Table 4.
Suggestive and significant QTL for trait hours of survival after challenge with A. hydrophila detected using PLINK (QFAM) and GenAbel (FASTA and GRAMMA) analyses in 21 L. rohita families
| LG | Pos | SNP | Test | N | Effect | Stat | P -value | Sig | GeneID |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
37.3 |
55086_181 |
FASTA |
963 |
-2.22(0.82) |
7.32 |
0.0068 |
|
Small heat shock |
| 1 |
37.3 |
55086_181 |
GRAMMA |
963 |
-1.18 (0.56) |
4.47 |
0.00538 |
|
Small heat shock |
| 2 |
43.9 |
121615_93 |
QFAM |
1021 |
|
-1.449 |
0.00675 |
|
|
| 2 |
47.4 |
6937_74 |
QFAM |
1022 |
|
1.48 |
0.00772 |
|
|
| 2 |
48.4 |
61599_86 |
QFAM |
1022 |
|
1.48 |
0.00708 |
|
|
| 2 |
48.4 |
83153_20 |
QFAM |
1022 |
|
1.48 |
0.00775 |
|
|
| 3 |
20.3 |
68284_87 |
GRAMMA |
979 |
-1.12 (0.57) |
3.85 |
0.00979 |
|
|
| 4 |
0 |
84080_123 |
GRAMMA |
978 |
1.05 (0.5) |
4.4 |
0.00575 |
|
|
| 4 |
0 |
84080_123 |
QFAM |
1021 |
|
1.708 |
0.00232 |
|
|
| 4 |
19.7 |
65405_244 |
FASTA |
979 |
-2.07(0.73) |
7.95 |
0.00482 |
|
|
| 4 |
19.7 |
65405_244 |
GRAMMA |
979 |
-1.26 (0.55) |
5.21 |
0.00268 |
|
|
| 4 |
46.8 |
110358_408 |
FASTA |
979 |
2.18(0.71) |
9.33 |
0.00226 |
|
c-type natriuretic peptide 1 precursor |
| 4 |
46.8 |
110358_408 |
GRAMMA |
979 |
1.3 (0.53) |
5.96 |
0.00131 |
* |
c-type natriuretic peptide 1 precursor |
| 4 |
46.8 |
110358_408 |
QFAM |
1022 |
|
2.058 |
0.00867 |
|
c-type natriuretic peptide 1 precursor |
| 5 |
9.6 |
4797_109 |
FASTA |
978 |
-1.57(0.55) |
8.06 |
0.00452 |
|
|
| 5 |
9.6 |
4797_109 |
GRAMMA |
978 |
-0.92 (0.41) |
5.06 |
0.00307 |
|
|
| 5 |
23.8 |
83820_94 |
FASTA |
979 |
-2.05(0.72) |
8.14 |
0.00434 |
|
Brain specific kinase 146 |
| 5 |
23.8 |
83820_94 |
GRAMMA |
979 |
-0.97 (0.48) |
4.12 |
0.00753 |
|
Brain specific kinase 146 |
| 5 |
38.3 |
1886_343 |
FASTA |
979 |
1.71(0.64) |
7.24 |
0.00712 |
|
loc100037090 protein |
| 5 |
38.3 |
1886_343 |
QFAM |
1022 |
|
1.826 |
0.00577 |
|
loc100037090 protein |
| 5 |
43.4 |
53540_630 |
FASTA |
976 |
2.76(0.92) |
9.03 |
0.00265 |
|
protein phosphatase regulatory subunit 10 |
| 5 |
43.4 |
53540_630 |
GRAMMA |
976 |
1.28 (0.59) |
4.71 |
0.00429 |
|
Protein phosphatase Regulatory subunit 10 |
| 5 |
43.4 |
75322_75 |
QFAM |
1022 |
|
-1.517 |
0.00759 |
|
|
| 7 |
23.4 |
62374_157 |
FASTA |
968 |
-3.59(1.04) |
11.99 |
0.00053 |
* |
|
| 7 |
23.4 |
62374_157 |
GRAMMA |
968 |
-2.26 (0.8) |
7.99 |
0.0002 |
** |
|
| 7 |
23.4 |
62374_157 |
QFAM |
1016 |
|
-4.763 |
0.0041 |
|
|
| 7 |
53.7 |
87974_385 |
GRAMMA |
979 |
-0.95 (0.48) |
3.96 |
0.00886 |
|
sec14-like 1 (cerevisiae) |
| 8 |
23.3 |
136056_232 |
GRAMMA |
979 |
-1.04 (0.47) |
4.89 |
0.00362 |
|
|
| 8 |
54.9 |
31265_40 |
QFAM |
1022 |
|
1.369 |
0.00338 |
|
cd22 antigen |
| 10 |
29.6 |
82862_249 |
FASTA |
979 |
-1.99(0.73) |
7.32 |
0.00683 |
|
|
| 10 |
29.6 |
82862_249 |
GRAMMA |
979 |
-1.11 (0.53) |
4.39 |
0.00582 |
|
|
| 12 |
31.1 |
57295_319 |
QFAM |
1022 |
|
-1.117 |
