Table 2 Candidate regions, SNPs with topmost score in LR-GWAS, and associated genes that were identified by at least two methods of selection signature analysis between the high- (HR) and low-resistant (LR) sheep cohorts
From: Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep
Reg | OAR | Start | Stop | Size (Mb) | Method | Top SNP (LR-GWAS) | No. of genes | Genes (Top genea) | P value* | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
ROH | LR-GWAS | FST | XP-EHH | |||||||||
1 | 1 | 122,490,001 | 122,680,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR1_122581225 | 4 | TIAM1, LOC105616413, LOC105616409, LOC105616407 | 3.10E-06 |
2 | 1 | 226,950,001 | 227,160,000 | 0.210 | ✗ | ✓ | ✓ | ✗ | oar3_OAR1_227042621 | 5 | GFM1, LXN, MLF1, RSRC1, LOC105603699 | 2.55E-06 |
3 | 1 | 253,380,001 | 253,660,000 | 0.280 | ✗ | ✓ | ✓ | ✓ | oar3_OAR1_253478525 | 4 | LOC105604371, SLCO2A1, RAB6B, TF | 2.70E-06 |
4 | 2 | 51,910,001 | 52,140,000 | 0.230 | ✗ | ✓ | ✓ | ✗ | oar3_OAR2_52043939 | 7 | RNF38, GNE, CLTA, CCIN, GLIPR2, LOC101111253, RECK | 2.72E-06 |
5 | 2 | 53,110,001 | 53,250,000 | 0.140 | ✗ | ✗ | ✓ | ✓ | oar3_OAR2_53171448 | 4 | C2H9orf131, DNAJB5, KIAA1045, LOC101110212 | 1.79E-06 |
6 | 2 | 62,970,001 | 63,160,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR2_63061644 | 3 | ANXA1, LOC105607837, LOC105607840 | 2.68E-06 |
7 | 2 | 84,550,001 | 84,740,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR2_84646297 | 4 | BNC2, LOC105608204, LOC105608202, LOC105608200 | 3.47E-06 |
8 | 2 | 85,810,001 | 86,140,000 | 0.330 | ✗ | ✓ | ✗ | ✓ | oar3_OAR2_86046574 | 2 | ADAMTSL1, TRNAC-GCA | 3.18E-06 |
9 | 2 | 201,150,001 | 201,380,000 | 0.230 | ✗ | ✓ | ✓ | ✓ | oar3_OAR2_201281356 | 5 | LOC101102297, C2H2orf69, TYW5, C2H2orf47, LOC105610167 | 2.72E-06 |
10 | 3 | 183,020,001 | 183,260,000 | 0.240 | ✓ | ✓ | ✓ | ✗ | oar3_OAR3_183165082 | 2 | TRNAC-GCA, DENND5B | 2.76E-06 |
11 | 3 | 193,980,001 | 194,170,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR3_194077322 | 1 | PDE3A | 2.65E-06 |
12 | 3 | 213,290,001 | 213,550,000 | 0.260 | ✗ | ✓ | ✓ | ✗ | oar3_OAR3_213385724 | 11 | PEX26, TUBA8, CDC42EP1, LGALS2, GGA1, SH3BP1, PDXP, LGALS1, NOL12, TRIOBP, TRNAG-CCC | 2.70E-06 |
13 | 3 | 224,020,001 | 224,277,781 | 0.258 | ✗ | ✓ | ✓ | ✗ | oar3_OAR3_224118862 | 11 | NCAPH2, ODF3B, KLHDC7B, SYCE3, CPT1B, CHKB, MAPK8IP2, ARSA, SHANK3, ACR, RABL2B | 3.35E-06 |
14 | 4 | 48,760,001 | 49,000,000 | 0.240 | ✗ | ✓ | ✓ | ✗ | oar3_OAR4_48859309 | 5 | CBLL1, SLC26A3, LOC105611149, DLD, LAMB1 | 2.82E-06 |
15 | 5 | 44,110,001 | 44,300,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR5_44206370 | 3 | LOC105607063, LOC101104574, LOC105607061 | 2.68E-06 |
16 | 5 | 105,810,001 | 106,000,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR5_105908550 | 1 | MAN2A1 | 2.56E-06 |
17 | 6 | 5,580,001 | 5,770,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR6_5672674 | 2 | LOC101115459, MAD2L1 | 2.60E-06 |
18 | 8 | 2,520,001 | 2,710,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR8_2618920 | 2 | MYO, IMPG1 | 2.55E-06 |
19 | 8 | 27,780,001 | 27,970,000 | 0.190 | ✗ | ✓ | ✓ | ✓ | oar3_OAR8_27875909 | 7 | AK9, ZBTB24, MICAL1, SMPD2, PPIL6, POLE4, CD164 | 2.72E-06 |
20 | 8 | 63,260,001 | 63,450,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | OAR8_68144751.1 | 1 | NHSL1 | 2.59E-06 |
21 | 9 | 27,550,001 | 27,740,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR9_27644689 | 3 | TRIB, LOC105611791, NSMCE2 | 2.63E-06 |
