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Table 2 Suggestive and significant QTL for trait hours of survival after WSSV challenge detected using PLINK (QFAM total) and GenAbel (FASTA and GRAMMAS) analyses in 7 P. monodon families

From: QTL for white spot syndrome virus resistance and the sex-determining locus in the Indian black tiger shrimp (Penaeus monodon)

LG Pos SNP Test N Effect Stat P-value Sig GeneID
1 60.3 39454_862 GRAMMAS 1007 1.14(0.53) 4.66 0.0032   unknown
2 0 47460_2015 QFAM 1024 -4.538 56.81 0.0094   dna p58 subunit
2 21.6 52022_4578 QFAM 1020 6.351 83.1 0.0049   plasminogen activator inhibitor 1 rna-binding protein
2 24.5 50149_330 FASTA 983 3.32(1.03) 10.49 0.0014   thyroid transcription factor 1-associated protein 26-like protein
2 24.5 50149_330 GRAMMAS 983 1.65(0.71) 5.44 0.0015   thyroid transcription factor 1-associated protein 26-like protein
2 30.5 52064_948 GRAMMAS 1007 0.95(0.49) 3.79 0.008   polymerase I polypeptide 194kda
2 36.6 36607_579 GRAMMAS 1006 -0.91(0.46) 3.94 0.0068   unknown
2 53.5 28698_101 GRAMMAS 965 -1.01(0.48) 4.4 0.0042   unknown
2 53.5 28698_101 FASTA 965 -1.75(0.65) 7.22 0.0082   unknown
2 61.8 51997_2402 QFAM 1023 -5.49 139.2 0.0009 * runt protein 1a
2 62.5 35650_1855 FASTA 1004 2.11(0.79) 7.23 0.0081   unknown
2 62.5 35650_1855 QFAM 1018 5.408 100.5 0.0085   unknown
3 14.6 38676_1386 QFAM 1021 -4.2 41.79 0.0069   actin-binding rho-activating
3 29.5 41442_2163 GRAMMAS 1006 -1.35(0.55) 5.99 0.0008 * flagellar hook-length control protein flik
3 29.5 41442_2163 FASTA 1006 -1.88(0.68) 7.62 0.0066   flagellar hook-length control protein flik
5 21.2 45605_1545 FASTA 1007 7.34(1.94) 14.26 0.0002 * ubiquitin domain-containing protein ubfd1
5 21.2 45605_1545 GRAMMAS 1007 2.42(1.06) 5.22 0.0018   ubiquitin domain-containing protein ubfd1
5 21.9 35133_160 FASTA 991 -2.98(0.96) 9.56 0.0023   unknown
5 21.9 35133_160 GRAMMAS 991 -1.42(0.65) 4.81 0.0028   unknown
5 22.3 44076_3116 GRAMMAS 1004 -1.15(0.49) 5.4 0.0015   vacuolar proton atpase
5 22.3 44076_3116 FASTA 1004 -1.82(0.65) 7.79 0.006   vacuolar proton atpase
5 87 45237_316 GridQTL 1024 11.96(2.44) 24 0.0048 *  
5 96.5 30527_111 FASTA 992 -1.88(0.68) 7.67 0.0064   unknown
6 17.3 29124_228 FASTA 1007 4.82(1.34) 12.88 0.0004 * paired-like homeodomain transcription factor 3
6 17.3 29124_228 GRAMMAS 1007 1.49(0.71) 4.42 0.0042   paired-like homeodomain transcription factor 3
6 39 50756_3741–46539_1081 GridQTL 1024 11.25(2.32) 23.54 0.0098 *  
6 42.8 33044_1018 FASTA 1007 3.65(1.15) 10.07 0.0018   erythrocyte band 7 integral membrane protein
8 45.4 52776_1335 QFAM 1021 5.849 56.79 0.0036   abb73282reverse transcriptase
9 10.4 42679_345 QFAM 1007 4.823 81.8 0.0039   unknown
9 59.9 48064_77 QFAM 1024 4.807 126.6 0.0072   unknown
11 24.7 60951_72 FASTA 1007 -3.46(1.14) 9.2 0.0028   unknown
11 24.7 60951_72 GRAMMAS 1007 -1.37(0.68) 4.05 0.0061   unknown
11 38.1 46551_1072 QFAM 1024 5.642 135.6 0.0016   multidrug resistance-associated protein 14
11 59.4 23272_344 FASTA 1007 3.52(1.33) 7.01 0.0091   26 s protease regulatory subunit
13 18 29098_2532 QFAM 1024 3.95 50.35 0.0076   actin-binding homolog 1
14 49.5 40042_2041 QFAM 1021 4.192 46.08 0.0046   unknown
15 27.2 32667_1134 QFAM 1023 -5.196 104.9 0.0067   usick-kaufman syndrome
15 47.8 44399_644 FASTA 1007 2.28(0.78) 8.61 0.0039   unknown
