A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

Robinson, Nicholas; Baranski, Matthew; Mahapatra, Kanta Das; Saha, Jatindra Nath; Das, Sweta; Mishra, Jashobanta; Das, Paramananda; Kent, Matthew; Arnyasi, Mariann; Sahoo, Pramoda Kumar

doi:10.1186/1471-2164-15-541

Table 5 Suggestive and significant QTL for trait dead or alive after challenge with A. hydrophila detected using PLINK (ASSOC) and GenAbel (FASTA and GRAMMA) analyses in 21 L. rohita families

From: A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

LG	Pos	SNP	Test	N	Effect	Stat	P-value	Sig	GeneID
1	37.3	55086_181	ASSOC	1022	0.102/0.146	9.07	0.00685		Small heat shock
1	37.3	61478_69	GRAMMA	979	-0.06 (0.03)	6.54	0.0095
1	44.1	116899_232	GRAMMA	979	0.07 (0.03)	6.69	0.00875
1	44.1	116899_232	ASSOC	1022	0.447/0.393	6.08	0.00625
3	29	89585_200	ASSOC	1022	0.27/0.329	8.62	0.00548		Cardiac ankyrin repeat protein
3	29	89585_200	GRAMMA	979	-0.07 (0.02)	6.9	0.00772		Cardiac ankyrin repeat protein
4	0.9	32879_80	FASTA	979	0.08 (0.03)	7.86	0.00505
4	0.9	32879_80	GRAMMA	979	0.08 (0.03)	8.44	0.00321
5	23.8	83820_94	GRAMMA	979	-0.07 (0.03)	6.71	0.00863		Brain specific kinase 146
6	46.9	67578_280	FASTA	979	0.15 (0.05)	9.04	0.00264		Nicotinamide nucleotide transhydrogenase
6	46.9	67578_280	GRAMMA	979	0.15 (0.05)	9.71	0.00158	*	Nicotinamide nucleotide transhydrogenase
6	46.9	67578_280	ASSOC	1022	0.097/0.063	8.03	0.00397		Nicotinamide nucleotide transhydrogenase
6	46.9	87896_2052	FASTA	979	0.17 (0.06)	7.43	0.00643		Complement protein component c7-1
6	46.9	87896_2052	GRAMMA	979	0.17 (0.06)	7.97	0.00419		Complement protein component c7-1
7	53.7	87974_385	FASTA	979	-0.08 (0.03)	7.18	0.00738		sec14-like 1 (cerevisiae)
7	53.7	87974_385	GRAMMA	979	-0.08 (0.03)	7.71	0.00487		sec14-like 1 (cerevisiae)
7	53.7	87974_385	ASSOC	1022	0.246/0.3	7.4	0.00568		sec14-like 1 (cerevisiae)
9	32.1	56368_90	GRAMMA	979	-0.07 (0.02)	6.98	0.00739		leucine-rich ppr-motif containing
10	26.1	54734_19	FASTA	979	0.08 (0.03)	6.75	0.00937
10	26.1	54734_19	GRAMMA	979	0.08 (0.03)	7.25	0.00633
10	34.8	133884_276	GRAMMA	979	-0.08 (0.03)	7.02	0.0072
13	26.9	65946_186	GRAMMA	979	-0.1 (0.04)	6.48	0.00985		Cytoskeleton associated protein 5
13	26.9	65946_186	ASSOC	1022	0.126/0.164	6.03	0.0083		Cytoskeleton associated protein 5
13	34.9	55609_284	FASTA	979	0.08 (0.03)	7	0.00816		Heavy subunit
13	34.9	55609_284	GRAMMA	979	0.08 (0.03)	7.51	0.00544		Heavy subunit
14	1.9	132996_241	FASTA	978	0.07 (0.02)	8.22	0.00415
14	1.9	132996_241	GRAMMA	978	0.07 (0.02)	8.82	0.00259
14	1.9	132996_241	ASSOC	1022	0.481/0.416	8.83	0.00448
14	12.5	112228_90	FASTA	979	0.08 (0.03)	9.4	0.00217
14	12.5	112228_90	GRAMMA	979	0.08 (0.03)	10.1	0.00127	*
14	12.5	112228_90	ASSOC	1022	0.33/0.269	8.99	0.00334