0.00924 |
|
|
| 12 |
37.8 |
52515_4545 |
QFAM |
1022 |
|
1.667 |
0.0088 |
|
titin a |
| 12 |
37.8 |
63497_114 |
QFAM |
1022 |
|
1.667 |
0.009 |
|
Unnamed protein product [Tetraodon nigroviridis] |
| 13 |
19.8 |
64435_287 |
QFAM |
1022 |
|
1.813 |
0.00376 |
|
Proline rich 5 |
| 14 |
1.9 |
132996_241 |
QFAM |
1021 |
|
1.646 |
0.00159 |
* |
|
| 14 |
12.5 |
112228_90 |
FASTA |
979 |
2.09(0.65) |
10.32 |
0.00132 |
* |
|
| 14 |
12.5 |
112228_90 |
GRAMMA |
979 |
1.02 (0.44) |
5.43 |
0.00216 |
|
|
| 14 |
24.1 |
96692_167 |
FASTA |
979 |
1.53(0.59) |
6.79 |
0.00918 |
|
Novel protein prickle-like family |
| 14 |
43.9 |
113696_50 |
FASTA |
976 |
-3.39(1.15) |
8.75 |
0.0031 |
|
Perforin 1 (pore forming protein) |
| 14 |
43.9 |
113696_50 |
GRAMMA |
976 |
-2.22 (0.91) |
5.92 |
0.00137 |
* |
Perforin 1 (pore forming protein) |
| 15 |
1.1 |
13736_229 |
GRAMMA |
979 |
-1 (0.5) |
4.01 |
0.00844 |
|
|
| 15 |
12.5 |
55466_266 |
QFAM |
1022 |
|
1.383 |
0.00078 |
* |
sept2 protein |
| 15 |
26.7 |
110434_333 |
FASTA |
979 |
-1.93(0.75) |
6.72 |
0.00956 |
|
t cell antigen receptor alpha chain c region |
| 15 |
26.7 |
110434_333 |
GRAMMA |
979 |
-1.18 (0.56) |
4.39 |
0.00584 |
|
t cell antigen receptor alpha chain c region |
| 15 |
28.9 |
54100_91 |
FASTA |
979 |
2.06(0.68) |
9.11 |
0.00255 |
|
cerebellin 1 precursor |
| 15 |
28.9 |
60130_224 |
FASTA |
978 |
-1.95(0.66) |
8.7 |
0.00318 |
|
|
| 15 |
28.9 |
60130_224 |
GRAMMA |
978 |
-0.99 (0.46) |
4.71 |
0.00429 |
|
|
| 15 |
54.4 |
94824_55 |
QFAM |
1022 |
|
-1.559 |
0.00057 |
* |
Adaptor-related protein complex mu 1 subunit |
| 16 |
23.8 |
115737_104 |
QFAM |
1020 |
|
-1.206 |
0.0094 |
|
mucin-5b precursor (mucin 5 subtype tracheobronchial) (high molecular weight salivary mucin mg1) (sublingual gland mucin) |
| 16 |
39.2 |
136477_76 |
QFAM |
1022 |
|
2.121 |
0.00687 |
|
sp2 transcription factor |
| 18 |
8.4 |
60684_109 |
GRAMMA |
978 |
-0.89 (0.45) |
3.88 |
0.00958 |
|
|
| 18 |
48.9 |
52766_1600 |
FASTA |
979 |
-1.8(0.69) |
6.81 |
0.00909 |
|
solute carrier family 25 (mitochondrial carrier phosphate carrier) member 25 |
| 18 |
49.9 |
116665_768 |
FASTA |
979 |
1.95(0.63) |
9.62 |
0.00193 |
* |
ptc7 protein phosphatase homolog (cerevisiae) |
| 18 |
49.9 |
116665_768 |
GRAMMA |
979 |
1.14 (0.46) |
6.04 |
0.00122 |
* |
ptc7 protein phosphatase homolog (cerevisiae) |
| 18 |
49.9 |
13427_160 |
FASTA |
979 |
2.06(0.67) |
9.48 |
0.00208 |
|
|
| 18 |
49.9 |
13427_160 |
GRAMMA |
979 |
1.13 (0.48) |
5.58 |
0.00188 |
* |
|
| 19 |
23.8 |
111569_63 |
FASTA |
979 |
2.49(0.77) |
10.44 |
0.00123 |
* |
tbt-binding protein |
| 19 |
23.8 |
111569_63 |
GRAMMA |
979 |
1.35 (0.55) |
6.07 |
0.00119 |
* |
tbt-binding protein |
| 20 |
0.8 |
54931_324 |
GRAMMA |
979 |
1.16 (0.59) |
3.86 |
0.0097 |
|
solute carrier family member 34 |
| 20 |
3.3 |
134730_80 |
FASTA |
970 |
-2.64(0.69) |
14.81 |
0.00012 |
** |
|
| 20 |
3.3 |
134730_80 |
GRAMMA |
970 |
-0.99 (0.41) |
5.89 |