16 11 42291_720 GRAMMAS 1007 2.13(0.93) 5.24 0.0018   adp-ribosylation factor-like 2 binding protein
16 11 42291_720 FASTA 1007 4(1.34) 8.91 0.0033   adp-ribosylation factor-like 2 binding protein
16 11 38195_1528 FASTA 1003 2.46(0.84) 8.52 0.0041   fanconi anemia group a protein homolog
16 23.4 45647_100 QFAM 1018 -4.662 56.63 0.009   glutamyl-trna amidotransferase subunit
16 38.1 35920_135 QFAM 1012 3.142 43.9 0.0018   unknown
16 39.2 5999_123 QFAM 1024 6.677 92.39 0.0049   unknown
17 8.3 39727_708 GRAMMAS 1007 0.82(0.41) 4.01 0.0063   unknown
17 26.7 26178_2213 QFAM 1018 -4.67 78.32 0.0067   bobby sox
17 29 47941_2759 FASTA 1007 2.75(1.01) 7.34 0.0076   alsin isoform 2
17 54 25133_74 to 36717_243 GridQTL 1024 22.90 (2.42) 89.81 0.0001 **  
18 15.1 44821_270 FASTA 1006 7.26(1.85) 15.34 0.0001 ** unknown
18 15.1 44821_270 GRAMMAS 1006 3.35(1.2) 7.83 0.0001 ** unknown
18 81.5 24411_90 GRAMMAS 1006 -0.9(0.46) 3.83 0.0076   unknown
19 34.8 35006_276 QFAM 1024 5.931 92.83 0.0011   alanyl-trna synthetase
19 44.5 14555_138 QFAM 1021 6.616 125.5 0.006   unknown
19 70.9 51029_2543 QFAM 1023 -3.578 40.82 0.0029   insulin receptor substrate 1
19 82.4 50096_1789 QFAM 1021 5.243 77.12 0.0005 * ankyrin repeat
20 23.1 36484_493 FASTA 1007 3.48(1.31) 7.01 0.0091   mitochondrial ribosomal protein l2
20 63.1 42447_399 GRAMMAS 1007 -1.14(0.57) 4.04 0.0062   unknown
20 63.1 42447_399 FASTA 1007 -2.26(0.84) 7.26 0.008   unknown
21 20.1 47262_891 GRAMMAS 1007 -0.93(0.45) 4.19 0.0053   myostatin 1b
21 20.1 47262_891 FASTA 1007 -1.75(0.66) 7.17 0.0084   myostatin 1b
21 20.1 47262_891 QFAM 1024 -4.787 82.96 0.0017   myostatin 1b
21 26 30265_1829 FASTA 1007 1.96(0.68) 8.44 0.0042   unknown
21 26 30265_1829 GRAMMAS 1007 0.88(0.43) 4.2 0.0052   unknown
21 28.5 29404_373 GRAMMAS 1007 1.26(0.63) 4.05 0.0061   unknown
21 28.8 19638_158 QFAM 1011 4.032 45.59 0.008   unknown
21 89.5 40988_772 GRAMMAS 1007 -0.98(0.5) 3.77 0.0082   c12orf66-like
22 9.1 52229_3858 GRAMMAS 1003 -1.08(0.55) 3.8 0.0079   nucleolar pre-ribosomal-associated protein 1-like
22 20.8 25410_46 GRAMMAS 986 -1.13(0.51) 4.96 0.0024   unknown
22 27.9 18472_352 FASTA 1007 -2.11(0.76) 7.69 0.0063   unknown
22 27.9 18472_352 GRAMMAS 1007 -0.98(0.49) 3.97 0.0066   unknown
22 27.9 18472_352 QFAM 1024 -5.815 104.9 0.0001 ** unknown
23 83.5 41044_732 QFAM 1024 5.885 110.7 0.0043   unknown
24 0.4 49156_279 GRAMMAS 1007 1.11(0.55) 4.13 0.0056   haspin
24 0.4 49156_279 FASTA 1007 2.21(0.81) 7.43 0.0073   haspin
24 50.3 51251_2007 QFAM 1018 -5.541 141.1 0.0023   cub-serine protease
25 0 44977_264 QFAM 1024 4.927 61.93 0.004   unknown
26 0.6 52048_2568 GRAMMAS 992 -1.12(0.57) 3.8 0.0079   adenosine monophosphate-protein transferase ficd homolog
26 0.6 52048_2568 QFAM 1009 -6.31 89.68 0.002   adenosine monophosphate-protein transferase ficd homolog
26 8.5 44451_587 QFAM 1023 5.597 76.98 0.0021   unknown
26 58.9 33059_367 QFAM 1024 -5.422 69.94 0.0059   unknown
27 40 18687_338-33729_523 GridQTL 1024 8.64(2.39) 13.04 0.018 *  
27 52.7 47625_1438 GRAMMAS 1006 -0.99(0.52) 3.7 0.0087   unknown
27 63.6 33004_1869 GRAMMAS 1007 -1.26(0.59) 4.51 0.0038   unknown
27 91.9 43302_1775 FASTA 1007 2.2(0.8) 7.54 0.0069   dead box atp-dependent rna helicase
27 91.9 43302_1775 GRAMMAS 1007 0.98(0.51) 3.73 0.0085   dead box atp-dependent rna helicase
27 101.7 49263_1068 GRAMMAS 1007 1.67(0.77) 4.73 0.003   unknown