22 | 9 | 33,820,001 | 34,010,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR9_33912632 | 2 | PCMTD1, ST18 | 2.60E-06 |
23 | 9 | 59,370,001 | 59,560,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR9_59469003 | 1 | LOC105611701 | 2.70E-06 |
24 | 11 | 6,640,001 | 6,830,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR11_6733973 | 1 | ANKFN1 | 2.82E-06 |
25 | 12 | 29,800,001 | 30,030,000 | 0.230 | ✗ | ✓ | ✓ | ✗ | oar3_OAR12_29939034 | 2 | KIF26B, LOC105616515 | 2.71E-06 |
26 | 12 | 54,300,001 | 54,490,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR12_54393290 | 4 | TNN, LOC105612227, KIAA0040, LOC105612225 | 2.58E-06 |
27 | 13 | 37,980,001 | 38,190,000 | 0.210 | ✗ | ✓ | ✓ | ✓ | oar3_OAR13_38099599 | 2 | SLC24A3, LOC105616699 | 2.30E-06 |
28 | 15 | 958,579 | 1,427,669 | 0.469 | ✓ | ✗ | ✗ | ✓ | s55467.1 | 5 | MRE11A, ANKRD49, AASDHPPT, KBTBD3, MSANTD4 | 1.46E-06 |
29 | 15 | 5,510,001 | 5,720,000 | 0.210 | ✗ | ✓ | ✓ | ✗ | oar3_OAR15_5627753 | 3 | MMP27, MMP20, MMP7 | 2.73E-06 |
30 | 15 | 17,290,001 | 17,690,000 | 0.400 | ✗ | ✓ | ✓ | ✓ | oar3_OAR15_17387492 | 3 | NPAT, ATM, C15H11orf65 | 3.01E-06 |
31 | 15 | 20,560,001 | 20,730,000 | 0.170 | ✗ | ✓ | ✓ | ✓ | oar3_OAR15_20686078 | 1 | LOC105602151 | 1.71E-06 |
32 | 16 | 1,420,001 | 1,610,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR16_1510505 | 4 | LOC105602434, SPDL1, LOC105602438, DOCK2 | 2.68E-06 |
33 | 16 | 2,280,001 | 2,470,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR16_2373107 | 3 | KCNIP1, KCNMB1, LOC105602444 | 2.93E-06 |
34 | 16 | 12,310,001 | 12,500,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR16_12408278 | 4 | LOC105602490, CD180, LOC105602489, MAST4 | 2.55E-06 |
35 | 16 | 16,060,001 | 16,250,000 | 0.190 | ✗ | ✓ | ✓ | ✓ | oar3_OAR16_16150781 | 1 | LOC105602500, LOC105602501 | 3.40E-06 |
36 | 16 | 53,590,001 | 53,780,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR16_53686329 | 2 | CDH18, TRNAW-CCA | 2.60E-06 |
37 | 18 | 23,520,001 | 23,880,000 | 0.360 | ✓ | ✓ | ✓ | ✗ | oar3_OAR18_23760534 | 2 | EFTUD1, MEX3B | 2.65E-06 |
38 | 18 | 33,990,001 | 34,180,000 | 0.190 | ✗ | ✓ | ✗ | ✓ | oar3_OAR18_34086919 | 1 | STXBP6 | 2.59E-06 |
39 | 18 | 39,710,001 | 40,000,000 | 0.290 | ✗ | ✓ | ✓ | ✗ | oar3_OAR18_39823086 | 1 | LOC105603171 | 3.14E-06 |
40 | 19 | 880,001 | 1,070,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR19_977383 | 3 | LOC105603323, LOC105603324, LOC105603325 | 2.60E-06 |
41 | 19 | 9,910,001 | 10,100,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR19_10008059 | 1 | STAC | 2.64E-06 |
42 | 21 | 38,480,001 | 38,690,000 | 0.210 | ✗ | ✓ | ✓ | ✗ | oar3_OAR21_38598176 | 7 | LOC105601927, LOC101106045, LOC101104869, LOC101106295, LOC105604093, LOC101106556, LOC101106809 | 2.89E-06 |
43 | 21 | 38,646,061 | 38,906,932 | 0.261 | ✓ | ✓ | ✓ | ✗ | oar3_OAR21_38573588 | 9 | LOC101106556, LOC101106809, LOC101105115, LOC101107054, PAG6, LOC105604095, LOC443348, LOC101107317, LOC101107562 | 2.83E-06 |
44 | 21 | 40,520,001 | 40,710,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR21_40617710 | 9 | STX5, WDR74, LOC101116519, SLC3A2, CHRM1, LOC101112776, TRNAE-UUC, LOC101117286, SLC22A8 | 2.89E-06 |
45 | 25 | 19,550,001 | 19,740,000 | 0.190 | ✗ | ✓ | ✓ | ✗ | oar3_OAR25_19649912 | 2 | REEP3, LOC101122571 | 2.60E-06 |
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