0.00141 |
* |
|
| 20 |
3.3 |
134730_80 |
QFAM |
1013 |
|
-2.504 |
0.0047 |
|
|
| 20 |
7.9 |
88771_72 |
FASTA |
954 |
-1.53(0.58) |
6.89 |
0.00866 |
|
|
| 20 |
9.4 |
103839_124 |
FASTA |
970 |
2.22(0.81) |
7.54 |
0.00603 |
|
|
| 20 |
9.4 |
103839_124 |
GRAMMA |
970 |
1.07 (0.54) |
3.86 |
0.00974 |
|
|
| 20 |
9.4 |
110140_1196 |
FASTA |
979 |
1.6(0.6) |
7.06 |
0.00787 |
|
glycerol-3-phosphate dehydrogenase |
| 20 |
9.4 |
110140_1196 |
GRAMMA |
979 |
0.82 (0.42) |
3.9 |
0.00938 |
|
glycerol-3-phosphate dehydrogenase |
| 20 |
11.1 |
59816_21 |
QFAM |
1022 |
|
-1.607 |
0.00152 |
* |
novel protein vertebrate stabilin 2 |
| 20 |
20.3 |
134434_222 |
FASTA |
978 |
-2.03(0.76) |
7.09 |
0.00776 |
|
|
| 20 |
21.6 |
20086_69 |
QFAM |
1022 |
|
1.556 |
0.00996 |
|
vacuolar protein sorting 4b |
| 21 |
47.1 |
111636_59 |
QFAM |
1022 |
|
1.417 |
0.0044 |
|
kiaa1219 protein |
| 21 |
51.1 |
54579_132 |
FASTA |
979 |
1.63(0.55) |
8.68 |
0.00321 |
|
|
| 21 |
51.1 |
54579_132 |
GRAMMA |
979 |
1.04 (0.43) |
5.95 |
0.00133 |
* |
|
| 22 |
6 |
88524_52 |
FASTA |
979 |
1.55(0.57) |
7.31 |
0.00687 |
|
|
| 22 |
6 |
88524_52 |
GRAMMA |
979 |
0.97 (0.44) |
4.9 |
0.00357 |
|
|
| 22 |
6.4 |
94914_114 |
FASTA |
979 |
2.07(0.68) |
9.2 |
0.00242 |
|
|
| 22 |
6.4 |
94914_114 |
GRAMMA |
979 |
0.86 (0.42) |
4.09 |
0.00775 |
|
|
| 22 |
22.3 |
58881_141 |
QFAM |
1022 |
|
-1.781 |
0.00352 |
|
tuberous sclerosis 1 |
| 22 |
23.2 |
554_399 |
FASTA |
979 |
-1.89(0.72) |
6.94 |
0.00841 |
|
dipeptidyl peptidase 7 |
| 22 |
23.2 |
554_399 |
GRAMMA |
979 |
-0.98 (0.5) |
3.86 |
0.00974 |
|
dipeptidyl peptidase 7 |
| 23 |
0 |
93296_256 |
FASTA |
978 |
3.71(0.95) |
15.3 |
0.00009 |
** |
loc795887 protein |
| 23 |
0 |
93296_256 |
GRAMMA |
978 |
2.28 (0.72) |
10.11 |
0.00003 |
*** |
loc795887 protein |
| 23 |
0.9 |
110253_351 |
FASTA |
979 |
2.35(0.77) |
9.27 |
0.00232 |
|
novel protein |
| 23 |
0.9 |
110253_351 |
GRAMMA |
979 |
1.27 (0.55) |
5.36 |
0.00232 |
|
novel protein |
| 23 |
27.4 |
64731_210 |
QFAM |
1022 |
|
1.41 |
0.00308 |
|
|
| 24 |
55.9 |
67606_298 |
FASTA |
979 |
-3.63(1.14) |
10.21 |
0.0014 |
* |
serine long chain base subunit 1 |
| 24 |
55.9 |
67606_298 |
GRAMMA |
979 |
-2.07 (0.83) |
6.25 |
0.00101 |
* |
serine long chain base subunit 1 |
| 25 | 46.1 | 54056_576 | FASTA | 979 | 1.7(0.65) | 6.87 | 0.00876 | n-ethylmaleimide sensitive fusion protein attachment protein alpha |
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 and GRAMMAS); Stat, test statistic linear regression coefficient for QFAM, chi-square with one degree of freedom for FASTA and GRAMMA analyses; P, point-wise empirical P-value (QFAM) or permuted P-value with one degree of freedom corrected for inflation factor lambda (FASTA and GRAMMA); Sig, significance after Bonferroni correction (*, P < 0.05; **, P < 0.01; ***, P < 0.001). GeneID, closest SNP homology from BLAST. Tests were considered suggestive when P < 0.01 before Bonferroni correction.