27 101.7 49263_1068 FASTA 1007 3.12(1.11) 7.94 0.0055   unknown
28 20.8 51400_2931 GRAMMAS 1006 1.32(0.63) 4.38 0.0043   unknown
28 20.8 51400_2931 QFAM 1019 4.917 43.37 0.0089   unknown
28 30.6 47112_509 FASTA 1006 -2.82(0.87) 10.63 0.0013   chorion peroxidase
29 29.7 52042_128 QFAM 1022 4.654 94.7 0.0065   multiple c2 domain and transmembrane region
29 44 43412_2186 GRAMMAS 1007 -1.35(0.71) 3.58 0.0099   gpi-anchor transamidase
29 53.7 32409_114 FASTA 1005 1.86(0.71) 6.92 0.0096   unknown
30 77.3 51299_1729 QFAM 1016 4.115 60.01 0.0047   breast carcinoma-amplified sequence 3 homolog isoform 1
31 14.7 36096_367 FASTA 1007 3.82(1.24) 9.49 0.0024   nucleostemin-like protein
32 36.6 47777_1061 FASTA 1002 -1.82(0.7) 6.85 0.01   exonuclease 3–5 domain-containing protein 2 isoform 1
32 36.6 47777_1061 QFAM 1012 -4.716 76.83 0.0035   exonuclease 3–5 domain-containing protein 2 isoform 1
34 32.3 24101_537 GRAMMAS 1007 -1.56(0.72) 4.67 0.0032   zinc finger protein 64-like
34 32.3 24101_537 FASTA 1007 -2.68(0.99) 7.25 0.008   zinc finger protein 64-like
36 29.6 30057_491 QFAM 1023 -5.252 75.55 0.009   unknown
36 32.1 49829_3826 QFAM 962 -4.221 71.99 0.0044   unknown
36 57.6 50839_3313 GRAMMAS 1007 1.72(0.81) 4.54 0.0037   transcriptional enhancer factor tef-
36 57.6 50839_3313 FASTA 1007 3.08(1.14) 7.33 0.0077   transcriptional enhancer factor tef-
38 36.1 35013_386 FASTA 1007 -2.31(0.72) 10.32 0.0016   unknown
38 36.1 35013_386 GRAMMAS 1007 -0.88(0.42) 4.36 0.0044   unknown
38 66.9 17589_451 GRAMMAS 1004 1.67(0.82) 4.12 0.0056   unknown
39 0.2 35101_271 QFAM 1021 4.295 57.77 0.0045   unknown
39 51.2 49386_1117 QFAM 1024 -5.859 109.8 0.0086   phospholipase c gamma
39 59.4 36972_442 FASTA 1004 -1.85(0.66) 7.82 0.0059   unknown
39 59.4 36972_442 GRAMMAS 1004 -0.83(0.42) 3.86 0.0074   unknown
40 22.9 51885_4402 QFAM 1024 5.687 50.84 0.007   chromodomain-helicase-dna-binding protein 1
40 68.1 11637_107 QFAM 1020 -7.046 129.7 0.0083   non-lysosomal glucosylceramidase
41 1.6 26900_757 QFAM 1021 -7.651 113.7 0.0079   unknown
42 59 35645_15 GRAMMAS 1005 0.99(0.46) 4.73 0.003   unknown
43 0.4 27976_64 GRAMMAS 990 -1.4(0.52) 7.3 0.0002 * unknown
43 0.4 27976_64 FASTA 990 -1.84(0.64) 8.39 0.0044   unknown
44 0 38601_555 FASTA 1007 -2.39(0.88) 7.41 0.0074   unknown
44 0 38601_555 GRAMMAS 1007 -1.1(0.57) 3.77 0.0081   unknown
44 3.2 42369_480 QFAM 1024 -5.011 91.99 0.0058   tbc1 domain family member 14 isoform a
44 26 51212_1738 QFAM 1024 6.066 107 0.0063   sodium bicarbonate transporter-like protein 11
44 40.4 20208_30 GRAMMAS 1007 1.55(0.79) 3.8 0.0078   unknown
  1. LG, linkage group; Pos, location on LG in centimorgans; N, number of progeny and parents analysed; Effect, allele substitution effect of the minor allele with standard error in parenthesis (FASTA, GRAMMAS and GridQTL), Beta (QFAM); Stat, test statistic linear regression coefficient for QFAM, chi-square with one degree of freedom for FASTA and GRAMMAS analyses, F-statistic for GridQTL; P, point-wise empirical P-value (QFAM), permuted P-value with one degree of freedom corrected for inflation factor lambda (FASTA and GRAMMAS) or chromosome-wide P search with permutation and bootstrap analysis (GridQTL); Sig, significance after Bonferroni correction (*P < 0.05; **P < 0.01). GeneID, closest SNP homology from BLAST. Tests were considered suggestive when P < 0.01 before Bonferroni correction.