snp30840-scaffold340-1887718 | snp30815-scaffold340-824448 | 6 | 24 | 13,498,678 | 14,563,391 | ALPK1, TIFA | |
| snp12525-scaffold148-867870 | snp12531-scaffold148-1222465 | 6 | 6 | 31,990,015 | 32,349,183 | ||
| snp12552-scaffold148-2118357 | snp12570-scaffold148-2915803 | 6 | 18 | 33,249,084 | 34,054,242 | ||
| snp12572-scaffold148-2999472 | snp12580-scaffold148-3342396 | 6 | 10 | 34,138,098 | 34,484,359 | ||
| snp26768-scaffold281-1436966 | snp26799-scaffold281-2778330 | 6 | 31 | 38,091,565 | 39,437,063 | ||
| snp7248-scaffold1268-14447 | snp54008-scaffold821-914173 | 6 | 36 | 39,985,135 | 41,385,076 | ||
| snp5662-scaffold1199-2118633 | snp12889-scaffold1498-459920 | 6 | 26 | 44,424,892 | 45,863,398 | DHX15, PI4K2B | |
| snp58085-scaffold94-5127553 | snp58098-scaffold94-5630065 | 6 | 28 | 70,454,815 | 70,959,830 | ||
| snp58100-scaffold94-5714186 | snp58110-scaffold94-6171823 | 6 | 37 | 71,044,898 | 71,495,883 |
1Chromosome, 2Location in base pairs, 3Based on the Ensembl database. ROH Runs of homozygosity