14	24.1	96692_167	FASTA	979	0.07 (0.02)	8.87	0.0029		Novel protein prickle-like family
14	24.1	96692_167	GRAMMA	979	0.07 (0.02)	9.52	0.00175	*	Novel protein prickle-like family
14	24.1	96692_167	ASSOC	1022	0.446/0.515	9.74	0.00588		Novel protein prickle-like family
14	47.1	4460_67	ASSOC	1022	0.372/0.46	8.29	0.0003	**
15	28.9	60130_224	FASTA	978	-0.08 (0.03)	8.64	0.00328
15	28.9	60130_224	GRAMMA	978	-0.08 (0.03)	9.28	0.00201
15	28.9	60130_224	ASSOC	1022	0.32/0.377	7.21	0.005
15	29.1	4834_117	FASTA	979	-0.07 (0.03)	6.92	0.00853		Novel protein
15	29.1	4834_117	GRAMMA	979	-0.07 (0.03)	7.43	0.00571		Novel protein
18	21.5	100422_182	ASSOC	1022	0.366/0.31	7.16	0.00972
18	35.5	75070_130	FASTA	979	0.1 (0.03)	10.37	0.00128	*
18	35.5	75070_130	GRAMMA	979	0.1 (0.03)	11.13	0.00072	*
18	35.5	75070_130	ASSOC	1022	0.241/0.183	10.12	0.00095	*
19	8.5	63493_143	GRAMMA	979	-0.06 (0.02)	6.54	0.00948
19	23.8	111569_63	FASTA	979	0.11 (0.03)	10.88	0.00097	*	tbt-binding protein
19	23.8	111569_63	GRAMMA	979	0.11 (0.03)	11.68	0.00053	*	tbt-binding protein
19	23.8	111569_63	ASSOC	1022	0.181/0.126	11.86	0.00106	*	tbt-binding protein
20	1.4	115437_120	GRAMMA	979	-0.1 (0.04)	6.46	0.00994		myosin heavy chain
20	3	55229_133	ASSOC	1022	0.342/0.284	7.97	0.00459		denn madd domain containing 2d
20	3	55229_133	FASTA	979	0.07 (0.03)	7.75	0.00537		denn madd domain containing 2d
20	3	55229_133	GRAMMA	979	0.07 (0.03)	8.32	0.00344		denn madd domain containing 2d
20	3.3	134730_80	FASTA	970	-0.07 (0.02)	8.75	0.00309
20	3.3	134730_80	GRAMMA	970	-0.07 (0.02)	9.39	0.00189	*
20	3.3	134730_80	ASSOC	1022	0.332/0.398	9.43	0.00392
20	9.4	110140_1196	FASTA	979	0.06 (0.02)	6.71	0.00959		glycerol-3-phosphate dehydrogenase
20	9.4	110140_1196	GRAMMA	979	0.06 (0.02)	7.21	0.00649		glycerol-3-phosphate dehydrogenase
20	9.4	110140_1196	ASSOC	1022	0.44/0.378	8	0.00638		glycerol-3-phosphate dehydrogenase
21	51.1	54579_132	ASSOC	1022	0.459/0.396	8.05	0.00374
23	0	93296_256	ASSOC	1022	0.135/0.092	9.15	0.00121	*	loc795887 protein
23	0	93296_256	FASTA	978	0.11 (0.04)	6.69	0.00967		loc795887 protein
23	0	93296_256	GRAMMA	978	0.11 (0.04)	7.19	0.00656		loc795887 protein
24	49	110996_58	ASSOC	1022	0.204/0.26	9.14	0.00508
24	49	110996_58	GRAMMA	979	-0.07 (0.03)	6.9	0.00773
24	51.5	110996_644	ASSOC	1022	0.086/0.124	7.95	0.00843
24	55.9	67606_298	ASSOC	1022	0.055/0.086	7.86	0.00404		serine long chain base subunit 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 and GRAMMAS) or frequency of minor allele in case/control (ASSOC); Stat, chi-square with one degree of freedom for ASSOC, FASTA and GRAMMA analyses; P, point-wise empirical P-value (ASSOC) 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.

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ISSN: 1471-2164

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