Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

Van Goor, Angelica; Ashwell, Christopher M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J.

doi:10.1186/s12864-016-2601-x

Table 2 Windows explaining a significant percentage (≥0.5) of genetic variance

From: Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

Windows explaining ≥ 0.5 % of genetic variance						SNP with highest model frequency within window
Trait^a	Chr	Pos (Mb)	% of genetic variance explained	Nb of SNPs	Freq of iterations with (P > 0)^b	SNP name^c	SNP pos (bp)^d	Model freq^e	Allele freq^f
pH20	18	3	1.29	401	0.94	AX-75894740	3342614	0.0111	0.652
pH20	28	4	1.01	328	0.85	AX-76384843	4097788	0.0090	0.294
pH20	28	3	0.64	437	0.92	AX-76383580	3856132	0.0092	0.294
pH20	18	6	0.58	342	0.86	AX-75894671	6670745	0.0075	0.340
pH28	12	7	0.55	302	0.81	AX-75723368	7630857	0.0070	0.288
pH28-20	6	4	0.66	350	0.86	AX-76958371	4259110	0.0074	0.724
pH28-20	10	16	0.50	372	0.89	AX-75591175	16460945	0.0066	0.298
pCO₂20	28	3	9.75	437	0.93	AX-76383461	3835952	0.0448	0.711
pCO₂20	28	4	4.49	328	0.89	AX-76385219	4167579	0.0239	0.706
pCO₂28	9	20	0.59	462	0.94	AX-75706074	19358758	0.0070	0.416
pCO₂28	1	110	0.54	194	0.38	AX-80866127	110487208	0.0098	0.510
pCO₂28	27	2	0.53	650	0.96	AX-76356017	2038872	0.0065	0.653
pCO₂28	10	3	0.50	447	0.91	AX-75607032	3037730	0.0069	0.626
pCO₂28-20	28	4	0.61	328	0.83	AX-76384843	4097788	0.0076	0.296
pCO₂28-20	23	2	0.57	388	0.86	AX-76282215	2594470	0.0071	0.435
pCO₂28-20	3	14	0.56	287	0.81	AX-76421954	14679413	0.0075	0.323
pCO₂28-20	10	1	0.50	393	0.86	AX-75601081	1816619	0.0080	0.339
pO₂28	13	5	0.57	277	0.79	AX-75758019	5130673	0.0070	0.531
BE20	18	3	0.68	401	0.93	AX-75894740	3342614	0.0103	0.652
BE20	18	6	0.52	342	0.84	AX-75906711	6859485	0.0078	0.554
BE28	27	2	0.70	650	0.97	AX-76359325	2733806	0.0076	0.473
BE28	1	172	0.54	202	0.67	AX-75342016	172010216	0.0094	0.683
BE28	21	4	0.50	521	0.91	AX-76247040	4491122	0.0078	0.321
HCO₃28	Z	30	4.11	74	0.47	AX-77209983	30284984	0.1864	0.671
HCO₃28	Z	8	3.10	24	0.27	AX-80958477	8485438	0.0719	0.357
HCO₃28	Z	5	2.22	62	0.33	AX-80834191	5042699	0.0931	0.634
HCO₃28	Z	33	2.09	45	0.28	AX-80973925	33940034	0.0543	0.608
HCO₃28	Z	35	1.67	128	0.50	AX-80901519	35319963	0.0589	0.379
HCO₃28	Z	7	1.47	2	0.9	AX-77264084	7705768	0.0806	0.311
HCO₃28	Z	70	1.45	55	0.28	AX-77257752	70210948	0.0625	0.376
HCO₃28	Z	69	1.31	113	0.40	AX-80879264	69810199	0.0525	0.370
HCO₃28	6	25	0.75	325	0.86	AX-76932184	25826439	0.0083	0.466
HCO₃28	Z	71	0.74	183	0.62	AX-80943753	71554374	0.0520	0.360
HCO₃28	6	26	0.53	291	0.83	AX-76933234	26203623	0.0092	0.493
TCO₂28	Z	69	3.63	113	0.46	AX-80879264	69810199	0.1357	0.370
TCO₂28	Z	30	3.04	74	0.44	AX-77209983	30284984	0.1424	0.671
TCO₂28	Z	8	2.30	24	0.25	AX-80958477	8485438	0.0859	0.357
TCO₂28	Z	33	1.73	45	0.28	AX-80973925	33940034	0.0667	0.608
TCO₂28	Z	5	1.60	62	0.29	AX-80834191	5042699	0.0700	0.634
