Table 4 Candidate regions, associated genes and QTLs that overlapped between at least two methods of detecting selection signatures.
From: Genome-wide insights on gastrointestinal nematode resistance in autochthonous Tunisian sheep
Reg | OAR | Start | Stop | Size (Mb) | Method | Top SNP (LR-GWAS) | P_value* | No. of genes | Genes (Top genea) | QTL, Trait name | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 1 | 109,500,001 | 109,800,000 | 0.300 | – | LR | FST | – | OAR1_109621789 | 0.00047 | 7 | CASQ1, PEA15, DCAF8, PEX19, COPA, NCSTN, VANGL2 | FECGEN (QTL#13987), Fecal egg count |
2 | 1 | 111,479,835 | 111,679,835 | 0.200 | – | LR | – | XP-EHH | OAR1_111579835 | 0.00012 | 3 | OLFML2B, SNORA70, ENSOARG00000025560 | FECGEN (QTL #13987), Fecal egg count |
3 | 1 | 116,100,001 | 116,254,820 | 0.155 | ROH | – | – | XP-EHH | OAR1_116606247 | 0.00940 | 1 | FAM78B | FECGEN (QTL #13987), Fecal egg count |
4 | 2 | 60,224,723 | 60,504,322 | 0.280 | – | LR | – | XP-EHH | OAR2_60345435 | 0.00001 | 1 | PCSK5 | HCWT (QTL#14279), Hot carcass weight; BW (QTL#14280), Body weight slaughter |
5 | 2 | 203,600,001 | 203,800,000 | 0.200 | – | LR | FST | XP-EHH | OAR2_215596955.1 | 0.00018 | 2 | BMPR2, FAM117B | HCWT (QTL#14279, 14253), Hot carcass weight; BW (QTL# 14280, 14254), Body weight slaughter |
6 | 3 | 4,000,001 | 4,300,000 | 0.300 | – | LR | – | XP-EHH | OAR3_4118423 | 0.00011 | 5 | AK8, GTF3C4, DDX31, AK8, BARX1, CFAP77 | HFEC (QTL#12897), Haemonchus contortus FEC |
7 | 3 | 26,314,565 | 26,514,565 | 0.200 | – | LR | – | XP-EHH | OAR3_26114621 | 0.00001 | 3 | RDH14 (LOC105601856), LOC101102216, RDH14 U6 | TFEC_1 (QTL #14155), Trichostrongylus colubriformis FEC |
8 | 3 | 201,773,340 | 202,015,539 | 0.242 | – | LR | FST | – | OAR3_201915539 | 0.00006 | 7 | HEBP1, GPRC5D, GPRC5A, DDX47, HEBP1, CDKN1B, U6, SEC61B | NFEC (QTL #12882), Nematodirus FEC; FECGEN (QTL #16023), Fecal egg count |
9 | 4 | 35,495,115 | 35,695,115 | 0.200 | ROH | LR | – | – | OAR4_35595115 | 0.00047 | 3 | SEMA3D, U6, ENSOARG00000015210 | BW (QTL# 17232), Body weight |
10 | 5 | 41,700,001 | 42,000,000 | 0.300 | – | LR | – | XP-EHH | OAR5_41807859 | 0.00071 | 9 | PDHB, SOWAHA, SHROOM1, PDHB, GDF9, UQCRQ, LEAP2, AFF4, ZCCHC10, HSPA4 | BIRTH_WT (QTL# 12934), Body weight (birth) |
11 | 5 | 51,800,001 | 52,200,000 | 0.400 | – | LR | – | XP-EHH | OAR5_51959486 | 0.00015 | 1 | NR3C1 | BIRTH_WT (QTL# 12934), Body weight (birth) |
12 | 5 | 60,100,001 | 60,400,000 | 0.300 | – | LR | – | XP-EHH | OAR5_60271682 | 0.00036 | 3 | SLC2A1, SLC2A2, FAT2 | BIRTH_WT (QTL# 12934), Body weight (birth) |
13 | 5 | 19,583,479 | 19,802,720 | 0.219 | – | LR | – | XP-EHH | OAR5_19741661 | 0.00012 | 4 | SLC22A5, SLC22A4, PDLIM4, P4HA2 | BIRTH_WT (QTL# 12934), Body weight (birth) |
14 | 5 | 49,789,923 | 49,930,854 | 0.141 | ROH | LR | FST | XP-EHH | OAR5_49867927 | 0.00002 | 3 | LOC101104745 (PCDHGA1, (PCDHGA2), ENSOARG00000000218 | BIRTH_WT (QTL# 12934), Body weight (birth) |
15 | 6 | 59,200,001 | 59,500,000 | 0.300 | – | LR | – | XP-EHH | OAR6_59306993 | 0.00031 | 4 | RHOH, U6, CHRNA9, RHOH, RBM47 | FECGEN (QTL#16024), Fecal egg count |
16 | 6 | 66,102,303 | 66,300,000 | 0.198 | – | LR | – | XP-EHH | OAR6_66202303 | 2 | ATP10D, CORIN | BW (QTL#14284), Body weight (slaughter) | |
17 | 7 | 71,965,934 | 72,165,934 | 0.200 | – | LR | – | XP-EHH | OAR7_72145128 | 0.00002 | 3 | KCNH5, U6, ENSOART00000001032 | – |
