Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice

Leamy, Larry J; Kelly, Scott A; Nietfeldt, Joseph; Legge, Ryan M; Ma, Fangrui; Hua, Kunjie; Sinha, Rohita; Peterson, Daniel A; Walter, Jens; Benson, Andrew K; Pomp, Daniel

doi:10.1186/s13059-014-0552-6

Table 2 QTL statistics for the IgA traits in the G ₁₀ mouse population

From: Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice

Trait	*IghV* gene	Ch	Location (Mb)	CI (Mb)	LOD	A	d	%	Interaction
B182	IghV2-6-1	1	70.1	69.2-73.1	4.21	0.206	0.166	6.44
B48	IghV14-4	4	117.5	106.0-124.5	4.64*	0.037	-0.234	6.66
		12	112.3	108.8-118.1	4.63*	0.210	-0.082	8.60
B30	IghV1-26	6	137.8	130.6-143.3	4.59*	0.221	0.112	8.91
		12	114.5	109.1-120.0	3.94	0.147	-0.022	7.47
B122	IghV1S17	7	4.3	3.6-16.2	4.57*	-0.139	0.188	7.22
B81	IghV1-75	8	91.5	90.6-92.8	4.07	0.144	0.367	6.51	Sex (M,F)
		12	114.5	114.0-120.0	21.29*	-0.530	0.257	38.01
		19	42.8	42.1-47.7	3.94	-0.197	0.199	5.67
B207	IghV5-12-1	9	27.3	18.8-32.9	3.98	-0.081	-0.325	6.37
		12	114.5	114.0-120.0	26.11*	0.689	0.306	42.76
B218	IghV5-6-2	9	22.8	13.7-31.8	4.13	-0.067	-0.351	6.65
		12	114.5	114.0-120.0	24.85*	0.701	0.271	41.87
B44	IghV14-2	12	114.5	114.0-120.0	13.74*	-0.325	0.128	23.17
B76	IghV1-7	12	114.5	114.0-120.0	5.07*	0.158	-0.036	9.55
B88	IghV1-81	12	114.5	114.0-120.0	19.31*	-0.472	0.174	36.27
B89	IghV1-82	12	114.5	110.9-120.0	5.07*	0.160	0.019	10.26
B57	IghV1-52	12	114.5	114.0-120.0	4.78*	0.187	-0.027	9.63
B23	IghV1-22	12	114.5	114.0-120.0	10.35*	-0.028	0.009	20.36
B17	IghV1-20	12	114.5	114.0-120.0	13.74*	0.344	0.030	26.70
B37	IghV1-34	12	114.5	114.0-120.0	26.32*	0.540	0.258	43.19
B14	IghV1-18	12	114.5	114.0-120.0	14.55*	-0.337	0.141	28.03
B80	IghV1-74	12	112.3	108.8-118.1	6.12*	-0.256	0.058	11.84
B42	IghV1-4	12	114.5	114.0-120.0	15.14*	-0.432	0.142	27.61
B71	IghV1-63	12	114.5	114.0-120.0	7.87*	0.300	0.069	14.67
B91	IghV1-84	12	114.5	114.0-120.0	23.21*	0.505	0.170	40.59
B72	IghV1-64	12	114.5	114.0-120.0	42.12*	-0.728	0.446	55.90
B54	IghV1-5	12	114.5	114.0-120.0	12.00*	0.361	0.061	23.32
		13	37.6	35.4-41.8	4.50*	-0.213	0.031	8.41
B87	IghV1-80	12	114.5	114.0-120.0	34.33*	-0.700	0.488	49.98
B15	IghV1-19	12	114.5	114.0-120.0	8.66*	-0.294	0.171	16.25
B78	IghV1-71	12	114.5	114.0-120.0	5.45*	-0.279	0.083	9.80
B93	IghV1-9	12	114.5	114.0-120.0	52.78*	-0.913	0.630	70.88
B61	IghV1-55	12	114.5	114.0-120.0	43.09*	-0.791	0.484	61.04
B79	IghV1-72	12	114.5	114.0-120.0	46.20*	-0.846	0.558	61.53
B73	IghV1-66	12	114.5	114.0-120.0	12.00*	-0.382	0.108	22.15
B43	IghV14-1	12	114.5	114.0-120.0	9.53*	-0.386	0.194	16.72
B55	IghV1-50	12	114.5	118.3-120.9	13.31*	-0.436	0.166	22.83
B46	IghV14-3	12	114.5	114.0-120.0	52.85*	0.979	0.529	65.56
		18	82.1	77.7-84.3	4.48*	-0.421	0.675	11.98
B92	IghV1-85	12	114.5	114.0-120.0	31.70*	-0.794	0.465	51.35
B64	IghV1-59	12	114.5	114.0-120.0	15.30*	-0.541	0.172	26.78
B60	IghV1-54	12	114.5	114.0-120.0	27.34*	-0.699	0.537	45.98
B82	IghV1-76	12	114.5	114.0-120.0	29.75*	-0.606	0.338	48.99
B10	IghV1-14	12	114.5	114.0-120.0	29.75*	1.098	0.843	69.66
B40	IghV1-37	12	114.5	110.9-120.0	4.02	0.230	-0.048	7.37
B153	IghV1S61	12	114.5	114.0-120.0	62.17*	1.189	0.733	74.98
B234	IghV6-3	12	114.5	114.0-120.0	5.60*	-0.235	0.154	11.23
B83	IghV1-77	12	114.5	114.0-120.0	15.01*	-0.400	0.254	28.59
B114	IghV1S135	12	114.5	114.0-120.0	43.97*	0.988	0.471	64.30
B217	IghV5-6-1	12	114.5	114.0-120.0	34.60*	-0.766	0.438	54.28
B223	IghV5-9	12	114.5	114.0-120.0	19.14*	0.544	0.280	33.41
B63	IghV1-58	12	114.5	114.0-120.0	22.02*	-0.667	0.222	38.12
B189	IghV2-6-8	12	114.5	114.0-120.0	9.23*	0.376	0.098	16.43
B175	IghV2-3	12	114.5	114.0-120.0	14.48*	-0.481	0.277	26.82
B196	IghV3-4	12	114.5	112.3-120.0	12.45*	0.445	0.100	24.31
B75	IghV1-69	17	33.7	31.6-38.0	4.70*	0.177	0.108	8.02
B195	IghV3-3	17	33.7	31.9-42.6	12.83*	0.348	0.394	18.80
		17	45.6	43.6-48.7	12.81*	0.447	0.495	29.33
		18	82.1	79.6-84.3	6.38*	-0.445	0.724	18.79
B178	IghV2-4-1	18	53.9	52.9-58.5	4.25*	0.089	0.173	6.98
B59	IghV1-53	19	42.1	37.9-42.8	4.20	-0.008	-0.118	5.73

Shown are all QTLs affecting the IgA traits that had LOD scores reaching the suggestive or significant (*) experiment-wise level of significance. The chromosome (Ch) location of the peak and confidence intervals (CI) of each QTL is given in Mb (from NCBI Build 37). Also shown is the percentage contribution (%) of each QTL to the total variance of each trait, and its additive (a), dominance (d) genotypic effects (bolded values indicate significance). Sex (M,F) = an interaction of the QTL with sex, where the QTL is significant in both sexes but has a greater effect in females.

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