TCO₂28	Z	7	1.23	2	0.7	AX-77264084	7705768	0.0707	0.311
TCO₂28	Z	70	0.91	55	0.26	AX-77257752	70210948	0.0434	0.376
TCO₂28	Z	35	0.80	128	0.48	AX-80901519	35319963	0.0419	0.379
TCO₂28	6	25	0.66	325	0.85	AX-76932184	25826439	0.0080	0.466
TCO₂28	26	3	0.51	616	0.98	AX-80958155	3785485	0.0079	0.513
TCO₂28-20	10	5	0.51	515	0.93	AX-75615576	5758221	0.0067	0.355
K20	10	16	0.76	372	0.92	AX-75589587	16018566	0.0041	0.249
K20	10	18	0.53	496	0.96	AX-75597981	18294286	0.0038	0.278
K20	12	17	0.53	242	0.72	AX-75701199	17759131	0.0043	0.646
K20	26	3	0.50	616	0.96	AX-76340450	3273628	0.0036	0.180
K28-20	12	16	1.29	246	0.75	AX-75696568	16220734	0.0036	0.650
K28-20	12	17	0.69	242	0.70	AX-75701149	17743731	0.0043	0.633
iCa28	26	3	0.52	616	0.96	AX-76343628	3922118	0.0076	0.550
Hct28	14	11	1.78	391	0.94	AX-75776707	11791127	0.0096	0.502
Hct28	1	169	1.17	196	0.83	AX-75336362	169571235	0.0110	0.714
Hct28	28	3	1.01	437	0.92	AX-76384000	3944019	0.0116	0.397
Hct28	28	4	0.93	328	0.91	AX-76385356	4197143	0.0113	0.408
Hct28	22	3	0.88	573	0.95	AX-76269662	3474970	0.0072	0.513
Hct28	10	16	0.59	372	0.90	AX-75589730	16057907	0.0070	0.254
Hb28	14	11	1.64	391	0.95	AX-75776707	11791127	0.0091	0.502
Hb28	1	169	1.33	196	0.83	AX-75337336	169979876	0.0121	0.322
Hb28	28	3	0.96	437	0.91	AX-76384000	3944019	0.0112	0.397
Hb28	28	4	0.94	328	0.92	AX-76385356	4197143	0.0103	0.408
Hb28	22	3	0.79	573	0.95	AX-76269662	3474970	0.0073	0.513
Hb28	10	16	0.60	372	0.90	AX-75590148	16177101	0.0077	0.295
Hb28	1	170	0.50	176	0.65	AX-75337520	170074107	0.0083	0.676
Hb28-20	22	3	1.71	573	0.96	AX-76272400	3857927	0.0072	0.533
sO₂28	25	0	1.23	364	0.91	AX-75758019	5130673	0.0070	0.531
sO₂28	24	3	0.55	581	0.94	AX-76328225	36480	0.0111	0.618
sO₂28-20	17	6	0.53	324	0.83	AX-75872796	6506736	0.0066	0.412
sO₂28-20	17	7	0.53	467	0.88	AX-75875111	7125729	0.0066	0.172
Glu20	10	4	0.67	548	0.95	AX-80975590	4452892	0.0067	0.740
Glu28	22	3	1.09	573	0.94	AX-76273189	3966852	0.0070	0.585
Glu28	Z	5	0.79	62	0.28	AX-80834191	5042699	0.0246	0.634
Glu28	Z	70	0.74	55	0.24	AX-77257752	70210948	0.0266	0.376
Glu28	Z	69	0.64	113	0.42	AX-80879264	69810199	0.0187	0.371

^aBlood chemistry components were measured pre-heat (day 20), on the seventh day of heat treatment (day 28), and the calculated differential due to heat (day 28–20)
^bFrequency in which the window was included in the MCMC iterations (post-burn-in)
^cSNP within the specified window which was most frequently included in the MCMC iterations (post-burn-in), and is therefore predicted to have the greatest effect on the phenotype
^dPosition of SNPs in base pairs on Gallus-gallus (version 4.0) chromosome
^eFrequency in which the SNP was included in the MCMC iterations (post-burn-in) model
^fAllele frequency of the SNP in the genotyped population (N = 458)

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