18 | 8 | 85,300,001 | 85,600,000 | 0.300 | – | LR | FST | – | OAR8_86573428 | 0.00019 | 2 | PACRG, QKI | LATRICH_2 (QTL #11289912900), Trichostrongylus adult and larva count; FECGEN (QTL# 16025), Fecal egg count |
19 | 10 | 18,948,900 | 19,000,000 | 0.051 | ROH | – | – | XP-EHH | OAR10_18864674 | 0.00490 | 1 | ENSOARG00000005934 | FATWT (QTL#14292), fat weight in carcass; LMYP (QTL #14295), Lean meat yield percentage |
20 | 11 | 18,200,001 | 18,400,000 | 0.200 | – | LR | – | XP-EHH | OAR11_18201426 | 0.00001 | 4 | EVI2A, EVI2B, OMG, NF1 | LATRICH_2 (QTL #12901), Trichostrongylus adult and larva count |
21 | 11 | 43,600,001 | 43,900,000 | 0.300 | – | LR | FST | – | OAR11_43778741 | 0.00015 | 5 | ITGA2B, GPATCH8, FZD2, CCDC43, DBF4B | LATRICH_2 (QTL #12901), Trichostrongylus adult and larva count |
22 | 11 | 45,300,001 | 45,600,000 | 0.300 | – | LR | FST | – | OAR11_45447832 | 0.00029 | 2 | MAPT, KANSL1 | LATRICH_2 (QTL #12901), Trichostrongylus adult and larva count, IGA (QTL #95626), Immunoglobulin A level |
23 | 12 | 74,300,001 | 74,351,694 | 0.052 | – | LR | – | XP-EHH | OAR12_74469905 | 0.00001 | 1 | CRB1 | IGA (QTL #95627), Immunoglobulin A level |
24 | 13 | 28,900,001 | 29,300,000 | 0.400 | – | LR | FST | – | OAR13_29024037 | 0.00073 | 2 | FAM171A1, ITGA8 | SAOS (QTL #17198), Salmonella abortusovis susceptibility |
25 | 14 | 33,865,674 | 34,065,674 | 0.200 | – | LR | – | XP-EHH | OAR14_34068678 | 0.00021 | 11 | TERB1, NAE1, CA7, PDP2, CDH16, RRAD, CIAO2B (FAM96B), CES2, CES3, CES4A, CBFB | NFEC (QTL #12892), Nematodirus FEC; NFEC (QTL #12893), Nematodirus FEC |
26 | 14 | 35,554,237 | 35,796,467 | 0.242 | ROH | LR | FST | – | OAR14_35677446 | 0.00050 | 5 | TANGO6, CHTF8, UTP4, SNTB2, ENSOARG00000003488 | NFEC (QTL #12892), Nematodirus FEC; NFEC (QTL #12893), Nematodirus FEC |
27 | 17 | 34,359,503 | 34,611,364 | 0.252 | – | LR | FST | – | OAR17_34459503 | 0.00055 | 4 | FGF2 (SPATA5), NUDT6, U4, ENSOARG00000023095 | – |
28 | 17 | 58,100,001 | 58,578,009 | 0.478 | – | LR | FST | XP-EHH | OAR17_58269871 | 0.00071 | 1 | MED13L | – |
29 | 17 | 18,417,447 | 18,500,000 | 0.083 | – | LR | – | XP-EHH | OAR17_18517447 | 0.00017 | 1 | ENSOARG00000025659 | FECGEN (QTL #16031), Fecal egg count; IGA (QTL #95633), Immunoglobulin A level |
30 | 18 | 17,337,561 | 17,537,561 | 0.200 | – | LR | – | XP-EHH | OAR18_17468231 | 0.00001 | – | – | SAOS (QTL #17199), Salmonella abortusovis susceptibility |
31 | 18 | 20,100,001 | 20,400,000 | 0.300 | – | LR | – | XP-EHH | OAR18_20256893 | 0.00031 | 9 | TICRR, KIF7, PLIN1, PEX11A, WDR93, TRNAK-CUU, MESP2, ANPEP | WORMCT (QTL#19806), Worm count; SAOS (QTL #17199), Salmonella abortusovis susceptibility |
32 | 21 | 38,800,001 | 39,100,000 | 0.300 | – | LR | – | XP-EHH | OAR21_38935734 | 0.00010 | 1 | PAG6 | PEPSL (QTL#126104, 126105, 126106) Pepsinogen level; CEOSIN (QTL#14157), Change in eosinophil number; SAOS (QTL #17195), Salmonella abortusovis susceptibility |
33 | 24 | 3,724,161 | 3,927,939 | 0.204 | – | LR | – | XP-EHH | OAR24_3802371 | 0.00001 | 9 | C16orf96, MGRN1, NUDT16L1, ANKS3, SEPTIN12 (SEPT12), ROGDI, GLYR1, C24H16orf71, ENSOARG00000003885 | BONE_WT (QTL#14315), Bone weight in carcass |
34 | 25 | 14,000,001 | 14,300,000 | 0.300 | – | LR | – | XP-EHH | OAR25_14136891 | 0.00091 | 1 | BICC1 | – |
35 | 26 | 42,900,001 | 42,931,347 | 0.031 | – | LR | FST | XP-EHH | OAR26_43044064 | 0.00002 | 1 | ZNF385D | – |
