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

Robinson, Nicholas A; Gopikrishna, Gopalapillay; Baranski, Matthew; Katneni, Vinaya Kumar; Shekhar, Mudagandur S; Shanmugakarthik, Jayakani; Jothivel, Sarangapani; Gopal, Chavali; Ravichandran, Pitchaiyappan; Gitterle, Thomas; Ponniah, Alphis G

doi:10.1186/1471-2164-15-731

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

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.

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ISSN: 1471-2164

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